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Fang J, Sheng Z, Liu J, Li C, Lyu T, Wang Z, Zhang H. Interference of microplastics on autotrophic microbiome in paddy soils: Shifts in carbon fixation rate, structure, abundance, co-occurrence, and assembly process. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134783. [PMID: 38824776 DOI: 10.1016/j.jhazmat.2024.134783] [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: 03/15/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Autotrophic microorganisms play a crucial role in soil CO2 assimilation. Although microplastic pollution is recognized as a significant global concern, its precise impact on carbon sequestration by autotrophic microorganisms in agroecosystem soil remains poorly understood. This study conducted microcosm experiments to explore how conventional polystyrene (PS) and biodegradable poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) microplastics affect carbon fixation rates (CFRs) and the community characteristics of soil autotrophic microorganisms in paddy agroecosystems. The results showed that compared with the control groups, 0.5 % and 1 % microplastic treatments significantly reduced soil CFRs by 11.8 - 24.5 % and 18.7 - 32.3 %, respectively. PS microplastics exerted a stronger inhibition effect on CFRs than PHBV microplastics in bulk soil. However, no significant difference was observed in the inhibition of CFRs by both types of microplastics in rhizosphere soils. Additionally, PS and PHBV microplastics altered the structure of autotrophic microbial communities, resulting in more stochastically dominated assembly and looser, more fragile coexistence networks compared to control groups. Moreover, microplastics drove the changes in autotrophic microbial carbon fixation primarily through their direct interference and the indirect effect by increasing soil organic carbon levels. Our findings enhance the understanding and predictive capabilities regarding the impacts of microplastic pollution on carbon sinks in agricultural soils.
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Affiliation(s)
- Jiaohui Fang
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Zihao Sheng
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Jian Liu
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Changchao Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Tianshu Lyu
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Zhenyang Wang
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu 273100, China.
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Wang X, Wang J, Zou Y, Bie Y, Mahmood A, Zhang L, Liao L, Song Z, Liu G, Zhang C. Urea fertilization increased CO 2 and CH 4 emissions by enhancing C-cycling genes in semi-arid grasslands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120718. [PMID: 38537467 DOI: 10.1016/j.jenvman.2024.120718] [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: 09/14/2023] [Revised: 03/10/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
Global climate change is predicted to increase exogenous N input into terrestrial ecosystems, leading to significant changes in soil C-cycling. However, it remains largely unknown how these changes affect soil C-cycling, especially in semi-arid grasslands, which are one of the most vulnerable ecosystems. Here, based on a 3-year field study involving N additions (0, 25, 50, and 100 kg ha-1 yr-1 of urea) in a semi-arid grassland on the Loess Plateau, we investigated the impact of urea fertilization on plant characteristics, soil properties, CO2 and CH4 emissions, and microbial C cycling genes. The compositions of genes involved in C cycling, including C fixation, degradation, methanogenesis, and methane oxidation, were determined using metagenomics analysis. We found that N enrichment increased both above- and belowground biomasses and soil organic C content, but this positive effect was weakened when excessive N was input (N100). N enrichment also altered the C-cycling processes by modifying C-cycle-related genes, specifically stimulating the Calvin cycle C-fixation process, which led to an increase in the relative abundance of cbbS, prkB, and cbbL genes. However, it had no significant effect on the Reductive citrate cycle and 3-hydroxypropionate bi-cycle. N enrichment led to higher soil CO2 and CH4 emissions compared to treatments without added N. This increase showed significant correlations with C degradation genes (bglA, per, and lpo), methanogenesis genes (mch, ftr, and mcr), methane oxidation genes (pmoA, pmoB, and pmoC), and the abundance of microbial taxa harboring these genes. Microbial C-cycling genes were primarily influenced by N-induced changes in soil properties. Specifically, reduced soil pH largely explained the alterations in methane metabolism, while elevated available N levels were mainly responsible for the shift in C fixation and C degradation genes. Our results suggest that soil N enrichment enhances microbial C-cycling processes and soil CO2 and CH4 emissions in semi-arid ecosystems, which contributes to more accurate predictions of ecosystem C-cycling under future climate change.
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Affiliation(s)
- Xiaojun Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Shaanxi, 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Science, Shaanxi, 712100, PR China
| | - Jie Wang
- College of Forestry, Guizhou University, Guiyang, 550025, PR China
| | - Yanuo Zou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Shaanxi, 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Science, Shaanxi, 712100, PR China
| | - Yujing Bie
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Shaanxi, 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Science, Shaanxi, 712100, PR China
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Lu Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Shaanxi, 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Science, Shaanxi, 712100, PR China
| | - Lirong Liao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Shaanxi, 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Science, Shaanxi, 712100, PR China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Shaanxi, 712100, PR China
| | - Guobin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Shaanxi, 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Science, Shaanxi, 712100, PR China.
| | - Chao Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Shaanxi, 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Science, Shaanxi, 712100, PR China.
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Wei W, Shi X, Wang M, Zhou Z. Manure application maintained the CO 2 fixation activity of soil autotrophic bacteria but changed its ecological characteristics in an entisol of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169630. [PMID: 38154636 DOI: 10.1016/j.scitotenv.2023.169630] [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: 11/14/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
The response of soil autotrophs to anthropogenic activities has attracted increasing attention against the background of global change. Here, three entisol plots under different fertilizing regimes, including no fertilization (CK), manure (M), and a combined application of chemical fertilizer and manure (NPKM) were selected, and then the soil RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) activity and cbbl (gene encoding the large subunit of RubisCO) composition were measured to indicate the activity and community of autotrophic bacteria, respectively. The results revealed that the RubisCO activity of CK showed no difference from that of M but was significantly higher than that of NPKM. The CK and M had the lowest and highest soil cbbl abundance, respectively. The α-diversity of soil cbbl-carrying bacteria showed no significant difference among these treatments, whereas they showed significantly different community structures of cbbl-carrying bacteria. Meanwhile, compared with CK, M had significantly lower abundances of bacterial species with the functions of nitrogen fixation (Azoarcus sp.KH32C) or detoxification (Methylibium petroleiphilum), indicating that manure application might have an inhibiting potential to some beneficial autotrophic bacterial species in this entisol.
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Affiliation(s)
- Wanling Wei
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400715, China; The National Monitoring Base for Purple Soil Fertility and Fertilizer Efficiency, Southwest University, Chongqing 400715, China
| | - Mingxia Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Zhifeng Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China.
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Wang Y, Huang Y, Zeng Q, Liu D, An S. Biogeographic distribution of autotrophic bacteria was more affected by precipitation than by soil properties in an arid area. Front Microbiol 2023; 14:1303469. [PMID: 38173682 PMCID: PMC10761425 DOI: 10.3389/fmicb.2023.1303469] [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: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction Autotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood. Methods Herein, we conducted a 391-km north to south transect (mean annual precipitation <600 mm) survey in the Loess Plateau of China, to investigate the biogeographic distributions of autotrophic bacteria (RubisCO cbbL and cbbM genes) and the environmental drivers across different latitude sites with clear vegetational and climatic gradients. Results and discussion The soils in northern region with lower precipitation are dominated by grassland/forest, which is typically separated from the soils in southern region with higher precipitation. The community structure of autotrophic bacterial cbbL and cbbM genes generally differed between the soils in the southern and northern Loess Plateau, suggesting that precipitation and its related land use practices/ecosystem types, rather than local soil properties, are more important in shaping the soil autotrophic microorganisms. The cbbL-containing generalist OTUs were almost equally abundant across the northern and southern Loess Plateau, while the cbbM-containing bacterial taxa were more prevalent in the low precipitation northern region. Such differences indicate differentiate distribution patterns of cbbM- and cbbL-containing bacteria across the north to south transect. Our results suggest that the community composition and the differentiate distributions of soil cbbL- and cbbM-containing bacterial communities depend on precipitation and the related ecosystem types in the north to south transect in the Loess Plateau of China.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Yimei Huang
- College of Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Quanchao Zeng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, Shaanxi Province, China
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Das SR, Nayak BK, Dey S, Sarkar S, Chatterjee D, Saha S, Sarkar D, Pradhan A, Saha S, Nayak AK. Potential soil organic carbon sequestration vis-a-vis methane emission in lowland rice agroecosystem. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1099. [PMID: 37632560 DOI: 10.1007/s10661-023-11673-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Mitigating the atmospheric greenhouse effect while enhancing the inherent soil quality and productive capacity is possible through soil carbon (C) sequestration, which has a significant potential to counteract the adverse effects of agroecosystem level C emission through natural and anthropogenic means. Although rice is the most important food in India, feeding more than 60% of the country's population, it is commonly blamed for significant methane (CH4) emissions that accelerate climate change. Higher initial soil organic matter concentrations would create more CH4 under the flooded soil conditions, as reducible soil C is a prerequisite for CH4 generation. In India, rice is generally cultivated in lowlands under continuous flooding. Less extensive organic matter breakdown in lowland rice agroecosystems often significantly impacts the dynamics of soil active and passive C pools. Change from conventional to conservation agriculture might trap a significant quantity of SOC. The study aims to investigate the potential of rice-based soils to sequester C and reduce the accelerated greenhouse effects through modified farming practices, such as crop residue retention, crop rotation, organic farming, varietal selection, conservation agriculture, integrated nutrient management, and water management. Overall, lowland rice agroecosystems can sequester significant amounts of SOC, but this potential must be balanced against the potential for CH4 emissions. Management practices that reduce CH4 emissions while increasing soil C sequestration should be promoted and adopted to maximize the sustainability of rice agroecosystems. This review is important for understanding the effectiveness of the balance between SOC sequestration and CH4 emissions in lowland rice agroecosystems for adopting sustainable agricultural practices in the context of climate change.
