1
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Zhang X, Liang Q, Wang G, Zhang H, Zhang A, Tan Y, Bol R. Incorporating straw into intensively farmed cropland soil can reduce N 2O emission via inhibition of nitrification and denitrification pathways. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118115. [PMID: 37196616 DOI: 10.1016/j.jenvman.2023.118115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
Straw incorporation (SI) combined with N fertilizer has been shown to affect soil N2O emission and N-related functional microbes in agriculture. However, the responses of N2O emission, community structure of nitrifiers and denitrifiers and related microbial functional genes to straw management strategies in the winter wheat season in China remain unclear. Here, we conducted a two-season experiment in a winter wheat field in Ningjing County, northern China, to examine four treatments: no fertilizer with (N0S1) and without maize straw (N0S0); N fertilizer with (N1S1) and without maize straw (N1S0), and their effects on N2O emissions, soil chemical parameters, crop yield, as well as the dynamics of nitrifying and denitrifying microbial communities. We found that seasonal N2O emissions decreased by 7.1-11.1% (p < 0.05) in N1S1 as compared to N1S0, without significant difference between N0S1 and N0S0. In combination with N fertilization, SI increased the yield by 2.6-4.3%, altered the microbial community composition, increased Shannon and ACE indexes, and decreased the abundance of AOA (9.2%), AOB (32.2%; p < 0.05), nirS (35.2%; p < 0.05), nirK (21.6%; p < 0.05) and nosZ (19.2%). However, in the absence of N fertilizer, SI promoted the major genera of Nitrosavbrio (AOB), unclassifiied_Gammaproteobacteria, Rhodanobacter (nirS), Sinorhizobium (nirK), which strongly correlated positively with N2O emissions. Thereby, a negative interaction effect between SI and N fertilizer on AOB and nirS emphasized that SI could offset the increase of N2O emission caused by fertilization. Soil moisture and NO3- concentration were the major factors affecting N-related microbial community structure. Our study reveals that SI suppressed N2O emission significantly and simultaneously decreased the abundance of N-related functional genes and altered denitrifying bacterial community composition. We conclude that SI helps to enhance yield and alleviate fertilizer-induced environmental costs in intensively farmed fields in northern China.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Resources and Environmental Sciences, Hebei Agricultural University, Baoding, 071000, China.
| | - Qing Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Resources and Environmental Sciences, Hebei Agricultural University, Baoding, 071000, China
| | - Guiyan Wang
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, Hebei, 071001, China
| | - Haowen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Resources and Environmental Sciences, Hebei Agricultural University, Baoding, 071000, China
| | - Aijun Zhang
- Mountainous Area Research Institute of Hebei Province, Baoding, 071000, China
| | - Yuechen Tan
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, 100091, China
| | - Roland Bol
- Institute of Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany; School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, LL57 2UW, UK
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2
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Niu Y, Hu W, Zhou T, He B, Chen X, Li Y. Diversity of nirS and nirK denitrifying bacteria in rhizosphere and non-rhizosphere soils of halophytes in Ebinur Lake Wetland. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2070030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Yanhui Niu
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Wenge Hu
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Tingting Zhou
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Bo He
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Xuemei Chen
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Yang Li
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
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3
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Li X, Deng Q, Zhang Z, Bai D, Liu Z, Cao X, Zhou Y, Song C. The role of sulfur cycle and enzyme activity in dissimilatory nitrate reduction processes in heterotrophic sediments. CHEMOSPHERE 2022; 308:136385. [PMID: 36096301 DOI: 10.1016/j.chemosphere.2022.136385] [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] [Received: 06/26/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
The dissimilatory nitrate (NO3-) reduction processes (DNRPs) play an important role in regulating the nitrogen (N) balance of aquatic ecosystem. Organic carbon (OC) and sulfur are important factors that influence the DNRPs. In this study, we investigated the effects of sulfur cycle and enzyme activity on DNRPs in the natural and human-modified heterotrophic sediments. Quarterly monitoring of anaerobic ammonium oxidation, denitrification (DNF), and dissimilatory NO3- reduction to ammonium (DNRA) in sediments was conducted using 15N isotope tracing method. qPCR and high-throughput sequencing were applied to characterize the DNF and DNRA microbial abundances and communities. Results showed that instead of the OC, the glucosidase activity (GLU) was the key driver of the DNRPs. Furthermore, instead of the ratio of OC to NO3-, the GLU and the ratio of OC to sulfide (C/S) correctly indicated the partitioning of DNRPs in this study. We deduced that the sulfur reduction processes competed with the DNRPs for the available OC. In addition, the inhibitory effect of sulfide (final product of the sulfur reduction processes) on the DNRPs bacterial community were observed, which suggested a general restrictive role of the sulfur cycle in the regulation and partitioning of the DNRPs in heterotrophic sediments.
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Affiliation(s)
- Xiaowen Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Qinghui Deng
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, PR China.
| | - Zhimin Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Dong Bai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China.
| | - Zhenghan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China.
| | - Xiuyun Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Yiyong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Chunlei Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
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4
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Walker JB, Rinehart S, Greenberg‐Pines G, White WK, DeSantiago R, Lipson DA, Long JD. Aboveground competition influences density‐dependent effects of cordgrass on sediment biogeochemistry. Ecol Evol 2022; 12:e8722. [PMID: 35356584 PMCID: PMC8939245 DOI: 10.1002/ece3.8722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/08/2022] [Accepted: 02/22/2022] [Indexed: 11/06/2022] Open
Abstract
Interspecific interactions between plants influence plant phenotype, distribution, abundance, and community structure. Each of these can, in turn, impact sediment biogeochemistry. Although the population and community level impacts of these interactions have been extensively studied, less is known about their effect on sediment biogeochemistry. This is surprising given that many plants are categorized as foundation species that exert strong control on community structure. In southern California salt marshes, we used clipping experiments to manipulate aboveground neighbor presence to study interactions between two dominant plants, Pacific cordgrass (Spartina foliosa) and perennial pickleweed (Sarcocornia pacifica). We also measured how changes in cordgrass stem density influenced sediment biogeochemistry. Pickleweed suppressed cordgrass stem density but had no effect on aboveground biomass. For every cordgrass stem lost per square meter, porewater ammonium increased 0.3–1.0 µM. Thus, aboveground competition with pickleweed weakened the effects of cordgrass on sediment biogeochemistry. Predictions about plant–soil feedbacks, especially under future climate scenarios, will be improved when plant–plant interactions are considered, particularly those containing dominant and foundation species.