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Affiliation(s)
- Saikat Ranjan Das
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | | | - Souvik Dey
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741252, India
| | - Suman Sarkar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | | | - Saurav Saha
- ICAR-Research Complex for North Eastern Hill Region, Tadong, Sikkim, 737102, India
| | - Dibyendu Sarkar
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741252, India
| | - Abhijit Pradhan
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Sanjoy Saha
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
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Fang J, Tao Y, Liu J, Lyu T, Yang X, Ma S, Dong J, Dou H, Zhang H. Effects of emergent plants on soil carbon-fixation and denitrification processes in freshwater and brackish wetlands in a watershed in northern China. GEODERMA 2023; 430:116311. [DOI: 10.1016/j.geoderma.2022.116311] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
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Tang H, Wen L, Shi L, Li C, Cheng K, Li W, Xiao X. Effects of Long-Term Fertilizer Practices on Rhizosphere Soil Autotrophic CO 2-Fixing Bacteria under Double Rice Ecosystem in Southern China. J Microbiol Biotechnol 2022; 32:1292-1298. [PMID: 36224752 PMCID: PMC9668096 DOI: 10.4014/jmb.2205.05055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022]
Abstract
Soil autotrophic bacterial communities play a significant role in the soil carbon (C) cycle in paddy fields, but little is known about how rhizosphere soil microorganisms respond to different long-term (35 years) fertilization practices under double rice cropping ecosystems in southern China. Here, we investigated the variation characteristics of rhizosphere soil RubisCO gene cbbL in the double rice ecosystems of in southern China where such fertilization practices are used. For this experiment we set up the following fertilizer regime: without any fertilizer input as a control (CK), inorganic fertilizer (MF), straw returning (RF), and organic and inorganic fertilizer (OM). We found that abundances of cbbL, 16S rRNA genes and RubisCO activity in rhizosphere soil with OM, RF and MF treatments were significantly higher than that of CK treatment. The abundances of cbbL and 16S rRNA genes in rhizosphere soil with OM treatment were 5.46 and 3.64 times higher than that of CK treatment, respectively. Rhizosphere soil RubisCO activity with OM and RF treatments increased by 50.56 and 45.22%, compared to CK treatment. Shannon and Chao1 indices for rhizosphere soil cbbL libraries with RF and OM treatments increased by 44.28, 28.56, 29.60, and 23.13% compared to CK treatment. Rhizosphere soil cbbL sequences with MF, RF and OM treatments mainly belonged to Variovorax paradoxus, uncultured proteobacterium, Ralstonia pickettii, Thermononospora curvata, and Azoarcus sp.KH33C. Meanwhile, cbbL-carrying bacterial composition was obviously influenced by soil bulk density, rhizosphere soil dissolved organic C, soil organic C, and microbial biomass C contents. Fertilizer practices were the principal factor influencing rhizosphere soil cbbL-carrying bacterial communities. These results showed that rhizosphere soil autotrophic bacterial communities were significantly changed under conditions of different long-term fertilization practices Therefore, increasing rhizosphere soil autotrophic bacteria community with crop residue and organic manure practices was found to be beneficial for management of double rice ecosystems in southern China.
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Affiliation(s)
- Haiming Tang
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China,Corresponding authors H. Tang Phone: +86 731 84696102 Fax: +86 731 84691581 E-mail:
| | - Li Wen
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Lihong Shi
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China,
L. Shi E-mail:
| | - Chao Li
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Kaikai Cheng
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Weiyan Li
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Xiaoping Xiao
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
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Peng B, Zhao S, Banerjee S, Mai W, Tian C. Contrasting effect of irrigation practices on the cotton rhizosphere microbiota and soil functionality in fields. FRONTIERS IN PLANT SCIENCE 2022; 13:973919. [PMID: 36330236 PMCID: PMC9623166 DOI: 10.3389/fpls.2022.973919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Drip irrigation under plastic film mulch is a common agricultural practice used to conserve water. However, compared to traditional flood irrigation with film mulch, this practice limit cotton root development from early flowering stage and may cause premature senescence in cotton. Changes of root will consequently shape the composition and activity of rhizosphere microbial communities, however, the effect of this farming practice on cotton rhizosphere microbiota remains poorly understood. This study investigated rhizosphere bacteria and soil functionality in response to different irrigation practices -including how changes in rhizosphere bacterial diversity alter soil nutrient cycling. Drip irrigation under plastic film mulch was shown to enhance bacterial diversity by lowering the salinity and increasing the soil moisture. However, the reduced root biomass and soluble sugar content of roots decreased potential copiotrophic taxa, such as Bacteroidetes, Firmicutes, and Gamma-proteobacteria, and increased potential oligotrophic taxa, such as Actinobacteria, Acidobacteria, and Armatimonadetes. A core network module was strongly correlated with the functional potential of soil. This module not only contained most of the keystone taxa but also comprised taxa belonging to Planctomycetaceae, Gemmatimonadaceae, Nitrosomonadaceae, and Rhodospirillaceae that were positively associated with functional genes involved in nutrient cycling. Drip irrigation significantly decreased the richness of the core module and reduced the functional potential of soil in the rhizosphere. Overall, this study provides evidence that drip irrigation under plastic film mulch alters the core bacterial network module and suppresses soil nutrient cycling.
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Affiliation(s)
- Bin Peng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Wenxuan Mai
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Li N, Wang B, Huang Y, Huang Q, Jiao F, An S. Response of cbbL-harboring microorganisms to precipitation changes in a naturally-restored grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156191. [PMID: 35618124 DOI: 10.1016/j.scitotenv.2022.156191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The impact of the long-term uneven precipitation distribution model on the diversity and community composition of soil C-fixing microorganisms in arid and semiarid grasslands remains unclear. In 2015, we randomly set up five experimental plots with precipitation gradients on the natural restoration grassland of the Loess Plateau (natural precipitation, NP; ± 40% natural precipitation: decreased precipitation (DP), DP40; increased precipitation (IP), IP40; ± 80% natural precipitation: DP80; IP80). In the third and fifth years after the experimental layout (spanned two years), we explored the cbbL-genes, which are functional genes in the Calvin cycle, harboring microbial diversity and community composition under different precipitation treatments. The results showed that the increase in mean annual precipitation significantly changed the cbbL-harboring microbial alpha diversity, especially when controlling for 40% natural precipitation. The response of the dominant microbial communities to interannual increased precipitation variation shifted from Gammaproteobacteria (Bradyrhizobium) to Betaproteobacteria (Variovorax). The structural equation model showed that precipitation directly affected the cbbL-harboring microbial diversity and community composition and indirectly by affecting soil NO3- (mg N kg -1), soil organic matter, dissolved organic N content, and above- and underground biomass. In conclusion, studying how cbbL-harboring microbial diversity and community composition respond to uneven precipitation variability provides new insights into the ecological processes of C-fixing microbes in semi-arid naturally-restored grasslands dominated by the Calvin cycle.
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Affiliation(s)
- Na Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Baorong Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimei Huang
- Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qian Huang
- Key Laboratory of Plant Nutrition and the Agro-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Feng Jiao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China.
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Yangling 712100, China.
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Ma S, Fang J, Liu J, Yang X, Lyu T, Wang L, Zhou S, Dou H, Zhang H. Differences in sediment carbon-fixation rate and associated bacterial communities in four wetland types in Hulun Lake Basin. CATENA 2022; 213:106167. [DOI: 10.1016/j.catena.2022.106167] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
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Ye C, Huang S, Sha C, Wu J, Cui C, Su J, Ruan J, Tan J, Tang H, Xue J. Changes of bacterial community in arable soil after short-term application of fresh manures and organic fertilizer. ENVIRONMENTAL TECHNOLOGY 2022; 43:824-834. [PMID: 32757721 DOI: 10.1080/09593330.2020.1807608] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The application of animal manure is highly recommended in agricultural production. However, the effect of different kinds of manures on bacterial community in farmland still remains unclear. In this study, a short-term field experiment was conducted to investigate the rapid effects of pig manure (PM), chicken manure (CM) and organic fertilizer (OF, composted by pig manure) application on soil physicochemical properties and soil bacterial community. The results showed that the application of CM and OF significantly increased soil bacterial richness (p < 0.05), mainly correlated with the increase of soil total nitrogen. Compared with CM and PM, OF had the greatest disturbance to soil bacterial structure. And total phosphorus showed the highest correlation with bacterial community. Meanwhile, the application of OF reduced the relative abundance of Actinobacteria, the organic matter synthetic bacteria, and Nitrospirae, the nitrifying bacteria, by 17.18% and 40.00%, respectively. 16S functional prediction analysis results shows that the application of OF increased the relative abundance of genes encoding Ribulose-1,5-bisphosphate carboxylase/oxyg (RuBsiCO), the genes involved in soil Calvin cycling, by 20.51%, and increased the relative abundance of genes encoding nitrous-oxide reductase by 44.86%. In conclusion, Short-term application of OF had greater disturbance to soil bacteria than CM and PM, and it had a significant influence on soil functional bacteria and genes involved in soil carbon and nitrogen cycling.
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Affiliation(s)
- Chunmei Ye
- College of Environmental Science and Engineering, Donghua University, Shanghai, People's Republic of China
| | - Shenfa Huang
- College of Environmental Science and Engineering, Donghua University, Shanghai, People's Republic of China
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Chenyan Sha
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Jianqiang Wu
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jinghua Su
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Junjie Ruan
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Juan Tan
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Hao Tang
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Jiajia Xue
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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Tang H, Li C, Shi L, Xiao X, Cheng K, Wen L, Li W. Effect of different long-term fertilizer managements on soil nitrogen fixing bacteria community in a double-cropping rice paddy field of southern China. PLoS One 2021; 16:e0256754. [PMID: 34469461 PMCID: PMC8409621 DOI: 10.1371/journal.pone.0256754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 08/13/2021] [Indexed: 11/28/2022] Open
Abstract
Soil microorganism plays an important role in nitrogen (N) fixation process of paddy field, but the related information about how soil microorganism that drive N fixation process response to change of soil phy-chemical characteristics under the double-cropping rice (Oryza sativa L.) paddy field in southern of China is need to further study. Therefore, the impacts of 34-years different long-term fertilization system on soil N-fixing bacteria community under the double-cropping rice paddy field in southern of China were investigated by taken chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method in this paper. The field experiment were set up four different fertilizer treatments: chemical fertilizer alone (MF), rice straw and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and unfertilized as a control (CK). This results showed that compared with CK treatment, the diversity index of cbbLR and nifH genes with OM and RF treatments were significantly increased (p<0.05), respectively. Meanwhile, the abundance of cbbLR gene with OM, RF and MF treatments were increased by 23.94, 12.19 and 6.70×107 copies g-1 compared to CK treatment, respectively. Compared with CK treatment, the abundance of nifH gene with OM, RF and MF treatments were increased by 23.90, 8.82 and 5.40×109 copies g-1, respectively. This results indicated that compared with CK treatment, the soil autotrophic azotobacter and nitrogenase activities with OM and RF treatments were also significantly increased (p<0.05), respectively. There were an obvious difference in features of soil N-fixing bacteria community between application of inorganic fertilizer and organic manure treatments. Therefore, this results demonstrated that abundance of soil N-fixing bacteria community in the double-cropping rice paddy field were increased by long-term applied with organic manure and crop residue managements.
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Affiliation(s)
- Haiming Tang
- Hunan Soil and Fertilizer Institute, Changsha, China
- * E-mail:
| | - Chao Li
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Lihong Shi
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Xiaoping Xiao
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Kaikai Cheng
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Li Wen
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Weiyan Li
- Hunan Soil and Fertilizer Institute, Changsha, China
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Wang J, Xie J, Li L, Luo Z, Zhang R, Wang L, Jiang Y. The Impact of Fertilizer Amendments on Soil Autotrophic Bacteria and Carbon Emissions in Maize Field on the Semiarid Loess Plateau. Front Microbiol 2021; 12:664120. [PMID: 34220750 PMCID: PMC8249863 DOI: 10.3389/fmicb.2021.664120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Soil autotrophic bacteria play a crucial role in regulating CO2 fixation and crop productivity. However, the information is limited to how fertilization amendments alter soil autotrophic bacterial community, crop yield, and carbon emission efficiency (CEE). Here, we estimated the impact of the structure and co-occurrence network of soil autotrophic bacterial community on maize yield and CEE. A long-term field experiment was conducted with five fertilization treatments in semiarid Loess Plateau, including no amendment (NA), chemical fertilizer (CF), chemical fertilizer plus commercial organic fertilizer (SC), commercial organic fertilizer (SM), and maize straw (MS). The results showed that fertilization amendments impacted the structure and network of soil Calvin-Benson-Bassham (CBB) (cbbL) gene-carrying bacterial community via changing soil pH and NO3-N. Compared with no amendment, the cbbL-carrying bacterial diversity was increased under the SC, SM, and MS treatments but decreased under the CF treatment. Soil autotrophic bacterial network contained distinct microbial modules that consisted of closely associated microbial species. We detected the higher abundances of soil cbbL-carrying bacterial genus Xanthobacter, Bradyrhizobium, and Nitrosospira. Structural equation modeling further suggested that the diversity, composition, and network of autotrophic bacterial community had strongly positive relationships with CEE and maize yield. Taken together, our results suggest that soil autotrophic bacterial community may drive crop productivity and CEE, and mitigate the atmospheric greenhouse effect.