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Affiliation(s)
- Janet B. Walker
- Department of Biology San Diego State University San Diego California USA
- Coastal and Marine Institute San Diego State University San Diego California USA
- Southern California Coastal Water Research Project Costa Mesa California USA
| | - Shelby Rinehart
- Department of Biology San Diego State University San Diego California USA
- Coastal and Marine Institute San Diego State University San Diego California USA
- Department of Biological Sciences University of Alabama Tuscaloosa Alabama USA
| | - Gabriel Greenberg‐Pines
- Department of Biology San Diego State University San Diego California USA
- Coastal and Marine Institute San Diego State University San Diego California USA
- Department of Zoology and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Wendi K. White
- Department of Biology San Diego State University San Diego California USA
- Coastal and Marine Institute San Diego State University San Diego California USA
- Department of Biology University of Massachusetts Boston Boston Massachusetts USA
| | - Ric DeSantiago
- Department of Biology San Diego State University San Diego California USA
- Coastal and Marine Institute San Diego State University San Diego California USA
- Department of Environmental Science and Policy University of California Davis Davis California USA
| | - David A. Lipson
- Department of Biology San Diego State University San Diego California USA
| | - Jeremy D. Long
- Department of Biology San Diego State University San Diego California USA
- Coastal and Marine Institute San Diego State University San Diego California USA
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5
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Yang Y, Liu H, Lv J. Response of N 2O emission and denitrification genes to different inorganic and organic amendments. Sci Rep 2022; 12:3940. [PMID: 35273224 PMCID: PMC8913736 DOI: 10.1038/s41598-022-07753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/09/2022] [Indexed: 11/10/2022] Open
Abstract
Denitrification is a key biochemical process in nitrogen cycling and nitrous oxide (N2O) production. In this study, the impacts of different inorganic and organic amendments (OAs) on the abundance of denitrifying genes (nirS, nirK and nosZ) and the level of N2O emission were examined with incubation experiments. Six treatments included the indicated applications: (i) no fertilization (CK); (ii) urea application alone (U); (iii) wheat straw plus urea (U + WS); (iv) pig manure plus urea (U + PM); (v) compost product plus urea (U + CP); and (vi) improved compost product plus urea (U + IC). The results indicated that all fertilization treatments increased accumulative N2O emissions compared with the CK treatment. The U + WS, U + PM and U + CP treatments increased N2O emissions by 2.12–141.3%, and the U + IC treatment decreased N2O emissions by 23.24% relative to the U treatment. nirK was the dominant denitrification gene rather than nirS and nosZ found in soil. Additionally, the highest abundance of nirK gene was that with the U + PM treatment, and the lowest was that with the U + IC treatment. Additionally, changes in the nirK gene were highly correlated with levels of dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and nitrate nitrogen (NO3–N). Automatic linear modeling revealed that N2O emission was closely related to the nirK gene, DOC and NO3–N. Overall, the use of urea and improved compost as co-amendments retarded N2O emission to a considerable degree compared with other OA additions.
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Affiliation(s)
- Yajun Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, People's Republic of China
| | - Hexiang Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, People's Republic of China
| | - Jialong Lv
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, People's Republic of China.
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6
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Tang H, Li C, Cheng K, Shi L, Wen L, Xiao X, Xu Y, Li W, Wang K. Effects of Short-Term Soil Tillage Management on Activity and Community Structure of Denitrifiers under Double- Cropping Rice Field. J Microbiol Biotechnol 2020; 30:1688-1696. [PMID: 32958734 PMCID: PMC9728280 DOI: 10.4014/jmb.2007.07012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
Soil physical and chemical characteristics, soil potential denitrification rates (PDR), community composition and nirK-, nirS- and nosZ-encoding denitrifiers were studied by using MiSeq sequencing, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment polymorphism (T-RFLP) technologies base on short-term (5-year) tillage field experiment. The 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), and rotary tillage with crop residue removed as control (RTO). The results indicated that soil organic carbon, total nitrogen and NH4+-N contents were increased with CT, RT and NT treatments. Compared with RTO treatment, the copies number of nirK, nirS and nosZ in paddy soil with CT, RT and NT treatments were significantly increased. The principal coordinate analysis indicated that tillage management and crop residue returning management were the most and the second important factors for the change of denitrifying bacteria community, respectively. Meanwhile, this study indicated that activity and community composition of denitrifiers with CT, RT and NT treatments were increased, compared with RTO treatment. This result showed that nirK, nirS and nosZ-type denitrifiers communities in crop residue applied soil had higher species diversity compared with crop residue removed soil, and denitrifying bacteria community composition were dominated by Gammaproteobacteria, Deltaproteobacteria, and Betaproteobacteria. Therefore, it is a beneficial practice to increase soil PDR level, abundance and community composition of nitrogen-functional soil microorganism by combined application of tillage with crop residue management.
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Affiliation(s)
- Haiming Tang
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China,Corresponding author Phone: +86-731-84696102 Fax: +86-731-84691581 E-mail :
| | - Chao Li
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China
| | - Kaikai Cheng
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China
| | - Lihong Shi
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China
| | - Li Wen
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China
| | - Xiaoping Xiao
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China
| | - Yilan Xu
- Hunan Biological and Electromechanical Polytechnic, Changsha 41017, P.R. China
| | - Weiyan Li
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China
| | - Ke Wang
- Hunan Soil and Fertilizer Institute, Changsha 4025, P.R. China
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7
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Yang Z, Guan Y, Bello A, Wu Y, Ding J, Wang L, Ren Y, Chen G, Yang W. Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China. PeerJ 2020; 8:e8844. [PMID: 32341890 PMCID: PMC7182023 DOI: 10.7717/peerj.8844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/02/2020] [Indexed: 11/20/2022] Open
Abstract
Organic fertilizer application could have an impact on the nitrogen cycle mediated by microorganisms in arable soils. However, the dynamics of soil ammonia oxidizers and denitrifiers in response to compost addition are less understood. In this study, we examined the effect of four compost application rates (0, 11.25, 22.5 and 45 t/ha) on soil ammonia oxidizers and denitrifiers at soybean seedling, flowering and mature stage in a field experiment in Northeast China. As revealed by quantitative PCR, compost addition significantly enhanced the abundance of ammonia oxidizing bacteria (AOB) at seedling stage, while the abundance of ammonia oxidizing archaea was unaffected across the growing season. The abundance of genes involved in denitrification (nirS, nirK and nosZ) were generally increased along with compost rate at seedling and flowering stages, but not in mature stage. The non-metric multidimensional scaling analysis revealed that moderate and high level of compost addition consistently induced shift in AOB and nirS containing denitrifers community composition across the growing season. Among AOB lineages, Nitrosospira cluster 3a gradually decreased along with the compost rate across the growing season, while Nitrosomonas exhibited an opposite trend. Network analysis indicated that the complexity of AOB and nirS containing denitrifiers network gradually increased along with the compost rate. Our findings highlighted the positive effect of compost addition on the abundance of ammonia oxidizers and denitrifiers and emphasized that compost addition play crucial roles in shaping their community compositions and co-occurrence networks in black soil of Northeast China.
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Affiliation(s)
- Zhongzan Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yupeng Guan
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yanxiang Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jiayi Ding
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Leiqi Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yuqing Ren
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Guangxin Chen
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
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8
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Wang C, Li J, Wu Y, Song Y, Liu R, Cao Z, Cui Y. Shifts of the nirS and nirK denitrifiers in different land use types and seasons in the Sanjiang Plain, China. J Basic Microbiol 2019; 59:1040-1048. [PMID: 31469176 DOI: 10.1002/jobm.201900192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 08/10/2019] [Indexed: 11/12/2022]
Abstract
Denitrification is a key nitrogen removal process that involves many denitrifying bacteria. In this study, the denitrification performance was estimated for soil samples from different land use types including farmland soil, restored wetland soil, and wetland soil. The quantitative real-time polymerase chain reaction results showed that the average abundance of nirS and nirK genes was notably affected by seasonal changes, increasing from 2.34 × 10 6 and 2.81 × 10 6 to 1.97 × 10 6 and 4.55 × 10 6 gene copies/g of dry soil, respectively, from autumn to spring. This suggests that the abundance of nirS and nirK denitrifiers in spring is higher than those in autumn. Furthermore, the abundance of nirS and nirK genes was higher in the farmland soil than in restored wetland soil and wetland soil in both seasons. According to the analyses of MiSeq sequencing of nirS and nirK genes, Halobacteriaceae could be used as a special strain to distinguish wetland soil from farmland soil and restored wetland soil. Furthermore, redundancy analysis indicated that the soil environmental variables of total carbon, total nitrogen, moisture content, and organic matter were the main factors affecting the community structures of nirS and nirK denitrifiers existing in wetland soil. These findings could contribute to understanding the differences in nirS and nirK denitrifiers between different land use types during seasonal changes.
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Affiliation(s)
- Chunyong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Juan Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuntao Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yi Song
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zicheng Cao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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9
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Zhang Y, Ji G, Wang C, Zhang X, Xu M. Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 244:47-54. [PMID: 30321711 DOI: 10.1016/j.envpol.2018.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/16/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
Excessive nitrogen (N) loadings from human activities have led to increased eutrophication and associated water quality impacts in China's coastal wetlands. Denitrification accounts for significant reduction of inorganic N to nitrous oxide (N2O) or dinitrogen gas (N2), and thereby curtails harmful effects of N pollution in coastal and marine ecosystems. However, the molecular drivers and limiting steps of denitrification in coastal wetlands are not well understood. Here, we quantified the abundances of functional genes involved in N cycling and determined denitrification rates using 15N paring technique in the coastal wetland sediments of Bohai Economic Rim in eastern China. Denitrification accounting for 80.7 ± 12.6% of N removal was the dominant pathway for N removal in the coastal wetlands. In comparison, anaerobic ammonium oxidation (ANAMMOX) removed up to 36.9 ± 7.3% of inorganic N. Structural equation modeling analysis indicated that the effects of ammonium on denitrification potential were mainly mediated by the relative abundances of nosZ/nirS, nirS/(narG + napA) and amoA/nirK. Denitrification was limited by the relative strength of two steps, namely N2O reduction to N2 and nitrite (NO2-) reduction to nitric oxide (NO). Our results suggest that the relative abundances of functional genes which are more stable than sediment chemical compounds in the context of environmental changes are indictive of denitrification potential in coastal wetlands.
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Affiliation(s)
- Yan Zhang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
| | - Chen Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Xuanrui Zhang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Ming Xu
- Department of Ecological, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
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10
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Zhang Y, Ji G. Quantitative responses of potential nitrification and denitrification rates to the size of microbial communities in rice paddy soils. CHEMOSPHERE 2018; 211:970-977. [PMID: 30119028 DOI: 10.1016/j.chemosphere.2018.08.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Nitrification and denitrification are important to nitrogen balance in agricultural ecosystems. However, the molecular drivers and limiting steps for these microbial processes in rice paddy soils are not well understood. Here, we assessed soil properties and abundances of functional genes affiliated with nitrification (amoA and nxrA), denitrification (nirS, nirK and nosZ), nitrate reduction (narG and napA) processes, and measured potential nitrification and denitrification rates (PNRs and PDRs) at 15 sites in Xiamen, China. The soil properties imposed indirect impacts on the potential rates by mediating the relative abundances of microbial communities. No significant relationships between the size of microbial communities and the potential rates were observed. Instead, we found the variables that best explained the variations in the PNRs and PDRs were AOB/nirS and (nirK + nirS)/nosZ, respectively. The PNRs were mainly limited by the relative strength of two steps, namely bacterial ammonium oxidation and nitrite into nitric oxide reduction, whereas the PDRs were mainly limited by the relative strength of the second and last denitrification steps. These results indicated that the dynamics of microbial communities based on the relative gene abundances are valuable in integrating fluctuations in soil physicochemical properties and are indictive of potential rates in paddy soils. Results of this study contribute to our quantitative understanding of the relative importance of soil physicochemical and biological factors in driving microbial potential in paddy soils.