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Affiliation(s)
- Jinbin Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China.,College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Junhong Xie
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China.,College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lingling Li
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China.,College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhuzhu Luo
- College of Resource and Environment, Gansu Agricultural University, Lanzhou, China
| | - Renzhi Zhang
- College of Resource and Environment, Gansu Agricultural University, Lanzhou, China
| | - Linlin Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China.,College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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14
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Wu S, Xi X, Fu X, Hu JJ, Zhang S, Wang L. Mixed electron donors synergistically enhance CO 2 fixation of non-photosynthetic microorganism communities through optimizing community structure to promote cbb gene transcription. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:16368-16379. [PMID: 33387320 DOI: 10.1007/s11356-020-12201-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Studies have shown that mixed electron donors (MEDs) can enhance the CO2-fixing efficiency of non-photosynthetic microbial communities (NPMCs), even up to the level of fixation observed when H2 is used as an electron donor. However, this promotion effect is not stable because its mechanism remains unclear. To elucidate the mechanisms involved, allowing further regulation and optimization of the MED system for improving the CO2-fixing efficiency of NPMCs consistently, cbb gene transcription level and efficiency, extracellular free organic carbon (EFOC) content as well as microbial structure of NPMCs under MED and other electron donor systems were investigated. MEDs synergistically promoted CO2 fixation efficiency of NPMCs, even producing levels seen when H2 was used as the electron donor. Subsequent experiments revealed that the cbb gene abundance and transcription level in the MED system were high compared with those in other single-electron donor systems; the concentration of EFOC per unit cell was relatively lower than that in any other electron donor system; and the system developed a large number of dominant heterotrophic bacteria such as Enterobacteriaceae and Vibrionaceae. Data analysis revealed a high negative correlation between EFOC concentration per unit cell and cbb gene abundance as well as gene transcription level. These results implied that MEDs can promote a complex microbial community structure enriched with high-efficiency heterotrophic bacteria, which can effectively reduce excessive EFOC generated by NPMCs in the CO2 fixation process, promoting overall cbb gene abundance and transcription level within the NPMC and thus enhancing CO2 fixation.
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Affiliation(s)
- Song Wu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Research Institute for Shanghai Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Xuefei Xi
- Shanghai Academy of Environmental Sciences, Shanghai, 200032, China
| | - Xiaohua Fu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Research Institute for Shanghai Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Jia-Jun Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Saiwei Zhang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Research Institute for Shanghai Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Lei Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
- Research Institute for Shanghai Pollution Control and Ecological Security, Shanghai, 200092, China.
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Qin J, Li M, Zhang H, Liu H, Zhao J, Yang D. Nitrogen Deposition Reduces the Diversity and Abundance of cbbL Gene-Containing CO 2-Fixing Microorganisms in the Soil of the Stipa baicalensis Steppe. Front Microbiol 2021; 12:570908. [PMID: 33737915 PMCID: PMC7961154 DOI: 10.3389/fmicb.2021.570908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/10/2021] [Indexed: 11/13/2022] Open
Abstract
CO2 fixation by autotrophic microbes has a significant effect on the carbon cycle in temperate grasslands. Nitrogen (N) deposition in soil has been steadily increasing for decades, which has consequences for soil microorganisms. However, the impact of this deposition on the diversity and abundance of CO2-fixing soil microorganisms remains unclear in temperate grasslands. In the present study, the cbbL gene, a key gene in the Calvin–Benson–Bassham cycle that encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, was used to study CO2-fixing microbes under different rates of N addition (0, 15, 30, 50, 100, and 150 kg N ha–1 yr–1) in a 9-year field experiment in a temperate grassland. The results showed that N addition led to significant reductions in cbbL gene abundance and genetic diversity and altered cbbL gene community composition. High N addition enhanced the relative abundances of Acidiferrobacterales and Rhizobiales but reduced those of Burkholderiales and Rhodobacterales. Structural equation modeling further revealed that N addition primarily reduced cbbL genetic diversity by increasing the soil NO3-N content and decreasing the soil pH. N addition indirectly reduced cbbL gene abundance, possibly by increasing the soil N/phosphorus (P) ratio and decreasing the soil pH. These findings suggest that N addition increases the soil available N and causes soil acidification, which may inhibit growth of CO2-fixing microbes to some extent.
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Affiliation(s)
- Jie Qin
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Ming Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Haifang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Hongmei Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Jianning Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Dianlin Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
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Tang H, Li C, Cheng K, Shi L, Wen L, Li W, Xiao X. Effect of different short-term tillage management on nitrogen-fixing bacteria community in a double-cropping paddy field of southern China. J Basic Microbiol 2020; 61:241-252. [PMID: 33351219 DOI: 10.1002/jobm.202000608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Accepted: 12/11/2020] [Indexed: 11/07/2022]
Abstract
Soil nitrogen (N)-fixing bacteria community plays an important role in the N cycling process in soil, but there is still limited information about how the soil microbes that drive this process to respond to combined application of tillage and crop residue management under the double-cropping rice (Oryza sativa L.) paddy field in southern of China. Therefore, the effects of 6-years short-term tillage treatment on soil N-fixing bacteria community under the double-cropping rice paddy field in southern China were studied by using the polymerase chain reaction-denaturing gradient gel electrophoresis method. The field experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), rotary tillage with crop residue removed as control (RTO). The results showed that the diversity index and richness index of cbbLR and nifH genes with CT, RT, and NT treatments were increased, compared with RTO treatment. Compared with RTO treatment, the abundance of cbbLR gene with CT, RT, and NT treatments were increased by 6.54, 4.73, and 2.78 times, respectively. Meanwhile, the abundance of nifH gene with CT, RT, and NT treatments were 5.32, 3.71, and 2.45 times higher than that of RTO treatment. The results also indicated that soil autotrophic Azotobacter and nitrogenase activity with CT and RT treatments were significantly higher (p < .05) than that of RTO treatment. There was an obvious difference in characteristic of soil N-fixing bacteria community between the application of crop residue and without crop residue input treatments. In summary, the results indicated that the abundance of N-fixing bacteria community in the double-cropping rice paddy field increased with conventional tillage and rotary tillage practice.
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Affiliation(s)
- Haiming Tang
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Chao Li
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Kaikai Cheng
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Lihong Shi
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Li Wen
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Weiyan Li
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Xiaoping Xiao
- Hunan Soil and Fertilizer Institute, Changsha, China
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Liao H, Qin F, Wang K, Zhang Y, Hao X, Chen W, Huang Q. Long-term chemical fertilization-driving changes in soil autotrophic microbial community depresses soil CO 2 fixation in a Mollisol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:141317. [PMID: 32814290 DOI: 10.1016/j.scitotenv.2020.141317] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 05/20/2023]
Abstract
Soil is the largest C pool in the terrestrial ecosystem. Numerous studies have been devoted to the decomposition of soil organic C as influenced by agricultural management. However, little is known about the effect of fertilization on the microbial CO2 fixation potential. Here, we examined the atmospheric CO2 fixation rates and structure of autotrophic cbbL-containing bacterial communities and accA-containing archaeal communities in response to 38 years of chemical and/or organic fertilizer application in a Mollisol. The autotrophic microbial abundance and community composition were analyzed by quantitative polymerase chain reaction and high throughput sequencing, respectively. Our results showed that chemical fertilization additions significantly decreased CO2 fixation rates by 57%, but organic manure use resulted in no notable differences compared to no fertilizer regimes (0.38 mg CO2 kg-1 soil d-1) through stable isotope methods. The declining soil pH and increasing Olsen-phosphorus in soils with chemical fertilization dramatically reduced the cbbL gene diversity and accA gene abundances and altered both the autotrophic bacterial and archaeal community compositions. The changes in CO2-fixation rate were more greatly attributed to the shifts in autotrophic bacterial community composition than to the diversity and abundance. The C fixation potentials were positively correlated with the relative abundances of Acidiphilium and Methylibium but were negatively related to those of Azospirillum and Nitrosospira. Both composition and abundance of the autotrophic archaeal community contributed together to the CO2 fixation activities. Our finding suggests that long-term chemical fertilization has a strong impact on the soil microbial CO2 fixation activity and autotrophic microorganisms in upland soils and highlight the important roles of the CO2 fixing process in soil organic carbon sequestration.