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Affiliation(s)
- Yan Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
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11
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Guo L, Wang X, Diao T, Ju X, Zheng L, Zhang X, Han X. N 2O emission contributions by different pathways and associated microbial community dynamics in a typical calcareous vegetable soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:2005-2013. [PMID: 30061078 DOI: 10.1016/j.envpol.2018.07.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 06/18/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Nitrous oxide, one of the powerful long-lived greenhouse gases, is emitted mainly through biological processes, especially from fertilized soil. It is critical to partition the contribution of different pathways to N2O emissions and the relevant characteristics of microbial communities to identify the key N2O processes. An microcosm was conducted to partition the N2O emissions from different pathways, and the changes in soil mineral nitrogen and various nitrifiers (amoA bacteria and amoA archaea) and denitrifiers (nirS, nirK, and nosZ) were also determined using qPCR and high-throughput sequencing methods. Different gas inhibitor combinations (i.e., 0.06% acetylene, pure oxygen, 0.06% acetylene in pure oxygen, and pure helium) were used to partition the N2O pathways. A 5% oxygen treatment, with and without acetylene, was also included so that the N2O emissions could be measured under lower oxygen partial pressure. Results showed that ammonia-oxidation (AO) and successive nitrifier denitrification (NiD) were the main pathways contributing to N2O emissions at the earlier period after ammonium sulfate application with the cumulative N2O emissions accounting for 30.9% and 59.2% of the total N2O emissions, respectively. The higher NiD N2O contributions occurred when the soil nitrite concentration appeared higher, especially under the lower oxygen conditions. Higher N2O emissions from AO and NiD were associated with the compositional proportion of some dominant AOB species. Denitrification contributed more N2O (63.6%-69.3%) in the later period during incubation, coinciding with the following characteristics for denitrifiers: a) lower nosZ/(nirS + nirK) ratio, b) more diversity in nirS, and c) different proportions of some dominant species in nirK. Our results demonstrated that higher AO and successive NiD were the main N2O emission pathways, suggesting that controlling the ammonium content and weakening the AO are critical in decreasing N2O emissions.
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Affiliation(s)
- Liping Guo
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xuedong Wang
- College of Resource Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Tiantian Diao
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotang Ju
- College of Resources and Environmental Sciences, Key Lab of Plant-Soil Interaction of MOE, China Agricultural University, Beijing 100093, China
| | - Lei Zheng
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Resource Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Xinyue Zhang
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xue Han
- Key Lab for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Xu H, Lin C, Chen W, Shen Z, Liu Z, Chen T, Wang Y, Li Y, Lu C, Luo J. Effects of pipe material on nitrogen transformation, microbial communities and functional genes in raw water transportation. WATER RESEARCH 2018; 143:188-197. [PMID: 29957407 DOI: 10.1016/j.watres.2018.06.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/15/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
Raw water transportation pipelines are vital in an urban water supply system for transporting raw water to drinking water treatment plants. This study investigated the effects of pipe material on nitrogen transformation, microbial communities and characteristics of related function genes in paint-lined steel pipe (PLSP) and cement-lined steel pipe (CLSP) raw water model systems. We established quantitative relationships between specific functional genes and change rates of nitrogen pollutants, which were verified by field investigation on nitrogen pollutant transformations in real raw water transportation systems. The results showed that the CLSP produced higher ammonia nitrogen (NH4+-N) transformation rates and higher effluent concentrations of nitrate nitrogen (NO3--N) and dissolved organic nitrogen (DON) than the PLSP. Both pipes achieved high and stable nitrite nitrogen (NO2--N) and low total nitrogen (TN) removal efficiency. Nitrification was found to be the dominant process in both model systems, especially in the CLSP. Characteristics of microbial communities and nitrogen functional genes, which were analysed by high-throughput pyrosequencing and quantitative polymerase chain reaction (qPCR), respectively, varied between the two pipe systems. Nitrogen transformation pathways, identified by path analysis, were also different between the PLSP and CLSP due to different microbial community characteristics and synergistic effects of nitrogen functional genes. In the CLSP, (NH4+-N→NO2--N) with part denitrification, was the primary transformation pathway of ammonia nitrogen (NH4+-N), while only ammonia oxidization contributed to NH4+-N transformation in the PLSP. (NO2--N→NO3--N) was the main pathway involved in NO2--N transformation and NO3--N accumulation. The TN removal showed complex relationships with nitrification, denitrification and nitrogen fixation processes. These findings provided molecular-level insights into nitrogen pollutant transformations during the transportation of raw water through different types of pipes and technical support for the selection of raw water pipe materials. In our study area, the Taihu basin, China, PLSP was better than CLSP for distributing raw water in a short transportation distance, due to the lower effluent concentrations of DON and NO3--N and less abundance of microorganisms.
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Affiliation(s)
- Hang Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China.
| | - Chenshuo Lin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Wei Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Zhen Shen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Zhigang Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China; Ningbo Water Supply Co., Ltd, No.348 Xinhe Road, Ningbo, 315041, China
| | - Taoyuan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Yueting Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Yang Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Chunhui Lu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Jian Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0355, USA
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Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization. Appl Environ Microbiol 2018; 84:AEM.01031-18. [PMID: 30006397 DOI: 10.1128/aem.01031-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/04/2018] [Indexed: 11/20/2022] Open
Abstract
Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO3) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the Nitrososphaera and B1 clades but shifted to clade A in the NL and NPM treatments. Nitrosospira cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of Nitrosospira cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that Nitrosospira cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization.IMPORTANCE The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. Nitrosospira cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.
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Liu H, Li J, Zhao Y, Xie K, Tang X, Wang S, Li Z, Liao Y, Xu J, Di H, Li Y. Ammonia oxidizers and nitrite-oxidizing bacteria respond differently to long-term manure application in four paddy soils of south of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:641-648. [PMID: 29597161 DOI: 10.1016/j.scitotenv.2018.03.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Nitrification plays an important role in the soil nitrogen (N) cycle, and fertilizer application may influence soil nitrifiers' abundance and composition. However, the effect of long-term manure application in paddy soils on nitrifying populations is poorly understood. We chose four long-term manure experimental fields in the south of China to study how the abundance and community structure of nitrifiers would change in response to long-term manure application using quantitative PCR and Miseq sequencing analyses. Our results showed that manure application significantly increased ammonia oxidizing archaea (AOA) abundance at the ChangSha (CS) and NanChang (NC) sites, while the abundance of ammonia oxidizing bacteria (AOB) represented 4.8- and 12.8- fold increases at the JiaXing (JX) and YingTan (YT) sites, respectively. Miseq sequencing of 16S rRNA genes indicated that manure application altered the community structure of nitrifying populations, especially at the NC and YT sites. The application of manure significantly changed AOA and nitrite oxidizing bacteria (NOB) community structures but not those of AOB, suggesting that AOA and NOB may be more sensitive to manures. Variation partitioning analysis (VPA) and redundancy analysis (RDA) indicated that soil pH, TN, NO3--N and water content were the main factors in shaping nitrifying communities. These findings suggest that nitrifiers respond diversely to manure application, and soil physiochemical properties play an important role in determining nitrifiers' abundance and communities with long-term manure addition.
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Affiliation(s)
- Haiyang Liu
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Jia Li
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Yan Zhao
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Kexin Xie
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Xianjin Tang
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Shaoxian Wang
- Institute of Soil & Fertilizer and Resource & Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, PR China
| | - Zhongpei Li
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Yulin Liao
- Soil and Fertilizer Institute of Hunan Province, Changsha, Hunan, PR China
| | - Jianming Xu
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Hongjie Di
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Yong Li
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China.
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Han X, Shen W, Zhang J, Müller C. Microbial adaptation to long-term N supply prevents large responses in N dynamics and N losses of a subtropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:1175-1187. [PMID: 29898524 DOI: 10.1016/j.scitotenv.2018.01.132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/13/2018] [Accepted: 01/14/2018] [Indexed: 06/08/2023]
Abstract
Atmospherically-deposited nitrogen (N) can stimulate complex soil N metabolisms and accumulations over time. Whether long-term (decadal) N deposition effects on soil N transformations and functional microbes differ from the short-term (annual) effects has rarely been assessed. Here we conducted a laboratory 15N tracing study with soil samples from a short-term (one year) N addition site and a long-term (12 years) site in a subtropical forest. The effects of simulated N deposition on soil N2O emissions, N transformation rates and microbial nitrifying and denitrifying genes were determined. Our results showed that: (1) long-term N addition did not change soil N2O fluxes significantly in comparison to the short-term N addition. Denitrification, heterotrophic nitrification and autotrophic nitrification contributed 53%, 28% and 18% to total N2O emissions, respectively. (2) Autotrophic nitrification was the dominant N transformation process, except for the high-N treatment at the long-term site. The magnitude of soil N transformation rates was significantly different among N addition treatments but not between short- and long-term N addition sites. However, long-term N addition changed the responses of specific N transformation rates to N addition markedly, especially for the rates of nitrification, organic N mineralization to NH4+, NO3- immobilization and dissimilatory NO3- reduction to NH4+ (DNRA). (3) Responses of ammonia oxidizing archaea and bacteria (AOA and AOB) were more variable than those of denitrifying N2O-producers (nirK) and denitrifying N2O-reducers (nosZ), particularly at the long-term site. (4) The close correlations among N2O flux, functional genes and soil properties observed at the short-term site were weakened at the long-term site, posing a decreased risk for N losses in the acid subtropical forest soil. There is evidence for an adaptation of functional microbial communities to the prevailing soil conditions and in response to long-term natural and anthropogenic N depositions.
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Affiliation(s)
- Xiaoge Han
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijun Shen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Tianhe District, Guangzhou 510650, China.
| | - Jinbo Zhang
- School of Geography Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Christoph Müller
- Department of Plant Ecology, Justus Liebig University Giessen, Heinrich-Buff Ring 26, 35392 Giessen, Germany; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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16
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Soil Media CO2 and N2O Fluxes Dynamics from Sand-Based Roadside Bioretention Systems. WATER 2018. [DOI: 10.3390/w10020185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Tao R, Wakelin SA, Liang Y, Hu B, Chu G. Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:739-749. [PMID: 28866401 DOI: 10.1016/j.scitotenv.2017.08.258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 06/07/2023]
Abstract
The effects of consecutive application of chemical fertilizer with or without organic fertilizer on soil N2O emissions and denitrifying community structure in a drip-irrigated field were determined. The four fertilizer treatments were (i) unfertilized, (ii) chemical fertilizer, (iii) 60% chemical fertilizer plus cattle manure, and (iv) 60% chemical fertilizer plus biofertilizer. The treatments with organic amendments (i.e. cattle manure and biofertilizer) reduced cumulative N2O emissions by 4.9-9.9%, reduced the N2O emission factor by 1.3-42%, and increased denitrifying enzyme activities by 14.3-56.2%. The nirK gene copy numbers were greatest in soil which received only chemical fertilizer. In contrast, nirS- and nosZ-copy numbers were greatest in soil amended with chemical fertilizer plus biofertilizer. Chemical fertilizer application with or without organic fertilizer significantly changed the community structure of nirK-type denitrifiers relative to the unfertilized soil. In comparison, the nirS- and nosZ-type denitrifier genotypes varied in treatments receiving organic fertilizer but not chemical fertilizer alone. The changes in the denitrifier communities were closely associated with soil organic carbon (SOC), NO3-, NH4+, water holding capacity, and soil pH. Modeling indicated that N2O emissions in this soil were primarily associated with the abundance of nirS type denitrifying bacteria, SOC, and NO3-. Overall, our findings indicate that (i) the organic fertilizers increased denitrifying enzyme activity, increased denitrifying-bacteria gene copy numbers, but reduced N2O emissions, and (ii) nirS- and nosZ-type denitrifiers were more sensitive than nirK-type denitrifiers to the organic fertilizers.