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Affiliation(s)
- Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Qin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuchen Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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Li M, Xu J, Jiang Z, Li Q. Molecular understanding of autotrophic CO2-fixing bacterial communities in composting based on RuBisCO genes analysis. J Biotechnol 2020; 320:36-43. [DOI: 10.1016/j.jbiotec.2020.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/31/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022]
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19
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Yang R, Xia X, Wang J, Zhu L, Wang J, Ahmad Z, Yang L, Mao S, Chen Y. Dose and time-dependent response of single and combined artificial contamination of sulfamethazine and copper on soil enzymatic activities. CHEMOSPHERE 2020; 250:126161. [PMID: 32092565 DOI: 10.1016/j.chemosphere.2020.126161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/04/2020] [Accepted: 02/08/2020] [Indexed: 06/10/2023]
Abstract
The widespread contamination of antibiotics and heavy metals results in imbalance in the ecosystem. However, the effect of the interaction between sulfamethazine (SM2) and copper (Cu) on soil enzymatic activities is unclear. Therefore, this study investigated the effect of single and combined artificial contamination of SM2 and Cu (0, 1.6 mmol kg-1 Cu and 0, 0.05, 0.2, 0.8 mmol kg-1 SM2) on soil enzymatic activities (urease, sucrose, phosphatase, and RubisCO). A single application of Cu at a concentration of 1.6 mmol kg-1 inhibited the urease, phosphatase and sucrase activities, while a stimulating effect on RubisCO activity was observed on day 7, 21, and 28 of incubation. The individual application of SM2 at higher concentration exhibited significant inhibition of sucrase, phosphatase, and urease activities while a stimulatory effect on RubisCO activity was observed on day 14 and 21 of incubation. The combined contamination of SM2 and Cu significantly inhibited the activities of urease, sucrase, and phosphatase. The effect of combined contamination of SM2 and Cu on the activity of RubisCO was different. The analysis results of interaction types show that there are synergistic or antagonistic effects between Cu and SM2, and these effects can amplify or reduce the effect of Cu or SM2 on soil enzyme activities. Integrated biological responses version 2 (IBRv2) analysis showed that the combined contamination of Cu and SM2 had a greater inhibitory or stimulatory effect on soil enzyme activities than the single contamination of Cu and SM2, depending upon dose and time.
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Affiliation(s)
- Rui Yang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Xiaoming Xia
- College of Plant Protection, Shandong Agricultural University, Taian, 271018, China.
| | - Jinhua Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Lusheng Zhu
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Jun Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Zulfiqar Ahmad
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, Hubei, 430072, China; Department of Environmental Sciences, University of California, Riverside, California, 92521, USA.
| | - Lili Yang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Shushuai Mao
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
| | - Yangyang Chen
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, PR China.
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Yue L, Kong W, Ji M, Liu J, Morgan-Kiss RM. Community response of microbial primary producers to salinity is primarily driven by nutrients in lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 696:134001. [PMID: 31454602 DOI: 10.1016/j.scitotenv.2019.134001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 06/10/2023]
Abstract
Higher microbial diversity was frequently observed in saline than fresh waters, but the underlying mechanisms remains unknown, particularly in microbial primary producers (MPP). MPP abundance and activity are notably constrained by high salinity, but facilitated by high nutrients. It remains to be ascertained whether and how nutrients regulate the salinity constraints on MPP abundance and community structure. Here we investigated the impact of nutrients on salinity constraints on MPP abundance and diversity in undisturbed lakes with a wide salinity range on the Tibetan Plateau. MPP community was explored using quantitative PCR, terminal restriction fragment length polymorphism and sequencing of cloning libraries targeting form IC cbbL gene. The MPP community structure was sorted by salinity into freshwater (salinity<1‰), saline (1‰ < salinity<29‰) and hypersaline (salinity>29‰) lakes. Furthermore, while MPP abundance, diversity and richness were significantly constrained with increasing salinity, these constraints were mitigated by enhancing total organic carbon (TOC) and total nitrogen (TN) contents in freshwater and saline lakes. In contrast, the MPP diversity increased significantly with the salinity in hypersaline lakes, due to the mitigation of enhancing TOC and TN contents and salt-tolerant MPP taxa. The mitigating effect of nutrients was more pronounced in saline than in freshwater and hypersaline lakes. The MPP compositions varied along salinity, with Betaproteobacteria dominating both the freshwater and saline lakes and Gammaproteobacteria dominating the hypersaline lakes. We concluded that high nutrients could mitigate the salinity constraining effects on MPP abundance, community richness and diversity. Our findings offer a novel insight into the salinity effects on primary producers and highlight the interactive effects of salinity and nutrients on MPP in lakes. These findings can be used as a baseline to illuminate the effects of increased anthropogenic activities altering nutrient dynamics on the global hydrological cycle and the subsequent responses thereof by MPP communities.
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Affiliation(s)
- Linyan Yue
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China.
| | - Mukan Ji
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinbo Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
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21
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Du Y, Wang T, Wang C, Anane PS, Liu S, Paz-Ferreiro J. Nitrogen fertilizer is a key factor affecting the soil chemical and microbial communities in a Mollisol. Can J Microbiol 2019; 65:510-521. [PMID: 30901528 DOI: 10.1139/cjm-2018-0683] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.
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Affiliation(s)
- Yan Du
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Tianye Wang
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Chengyu Wang
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Paul-Simon Anane
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Shuxia Liu
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Jorge Paz-Ferreiro
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne 3001, VIC, Australia
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22
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Wu X, Ge T, Yan W, Zhou J, Wei X, Chen L, Chen X, Nannipieri P, Wu J. Irrigation management and phosphorus addition alter the abundance of carbon dioxide-fixing autotrophs in phosphorus-limited paddy soil. FEMS Microbiol Ecol 2018; 93:4604778. [PMID: 29126231 DOI: 10.1093/femsec/fix154] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/07/2017] [Indexed: 11/14/2022] Open
Abstract
In this study, we assessed the interactive effects of phosphorus (P) application and irrigation methods on the abundances of marker genes (cbbL, cbbM, accA and aclB) of CO2-fixing autotrophs. We conducted rice-microcosm experiments using a P-limited paddy soil, with and without the addition of P fertiliser (P-treated-pot (P) versus control pot (CK)), and using two irrigation methods, namely alternate wetting and drying (AWD) and continuous flooding (CF). The abundances of bacterial 16S rRNA, archaeal 16S rRNA, cbbL, cbbM, accA and aclB genes in the rhizosphere soil (RS) and bulk soil (BS) were quantified. The application of P significantly altered the soil properties and stimulated the abundances of Bacteria, Archaea and CO2-fixation genes under CF treatment, but negatively influenced the abundances of Bacteria and marker genes of CO2-fixing autotrophs in BS soils under AWD treatment. The response of CO2-fixing autotrophs to P fertiliser depended on the irrigation management method. The redundancy analysis revealed that 54% of the variation in the functional marker gene abundances could be explained by the irrigation method, P fertiliser and the Olsen-P content; however, the rhizosphere effect did not have any significant influence. P fertiliser application under CF was more beneficial in improving the abundance of CO2-fixing autotrophs compared to the AWD treatment; thus, it is an ideal irrigation management method to increase soil carbon fixation.
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Affiliation(s)
- Xiaohong Wu
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China.,Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Changsha Observation and Research Station for the Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, No 644, Yuanda Second Road, Furong District, Changsha 410125, Hunan, China
| | - Tida Ge
- National Engineering Laboratory of Applied Technology for Forestry & Ecology in Southern China, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China
| | - Wende Yan
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China.,Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Changsha Observation and Research Station for the Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, No 644, Yuanda Second Road, Furong District, Changsha 410125, Hunan, China
| | - Juan Zhou
- National Engineering Laboratory of Applied Technology for Forestry & Ecology in Southern China, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China
| | - Xiaomeng Wei
- National Engineering Laboratory of Applied Technology for Forestry & Ecology in Southern China, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China
| | - Liang Chen
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China.,Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Changsha Observation and Research Station for the Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, No 644, Yuanda Second Road, Furong District, Changsha 410125, Hunan, China
| | - Xiangbi Chen
- National Engineering Laboratory of Applied Technology for Forestry & Ecology in Southern China, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China
| | - Paolo Nannipieri
- Department of Agrifood Production and Environmental Sciences, University of Firenze, Viale delle Cascine 15, Florence 50144, Italy
| | - Jinshui Wu
- National Engineering Laboratory of Applied Technology for Forestry & Ecology in Southern China, No 498, Shaoshan South Road, Tianxin District, Changsha 410004, Hunan, China
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Sauze J, Ogée J, Maron PA, Crouzet O, Nowak V, Wohl S, Kaisermann A, Jones SP, Wingate L. The interaction of soil phototrophs and fungi with pH and their impact on soil CO 2, CO 18O and OCS exchange. SOIL BIOLOGY & BIOCHEMISTRY 2017; 115:371-382. [PMID: 29200510 PMCID: PMC5666291 DOI: 10.1016/j.soilbio.2017.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/06/2017] [Accepted: 09/10/2017] [Indexed: 06/07/2023]
Abstract
The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (OCS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (α, β and γ) may have different affinities to CO2 and OCS and their expression should also vary between different microbial groups, differences in the community structure could impact the 'community-integrated' CA activity differently for CO2 and OCS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and OCS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototrophs. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototrophs abundance. OCS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. Our findings demonstrate that soil-atmosphere CO2, OCS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and supports the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and OCS.