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Affiliation(s)
- Rui Tao
- Department of Resources and Environmental Science, College of Agriculture, The Key Laboratory of Oasis Eco-agriculture of the Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, PR China
| | | | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Baowei Hu
- College of Life Science, Shaoxing University, Zhejiang 312000, PR China
| | - Guixin Chu
- Department of Resources and Environmental Science, College of Agriculture, The Key Laboratory of Oasis Eco-agriculture of the Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, PR China; College of Life Science, Shaoxing University, Zhejiang 312000, PR China.
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Li S, Song L, Gao X, Jin Y, Liu S, Shen Q, Zou J. Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System. Front Microbiol 2017; 8:409. [PMID: 28373862 PMCID: PMC5357657 DOI: 10.3389/fmicb.2017.00409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/27/2017] [Indexed: 11/22/2022] Open
Abstract
Manure composting is a significant source of atmospheric methane (CH4) and nitrous oxide (N2O) that are two potent greenhouse gases. The CH4 and N2O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH4 and N2O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH4 and N2O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH4-related functional genes (mcrA and pmoA genes) and N2O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH4 and N2O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH4+ together as the best predictors for CH4 fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N2O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH4 and N2O fluxes to elevated atmospheric CO2 concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.
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Affiliation(s)
- Shuqing Li
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Lina Song
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Xiang Gao
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Yaguo Jin
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Shuwei Liu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qirong Shen
- Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University Nanjing, China
| | - Jianwen Zou
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
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Zhang CJ, Shen JP, Sun YF, Wang JT, Zhang LM, Yang ZL, Han HY, Wan SQ, He JZ. Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe. FEMS Microbiol Ecol 2017; 93:3071446. [DOI: 10.1093/femsec/fix037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/11/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cui-Jing Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Fei Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong-Ling Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Hong-Yan Han
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Shi-Qiang Wan
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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20
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Wang JG, Xia F, Zeleke J, Zou B, Rhee SK, Quan ZX. An improved protocol with a highly degenerate primer targeting copper-containing membrane-bound monooxygenase genes for community analysis of methane- and ammonia-oxidizing bacteria. FEMS Microbiol Ecol 2016; 93:fiw244. [PMID: 27940646 DOI: 10.1093/femsec/fiw244] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/18/2016] [Accepted: 12/03/2016] [Indexed: 11/14/2022] Open
Abstract
The copper-containing membrane-bound monooxygenase (CuMMO) family comprises key enzymes for methane or ammonia oxidation: particulate methane monooxygenase (PMMO) and ammonia monooxygenase (AMO). To comprehensively amplify CuMMO genes, a two-step PCR strategy was developed using a newly designed tagged highly degenerate primer (THDP; degeneracy = 4608). Designated THDP-PCR, the technique consists of primary CuMMO gene-specific PCR followed by secondary PCR with a tag as a single primer. No significant bias in THDP-PCR amplification was found using various combinations of template mixtures of pmoA and amoA genes, which encode key subunits of the pMMO and AMO enzymes, respectively, from different microbes. THDP-PCR was successfully applied to nine different environmental samples and revealed relatively high contents of complete ammonia oxidation (Comammox)-related bacteria and a novel group of the CuMMO family. The levels of freshwater cluster methanotrophs obtained by THDP-PCR were much higher than those obtained by conventional methanotroph-specific PCR. The THDP-PCR strategy developed in this study can be extended to other functional gene-based community analyses, particularly when the target gene sequences lack regions of high consensus for primer design.
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Affiliation(s)
- Jian-Gong Wang
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Fei Xia
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jemaneh Zeleke
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Korea
| | - Zhe-Xue Quan
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
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Zhao Z, Hamdan N, Shen L, Nan H, Almajed A, Kavazanjian E, He X. Biomimetic Hydrogel Composites for Soil Stabilization and Contaminant Mitigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12401-12410. [PMID: 27762537 DOI: 10.1021/acs.est.6b01285] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We have developed a novel method to synthesize a hyper-branched biomimetic hydrogel network across a soil matrix to improve the mechanical strength of the loose soil and simultaneously mitigate potential contamination due to excessive ammonium. This method successfully yielded a hierarchical structure that possesses the water retention, ion absorption, and soil aggregation capabilities of plant root systems in a chemically controllable manner. Inspired by the robust organic-inorganic composites found in many living organisms, we have combined this hydrogel network with a calcite biomineralization process to stabilize soil. Our experiments demonstrate that poly(acrylic acid) (PAA) can work synergistically with enzyme-induced carbonate precipitation (EICP) to render a versatile, high-performance soil stabilization method. PAA-enhanced EICP provides multiple benefits including lengthening of water supply time, localization of cementation reactions, reduction of harmful byproduct ammonium, and achievement of ultrahigh soil strength. Soil crusts we have obtained can sustain up to 4.8 × 103 kPa pressure, a level comparable to cementitious materials. An ammonium removal rate of 96% has also been achieved. These results demonstrate the potential for hydrogel-assisted EICP to provide effective soil improvement and ammonium mitigation for wind erosion control and other applications.