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Affiliation(s)
- Joana Sauze
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | - Jérôme Ogée
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Olivier Crouzet
- INRA, UR 251 PESSAC, Centre Versailles-Grignon, RD 10, 78026 Versailles Cedex, France
| | - Virginie Nowak
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Steven Wohl
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | | | - Sam P. Jones
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | - Lisa Wingate
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
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24
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Zhang M, Liu X, Li Y, Wang G, Wang Z, Wen J. Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation. Sci Rep 2017; 7:474. [PMID: 28352108 PMCID: PMC5428726 DOI: 10.1038/s41598-017-00580-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/06/2017] [Indexed: 11/24/2022] Open
Abstract
To solve the competition problem of acidophilic bacteria and sulfate-reducing bacteria in the practical application of mine tailing bioremediation, research into the mechanisms of using different nutrients to adjust the microbial community was conducted. Competition experiments involving acidophilic bacteria and sulfate-reducing bacteria were performed by supplementing the media with yeast extract, tryptone, lactate, and glucose. The physiochemical properties were determined, and the microbial community structure and biomass were investigated using MiSeq sequencing and qRT-PCR, respectively. Four nutrients had different remediation mechanisms and yielded different remediation effects. Yeast extract and tryptone (more than 1.6 g/L) promoted sulfate-reducing bacteria and inhibited acidophilic bacteria. Lactate inhibited both sulfate-reducing and acidophilic bacteria. Glucose promoted acidophilic bacteria more than sulfate-reducing bacteria. Yeast extract was the best choice for adjusting the microbial community and bioremediation, followed by tryptone. Lactate kept the physiochemical properties stable or made slight improvements; however, glucose was not suitable for mine tailing remediation. Different nutrients had significant effects on the abundance of the second enzyme of the sulfate-reducing pathway (p < 0.05), which is the rate-limiting step of sulfate-reducing pathways. Nutrients changed the remediation effects effectively by adjusting the microbial community and the abundance of the sulfate-reducing rate-limiting enzyme.
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Affiliation(s)
- Mingjiang Zhang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Xingyu Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China.
| | - Yibin Li
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Guangyuan Wang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Zining Wang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Jiankang Wen
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
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25
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Ahn JH, Lee SA, Kim JM, Kim MS, Song J, Weon HY. Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices. J Microbiol 2016; 54:724-731. [PMID: 27796926 DOI: 10.1007/s12275-016-6463-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 11/29/2022]
Abstract
Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.
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Affiliation(s)
- Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Myung-Sook Kim
- Soil and Ferilization Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
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Hu Y, Wang L, Fu X, Yan J, Wu J, Tsang Y, Le Y, Sun Y. Salinity and nutrient contents of tidal water affects soil respiration and carbon sequestration of high and low tidal flats of Jiuduansha wetlands in different ways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 565:637-648. [PMID: 27208721 DOI: 10.1016/j.scitotenv.2016.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 06/05/2023]
Abstract
Soils were collected from low tidal flats and high tidal flats of Shang shoal located upstream and Xia shoal located downstream with different tidal water qualities, in the Jiuduansha wetland of the Yangtze River estuary. Soil respiration (SR) in situ and soil abiotic and microbial characteristics were studied to clarify the respective differences in the effects of tidal water salinity and nutrient levels on SR and soil carbon sequestration in low and high tidal flats. In low tidal flats, higher total nitrogen (TN) and lower salinity in the tidal water of Shang shoal resulted in higher TN and lower salinity in its soils compared with Xia shoal. These would benefit β-Proteobacteria and Anaerolineae in Shang shoal soil, which might have higher heterotrophic microbial activities and thus soil microbial respiration and SR. In low tidal flats, where soil moisture was high and the major carbon input was active organic carbon from tidal water, increasing TN was a more important factor than salinity and obviously enhanced soil microbial heterotrophic activities, soil microbial respiration and SR. While, in high tidal flats, higher salinity in Xia shoal due to higher salinity in tidal water compared with Shang shoal benefited γ-Proteobacteria which might enhance autotrophic microbial activity, and was detrimental to β-Proteobacteria in Xia shoal soil. These might have led to lower soil microbial respiration and thus SR in Xia shoal compared with Shang shoal. In high tidal flats, where soil moisture was relatively lower and the major carbon input was plant biomass that was difficult to degrade, soil salinity was the major factor restraining microbial activities, soil microbial respiration and SR.
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Affiliation(s)
- Yu Hu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Collaborative Innovation Center for Regional Environmental Quality, China
| | - Lei Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Collaborative Innovation Center for Regional Environmental Quality, China.
| | - Xiaohua Fu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Collaborative Innovation Center for Regional Environmental Quality, China
| | - Jianfang Yan
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Collaborative Innovation Center for Regional Environmental Quality, China
| | - Jihua Wu
- Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai 200433, China
| | - Yiufai Tsang
- Department of Science and Environmental Studies, Hong Kong Institute of Education, Hong Kong, China
| | - Yiquan Le
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Collaborative Innovation Center for Regional Environmental Quality, China
| | - Ying Sun
- Shanghai Jiuduansha Wetland Nature Reserve Administration, Shanghai 200135, China
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27
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Cai W, Li Y, Wang P, Niu L, Zhang W, Wang C. Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:15727-15738. [PMID: 27146525 DOI: 10.1007/s11356-016-6757-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/25/2016] [Indexed: 06/05/2023]
Abstract
Bisphenol A (BPA) and 4-nonylphenol (NP) are ubiquitous pollutants with estrogenic activity in aquatic environment and have attracted global concern due to their disruption of endocrine systems. This study investigated the spatial distribution characteristics of the bacterial groups involved in the degradation of BPA and NP within biofilms in an urban river using terminal restriction fragment length polymorphism based on 16S rRNA gene sequences. The effects of the pollution level and water parameters on these groups were also assessed. Hierarchical cluster analysis grouped the sampling sites into three clusters reflecting their varying nutrient pollution levels of relatively slight pollution (SP), moderate pollution (MP), and high pollution (HP) based on water quality data and Environmental Quality Standard for Surface Water of China (GB3838-2002). The BPA and NP concentration in river water ranged from 0.8 to 77.5 and 10.2 to 162.9 ng L(-1), respectively. Comamonadaceae, Pseudomonadaceae, Alcaligenaceae, Bacillaceae, Sphingomonadacea, Burkholderiaceae, and Rhizobiaceae were the dominant bacterial taxa involved in BPA and NP degradation, comprising an average of 9.8, 8.1, 7.6, 6.7, 6.2, 4.1, and 2.8 % of total sequences, respectively. The total abundance of these groups showed a slight upward trend and subsequently rapidly decreased with increasing pollution levels. The average proportion of Comamonadaceae in MP river sections was almost 1.5-2 times than that in SP or HP one. The distribution of functional groups was found related to environmental variables, especially pH, conductivity, ammonium nitrogen (NH3-N), and BPA. The abundance of Comamonadaceae and Rhizobiaceae was both closely related to higher values of pH and conductivity as well as lower concentrations of NP and BPA. Alcaligenaceae and Pseudomonadaceae were associated with higher concentrations of TP and CODMn and inversely correlated with DO concentration. This study might provide effective data on bacterial group changes in polluted urban rivers.
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Affiliation(s)
- Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
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28
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Xiang X, Gibbons SM, He JS, Wang C, He D, Li Q, Ni Y, Chu H. Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau. PeerJ 2016; 4:e2226. [PMID: 27478711 PMCID: PMC4950554 DOI: 10.7717/peerj.2226] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/15/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The Qinghai-Tibet Plateau (QTP) is home to the vast grassland in China. The QTP grassland ecosystem has been seriously degraded by human land use practices and climate change. Fertilization is used in this region to increase vegetation yields for grazers. The impact of long-term fertilization on plant and microbial communities has been studied extensively. However, the influence of short-term fertilization on arbuscular mycorrhizal fungal (AMF) communities in the QTP is largely unknown, despite their important functional role in grassland ecosystems. METHODS We investigated AMF community responses to three years of N and/or P addition at an experimental field site on the QTP, using the Illumina MiSeq platform (PE 300). RESULTS Fertilization resulted in a dramatic shift in AMF community composition and NP addition significantly increased AMF species richness and phylogenetic diversity. Aboveground biomass, available phosphorus, and NO3 (-) were significantly correlated with changes in AMF community structure. Changes in these factors were driven by fertilization treatments. Thus, fertilization had a large impact on AMF communities, mediated by changes in aboveground productivity and soil chemistry. DISCUSSION Prior work has shown how plants often lower their reliance on AMF symbioses following fertilization, leading to decrease AMF abundance and diversity. However, our study reports a rise in AMF diversity with fertilization treatment. Because AMF can provide stress tolerance to their hosts, we suggest that extreme weather on the QTP may help drive a positive relationship between fertilizer amendment and AMF diversity.
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Affiliation(s)
- Xingjia Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sean M. Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Chao Wang
- Department of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Dan He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Qian Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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29
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Ge T, Wu X, Liu Q, Zhu Z, Yuan H, Wang W, Whiteley AS, Wu J. Effect of simulated tillage on microbial autotrophic CO2 fixation in paddy and upland soils. Sci Rep 2016; 6:19784. [PMID: 26795428 PMCID: PMC4726159 DOI: 10.1038/srep19784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 12/18/2015] [Indexed: 11/09/2022] Open
Abstract
Tillage is a common agricultural practice affecting soil structure and biogeochemistry. To evaluate how tillage affects soil microbial CO2 fixation, we incubated and continuously labelled samples from two paddy soils and two upland soils subjected to simulated conventional tillage (CT) and no-tillage (NT) treatments. Results showed that CO2 fixation ((14)C-SOC) in CT soils was significantly higher than in NT soils. We also observed a significant, soil type- and depth-dependent effect of tillage on the incorporation rates of labelled C to the labile carbon pool. Concentrations of labelled C in the carbon pool significantly decreased with soil depth, irrespective of tillage. Additionally, quantitative PCR assays revealed that for most soils, total bacteria and cbbL-carrying bacteria were less abundant in CT versus NT treatments, and tended to decrease in abundance with increasing depth. However, specific CO2 fixation activity was significantly higher in CT than in NT soils, suggesting that the abundance of cbbL-containing bacteria may not always reflect their functional activity. This study highlights the positive effect of tillage on soil microbial CO2 fixation, and the results can be readily applied to the development of sustainable agricultural management.
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Affiliation(s)
- Tida Ge
- Changsha Research Station for Agricultural and Environmental Monitoring &Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Jiangshu, 210008, China
| | - Xiaohong Wu
- Changsha Research Station for Agricultural and Environmental Monitoring &Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.,Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Qiong Liu
- Changsha Research Station for Agricultural and Environmental Monitoring &Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.,ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Zhenke Zhu
- Changsha Research Station for Agricultural and Environmental Monitoring &Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.,ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Hongzhao Yuan
- Changsha Research Station for Agricultural and Environmental Monitoring &Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.,ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Wei Wang
- Changsha Research Station for Agricultural and Environmental Monitoring &Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - A S Whiteley
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China.,School of Earth and Environment, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jinshui Wu
- Changsha Research Station for Agricultural and Environmental Monitoring &Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.,ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
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30
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Yuan H, Ge T, Chen X, Liu S, Zhu Z, Wu X, Wei W, Whiteley AS, Wu J. Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice. MICROBIAL ECOLOGY 2015; 70:971-980. [PMID: 25956939 DOI: 10.1007/s00248-015-0621-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/23/2015] [Indexed: 06/04/2023]
Abstract
Elucidating the biodiversity of CO(2)-assimilating bacterial and algal communities in soils is important for obtaining a mechanistic view of terrestrial carbon sinks operating at global scales. "Red" acidic soils (Orthic Acrisols) cover large geographic areas and are subject to a range of management practices, which may alter the balance between carbon dioxide production and assimilation through changes in microbial CO(2)-assimilating populations. Here, we determined the abundance and diversity of CO(2)-assimilating bacteria and algae in acidic soils using quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) of the cbbL gene, which encodes the key CO(2) assimilation enzyme (ribulose-1,5-bisphosphate carboxylase/oxygenase) in the Calvin cycle. Within the framework of a long-term experiment (Taoyuan Agro-ecosystem, subtropical China), paddy rice fields were converted in 1995 to four alternative land management regimes: natural forest (NF), paddy rice (PR), maize crops (CL), and tea plantations (TP). In 2012 (17 years after land use transformation), we collected and analyzed the soils from fields under the original and converted land management regimes. Our results indicated that fields under the PR soil management system harbored the greatest abundance of cbbL copies (4.33 × 10(8) copies g(-1) soil). More than a decade after converting PR soils to natural, rotation, and perennial management systems, a decline in both the diversity and abundance of cbbL-harboring bacteria and algae was recorded. The lowest abundance of bacteria (0.98 × 10(8) copies g(-1) soil) and algae (0.23 × 10(6) copies g(-1) soil) was observed for TP soils. When converting PR soil management to alternative management systems (i.e., NF, CL, and TP), soil edaphic factors (soil organic carbon and total nitrogen content) were the major determinants of bacterial autotrophic cbbL gene diversity. In contrast, soil phosphorus concentration was the major regulator of algal cbbL community composition. Our results provide new insights into the diversity, abundance, and modulation of organisms responsible for microbial autotrophic CO(2) fixation in red acidic soils subjected to changing management regimes.
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Affiliation(s)
- Hongzhao Yuan
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Tida Ge
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China.
| | - Xiangbi Chen
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Shoulong Liu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Zhenke Zhu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Xiaohong Wu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
| | - Wenxue Wei
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- Taoyuan Agro-ecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Andrew Steven Whiteley
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
- School of Earth & Environment, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Jinshui Wu
- Changsha Research Station for Agricultural and Environmental Monitoring & Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology, Hunan, 410125, China
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Laccase activity is proportional to the abundance of bacterial laccase-like genes in soil from subtropical arable land. World J Microbiol Biotechnol 2015; 31:2039-45. [PMID: 26354020 DOI: 10.1007/s11274-015-1944-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
Abstract
Laccase enzymes produced by both soil bacteria and fungi play important roles in refractory organic matter turnover in terrestrial ecosystems. We investigated the abundance and diversity of fungal laccase genes and bacterial laccase-like genes in soil from subtropical arable lands, and identified which microbial group was associated with laccase activity. Compared with fungal laccase genes, the bacterial laccase-like genes had greater abundance, richness and Shannon-Wiener diversity. More importantly, laccase activity can be explained almost exclusively by the bacterial laccase-like genes, and their abundance had significant linear relationship with laccase activity. Thus, bacterial laccase-like gene has great potential to be used as a sensitive indicator of laccase enzyme for refractory organic matter turnover in subtropical arable lands.