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Affiliation(s)
- Zhi Zhao
- School for Engineering of Matter, Transport and Energy, Arizona State University , 781 E Terrace Rd, Tempe, Arizona 85287, United States
- The Center for Bio-inspired and Bio-mediated Geotechnics, Arizona State University , P.O. Box 873005, Tempe, Arizona 85287-3005, United States
| | - Nasser Hamdan
- The Center for Bio-inspired and Bio-mediated Geotechnics, Arizona State University , P.O. Box 873005, Tempe, Arizona 85287-3005, United States
| | - Li Shen
- School for Engineering of Matter, Transport and Energy, Arizona State University , 781 E Terrace Rd, Tempe, Arizona 85287, United States
| | - Hanqing Nan
- School for Engineering of Matter, Transport and Energy, Arizona State University , 781 E Terrace Rd, Tempe, Arizona 85287, United States
| | - Abdullah Almajed
- The Center for Bio-inspired and Bio-mediated Geotechnics, Arizona State University , P.O. Box 873005, Tempe, Arizona 85287-3005, United States
| | - Edward Kavazanjian
- The Center for Bio-inspired and Bio-mediated Geotechnics, Arizona State University , P.O. Box 873005, Tempe, Arizona 85287-3005, United States
| | - Ximin He
- School for Engineering of Matter, Transport and Energy, Arizona State University , 781 E Terrace Rd, Tempe, Arizona 85287, United States
- The Center for Bio-inspired and Bio-mediated Geotechnics, Arizona State University , P.O. Box 873005, Tempe, Arizona 85287-3005, United States
- The Biodesign Institute, Molecular Design and Biomimetics Center, Arizona State University , 727 E. Tyler St., Tempe, Arizona 85287-5001, United States
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Park JH, Choi O, Lee TH, Kim H, Sang BI. Pyrosequencing analysis of microbial communities in hollow fiber-membrane biofilm reactors system for treating high-strength nitrogen wastewater. CHEMOSPHERE 2016; 163:192-201. [PMID: 27529383 DOI: 10.1016/j.chemosphere.2016.07.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Wastewaters from swine farms, nitrogen-dealing industries or side-stream processes of a wastewater treatment plant (e.g., anaerobic digesters, sludge thickening processes, etc.) are characterized by low C/N ratios and not easily treatable. In this study, a hollow fiber-membrane biofilm reactors (HF-MBfR) system consisting of an O2-based HF-MBfR and an H2-based HF-MBfR was applied for treating high-strength wastewater. The reactors were continuously operated with low supply of O2 and H2 and without any supply of organic carbon for 250 d. Gradual increase of ammonium and nitrate concentration in the influent showed stable and high nitrogen removal efficiency, and the maximum ammonium and nitrate removal rates were 0.48 kg NH4(+)-N m(-3) d(-1) and 0.55 kg NO3(-)-N m(-3) d(-1), respectively. The analysis of the microbial communities using pyrosequencing analysis indicated that Nitrosospira multiformis, ammonium-oxidizing bacteria, and Nitrobacter winogradskyi and Nitrobacter vulgaris, nitrite-oxidizing bacteria were highly enriched in the O2-based HF-MBfR. In the H2-based HF-MBfR, hydrogenotrophic denitrifying bacteria belonging to the family of Thiobacillus and Comamonadaceae were initially dominant, but were replaced to heterotrophic denitrifiers belonging to Rhodocyclaceae and Rhodobacteraceae utilizing by-products induced from autotrophic denitrifying bacteria. The pyrosequencing analysis of microbial communities indicates that the autotrophic HF-MBfRs system well developed autotrophic nitrifying and denitrifying bacteria within a relatively short period to accomplish almost complete nitrogen removal.
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Affiliation(s)
- Jung-Hun Park
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea
| | - Okkyoung Choi
- The Research Institute of Industrial Science, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea
| | - Tae-Ho Lee
- The Research Institute of Industrial Science, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea
| | - Hyunook Kim
- Department of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-Ku, Seoul 02504, South Korea.
| | - Byoung-In Sang
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea.
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Huang C, Wu F, Yang W, Tan B, He W, Zhang J. Effects of snow thickness on the abundance of archaeal and bacterial amoA genes and gene transcripts during dwarf bamboo litter decomposition in an alpine forest on the eastern Tibetan Plateau. RUSS J ECOL+ 2016. [DOI: 10.1134/s106741361604010x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Niu L, Li Y, Wang P, Zhang W, Wang C, Cai W, Wang L. Altitude-scale variation in nitrogen-removal bacterial communities from municipal wastewater treatment plants distributed along a 3600-m altitudinal gradient in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 559:38-44. [PMID: 27054491 DOI: 10.1016/j.scitotenv.2016.03.175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/24/2016] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
Microbial ecological information on the nitrogen removal processes in wastewater treatment plants (WWTPs) has been of considerable importance as a means for diagnosing the poor performance of nitrogen removal. In this study, the altitude-scale variations in the quantitative relationships and community structures of betaproteobacteria ammonia-oxidizing bacteria (βAOB) and nitrite-reducing bacteria containing the copper-containing nitrite reductase gene (nirK-NRB) and the cytochrome cd1-containing nitrite reductase gene (nirS-NRB) were investigated in 18 municipal WWTPs distributed along a 3660-masl altitude gradient in China. An altitude threshold associated with the proportions of NRB to total bacteria, NRB to βAOB and nirK-NRB to nirS-NRB was detected at approximately 1500m above sea level (masl). Compared with the stable proportions below 1500masl, the proportions exhibited a pronounced decreasing trend with increased altitude above 1500masl. Spearman correlation analysis indicated that the trend was significantly driven by altitude as well as multiple wastewater and operational variables. The community structure dissimilarity of βAOB, nirK-NRB and nirS-NRB showed significant and positive correlations with altitudinal distance between WWTPs. Redundancy analyses indicated that the variation in community structures above 1500masl were predominantly associated with wastewater, followed by operation and altitude. In summary, although the variations of nitrogen-removal bacterial community in WWTPs were driven dominantly by wastewater and operational variables, altitude was also an important variable influencing the quantitative relationships and community structures of nitrogen-removal bacteria in WWTPs particularly above 1500masl.
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Affiliation(s)
- Lihua Niu
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Peifang Wang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Wenlong Zhang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Chao Wang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Wei Cai
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Linqiong Wang
- Ministry of Education Key laboratory of integrated regulation and resource development on shallow lakes, College of Environment, Hohai University, Nanjing 210098, PR China
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nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China. Appl Microbiol Biotechnol 2016; 100:8573-82. [PMID: 27311565 DOI: 10.1007/s00253-016-7659-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/29/2016] [Accepted: 06/01/2016] [Indexed: 11/27/2022]
Abstract
For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.