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Guo G, Kong W, Liu J, Zhao J, Du H, Zhang X, Xia P. Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau. Appl Microbiol Biotechnol 2015; 99:8765-76. [PMID: 26084890 DOI: 10.1007/s00253-015-6723-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/19/2015] [Accepted: 05/23/2015] [Indexed: 10/23/2022]
Abstract
Soil microbial autotrophs play a significant role in CO2 fixation in terrestrial ecosystem, particularly in vegetation-constrained ecosystems with environmental stresses, such as the Tibetan Plateau characterized by low temperature and high UV. However, soil microbial autotrophic communities and their driving factors remain less appreciated. We investigated the structure and shift of microbial autotrophic communities and their driving factors along an elevation gradient (4400-5100 m above sea level) in alpine grassland soils on the Tibetan Plateau. The autotrophic microbial communities were characterized by quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning/sequencing of cbbL genes, encoding the large subunit for the CO2 fixation protein ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). High cbbL gene abundance and high RubisCO enzyme activity were observed and both significantly increased with increasing elevations. Path analysis identified that soil RubisCO enzyme causally originated from microbial autotrophs, and its activity was indirectly driven by soil water content, temperature, and NH4 (+) content. Soil autotrophic microbial community structure dramatically shifted along the elevation and was jointly driven by soil temperature, water content, nutrients, and plant types. The autotrophic microbial communities were dominated by bacterial autotrophs, which were affiliated with Rhizobiales, Burkholderiales, and Actinomycetales. These autotrophs have been well documented to degrade organic matters; thus, metabolic versatility could be a key strategy for microbial autotrophs to survive in the harsh environments. Our results demonstrated high abundance of microbial autotrophs and high CO2 fixation potential in alpine grassland soils and provided a novel model to identify dominant drivers of soil microbial communities and their ecological functions.
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Affiliation(s)
- Guangxia Guo
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jinbo Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingxue Zhao
- Key Laboratory of Tibetan Environmental Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haodong Du
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pinhua Xia
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.,Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang, 550001, China
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Long XE, Yao H, Wang J, Huang Y, Singh BK, Zhu YG. Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7152-7160. [PMID: 25989872 DOI: 10.1021/acs.est.5b00506] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.
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Affiliation(s)
- Xi-En Long
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Huaiying Yao
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Juan Wang
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Ying Huang
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
- ‡Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Brajesh K Singh
- §Hawkesbury Institute for the Environment, University of Western Sydney, Penrith South DC, NSW 2751, Australia
| | - Yong-Guan Zhu
- †Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China
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Wu X, Ge T, Wang W, Yuan H, Wegner CE, Zhu Z, Whiteley AS, Wu J. Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil. Front Microbiol 2015; 6:379. [PMID: 26005435 PMCID: PMC4424977 DOI: 10.3389/fmicb.2015.00379] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 04/13/2015] [Indexed: 11/26/2022] Open
Abstract
The effect of different cropping systems on CO2 fixation by soil microorganisms was studied by comparing soils from three exemplary cropping systems after 10 years of agricultural practice. Studied cropping systems included: continuous cropping of paddy rice (rice-rice), rotation of paddy rice and rapeseed (rice-rapeseed), and rotated cropping of rapeseed and corn (rapeseed-corn). Soils from different cropping systems were incubated with continuous 14C-CO2 labeling for 110 days. The CO2-fixing bacterial communities were investigated by analyzing the cbbL gene encoding ribulose-1,5-bisphosphate carboxylase oxygenase (RubisCO). Abundance, diversity and activity of cbbL-carrying bacteria were analyzed by quantitative PCR, cbbL clone libraries and enzyme assays. After 110 days incubation, substantial amounts of 14C-CO2 were incorporated into soil organic carbon (14C-SOC) and microbial biomass carbon (14C-MBC). Rice-rice rotated soil showed stronger incorporation rates when looking at 14C-SOC and 14C-MBC contents. These differences in incorporation rates were also reflected by determined RubisCO activities. 14C-MBC, cbbL gene abundances and RubisCO activity were found to correlate significantly with 14C-SOC, indicating cbbL-carrying bacteria to be key players for CO2 fixation in these soils. The analysis of clone libraries revealed distinct cbbL-carrying bacterial communities for the individual soils analyzed. Most of the identified operational taxonomic units (OTU) were related to Nitrobacter hamburgensis, Methylibium petroleiphilum, Rhodoblastus acidophilus, Bradyrhizobium, Cupriavidus metallidurans, Rubrivivax, Burkholderia, Stappia, and Thiobacillus thiophilus. OTUs related to Rubrivivax gelatinosus were specific for rice-rice soil. OTUs linked to Methylibium petroleiphilum were exclusively found in rice-rapeseed soil. Observed differences could be linked to differences in soil parameters such as SOC. We conclude that the long-term application of cropping systems alters underlying soil parameters, which in turn selects for distinct autotrophic communities.
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Affiliation(s)
- Xiaohong Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
| | - Wei Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Hongzhao Yuan
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Zhenke Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
| | - Andrew S Whiteley
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China ; School of Earth and Environment, The University of Western Australia Crawley, WA, Australia
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
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35
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Liu JF, Sun XB, Yang GC, Mbadinga SM, Gu JD, Mu BZ. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration. Front Microbiol 2015; 6:236. [PMID: 25873911 PMCID: PMC4379918 DOI: 10.3389/fmicb.2015.00236] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.
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Affiliation(s)
- Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Xiao-Bo Sun
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Guang-Chao Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, University of Hong Kong Hong Kong, China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
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36
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Yousuf B, Kumar R, Mishra A, Jha B. Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities. PLoS One 2014; 9:e107025. [PMID: 25225969 PMCID: PMC4167329 DOI: 10.1371/journal.pone.0107025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/07/2014] [Indexed: 11/23/2022] Open
Abstract
Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO2 concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.
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Affiliation(s)
- Basit Yousuf
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - Raghawendra Kumar
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - Avinash Mishra
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
- * E-mail: (AM); (BJ)
| | - Bhavanath Jha
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
- * E-mail: (AM); (BJ)
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Li J, Zheng YM, Liu YR, Ma YB, Hu HW, He JZ. Initial copper stress strengthens the resistance of soil microorganisms to a subsequent copper stress. MICROBIAL ECOLOGY 2014; 67:931-941. [PMID: 24682341 DOI: 10.1007/s00248-014-0391-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/07/2014] [Indexed: 06/03/2023]
Abstract
To improve the prediction of essential ecosystem functioning under future environmental disturbances, it is of significance to identify responses of soil microorganisms to environmental stresses. In this study, we collected polluted soil samples from field plots with eight copper levels ranging from 0 to 3,200 mg Cu kg(-1) soil. Then, the soils with 0 and 3,200 mg Cu kg(-1) were selected to construct a microcosm experiment. Four treatments were set up including Cu0-C and Cu3200-C without further Cu addition, and Cu0-A and Cu3200-A with addition of 57.5 mg Cu kg(-1) soil. We measured substrate-induced respiration (SIR) and potential nitrification rate (PNR). Furthermore, the abundance of bacterial, archaeal 16S rRNA genes, ammonia-oxidizing bacteria and archaea amoA genes were determined through quantitative PCR. The soil microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP). For the field samples, the SIR and PNR as well as the abundance of soil microorganisms varied significantly between eight copper levels. Soil microbial communities highly differed between the low and high copper stress. In the microcosm experiment, the PNR and SIR both recovered while the abundance of soil microorganisms varied irregularly during the 90-day incubation. The differences of microbial communities measured by pairwise Bray-Curtis dissimilarities between Cu0-A and Cu0-C on day 0 were significantly higher after subsequent stress than before. However, the differences of microbial communities between Cu3200-A and Cu3200-C on day 0 changed little between after subsequent stress and before. Therefore, initial copper stress could increase the resistance of soil microorganisms to subsequent copper stress.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Xiao KQ, Bao P, Bao QL, Jia Y, Huang FY, Su JQ, Zhu YG. Quantitative analyses of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit genes (cbbL) in typical paddy soils. FEMS Microbiol Ecol 2013; 87:89-101. [DOI: 10.1111/1574-6941.12193] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ke-Qing Xiao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Peng Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Qiong-Li Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Yan Jia
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Fu-Yi Huang
- University of Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
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Wu X, Ge T, Yuan H, Li B, Zhu H, Zhou P, Sui F, O’Donnell AG, Wu J. Changes in bacterial CO2 fixation with depth in agricultural soils. Appl Microbiol Biotechnol 2013; 98:2309-19. [DOI: 10.1007/s00253-013-5179-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/04/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
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40
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Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics. Microbiol Res 2012; 168:165-73. [PMID: 23083746 DOI: 10.1016/j.micres.2012.09.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/20/2012] [Accepted: 09/17/2012] [Indexed: 12/22/2022]
Abstract
Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling.
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