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Li JG, Shen MC, Hou JF, Li L, Wu JX, Dong YH. Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce. Sci Rep 2016; 6:25305. [PMID: 27121918 PMCID: PMC4848521 DOI: 10.1038/srep25305] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/14/2016] [Indexed: 01/31/2023] Open
Abstract
Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3(-)-N, and NH4(+)-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.
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Affiliation(s)
- Jian-Gang Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, P.R. China
| | - Min-Chong Shen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Feng Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Xia Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, P.R. China
| | - Yuan-Hua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, P.R. China
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Braker G, Conrad R. Diversity, structure, and size of N(2)O-producing microbial communities in soils--what matters for their functioning? ADVANCES IN APPLIED MICROBIOLOGY 2016; 75:33-70. [PMID: 21807245 DOI: 10.1016/b978-0-12-387046-9.00002-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Nitrous oxide (N(2)O) is mainly generated via nitrification and denitrification processes in soils and subsequently emitted into the atmosphere where it causes well-known radiative effects. How nitrification and denitrification are affected by proximal and distal controls has been studied extensively in the past. The importance of the underlying microbial communities, however, has been acknowledged only recently. Particularly, the application of molecular methods to study nitrifiers and denitrifiers directly in their habitats enabled addressing how environmental factors influence the diversity, community composition, and size of these functional groups in soils and whether this is of relevance for their functioning and N(2)O production. In this review, we summarize the current knowledge on community-function interrelationships. Aerobic nitrification (ammonia oxidation) and anaerobic denitrification are clearly under different controls. While N(2)O is an obligatory intermediate in denitrification, its production during ammonia oxidation depends on whether nitrite, the end product, is further reduced. Moreover, individual strains vary strongly in their responses to environmental cues, and so does N(2)O production. We therefore conclude that size and structure of both functional groups are relevant with regard to production and emission of N(2)O from soils. Diversity affects on function, however, are much more difficult to assess, as it is not resolved as yet how individual nitrification or denitrification genotypes are related to N(2)O production. More research is needed for further insights into the relation of microbial communities to ecosystem functions, for instance, how the actively nitrifying or denitrifying part of the community may be related to N(2)O emission.
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Affiliation(s)
- Gesche Braker
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg, Germany.
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28
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Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil. Appl Microbiol Biotechnol 2016; 100:6815-6826. [DOI: 10.1007/s00253-016-7502-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 12/16/2022]
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29
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Zhang J, Zhou X, Chen L, Chen Z, Chu J, Li Y. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes. World J Microbiol Biotechnol 2016; 32:85. [DOI: 10.1007/s11274-016-2042-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/29/2016] [Indexed: 11/24/2022]
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Li X, Zhang M, Liu F, Li Y, He Y, Zhang S, Wu J. Abundance and distribution of microorganisms involved in denitrification in sediments of a Myriophyllum elatinoides purification system for treating swine wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:17906-17916. [PMID: 26165997 DOI: 10.1007/s11356-015-5041-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/05/2015] [Indexed: 06/04/2023]
Abstract
Environmental pollution from livestock production, particularly swine production, is often managed by the use of constructed wetlands, which incorporate plants such as Myriophyllum elatinoides as a means of treating wastewater. The M. elatinoides purification system has been shown to effectively remove, via nitrification and denitrification, more than 90% of the total nitrogen (TN) and 84% of the NH4 (+)-N produced in swine wastewater. However, the mechanisms of variation in aquatic environmental factors and how the interaction of these factors affects denitrification by microorganisms in sediments remain poorly understood. In this study, the impacts of dissolved oxygen (DO), TN, NH4(+)-N, and NO3(-)-N on the abundance, diversity, and community distribution of denitrifiers in the sediments from different concentrations and types of wastewater including tap water (CK), two strengths of synthetic wastewater: 200 mg NH4(+)-N L(-1) (T1) and 400 mg NH4(+)-N L(-1) (T2), swine wastewater diluted 50% (T3), and swine wastewater (T4) were investigated in a microcosm experiment. A significant improvement was observed in the abundance of denitrification genes (nirK and nirS) in response to increased NO3(-)-N and DO in the swine wastewater sediments. The abundance of these denitrification genes was highest in the T4 sediments compared with other treatments. Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the DO, TN, and NH4(+)-N positively impacted the richness index (S) of the nirK denitrifiers in T1, whereas the NO3(-)-N negatively affected the Simpson diversity index (D) of nirK and nirS denitrifiers in T3 and T4. However, the NO3(-)-N positively affected the nirK and nirS denitrifier community distribution, whereas the DO negatively affected the nirK and nirS denitrifier distribution in T3 and T4. These findings will be helpful in that they allow us to recognize the effects of environmental factors on the formation of the denitrifiers in the sediments in a M. elatinoides purification system.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
| | - Miaomiao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
| | - Yang He
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Shunan Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
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Bertagnolli AD, Meinhardt KA, Pannu M, Brown S, Strand S, Fransen SC, Stahl DA. Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:312-320. [PMID: 25504683 DOI: 10.1111/1758-2229.12250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
Ammonia-oxidizing thaumarcheota (AOA) and ammonia-oxidizing bacteria (AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene (amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass (Panicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. Nitrosotalea-like and Nitrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with Nitrososphaera and Nitrosospira cluster 3A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses.
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Affiliation(s)
- Anthony D Bertagnolli
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
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Li H, Weng BS, Huang FY, Su JQ, Yang XR. pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China. Appl Microbiol Biotechnol 2015; 99:6113-23. [PMID: 25744648 DOI: 10.1007/s00253-015-6488-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 12/11/2022]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
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Majeed MZ, Miambi E, Riaz MA, Brauman A. Characterization of N2O emission and associated bacterial communities from the gut of wood-feeding termite Nasutitermes voeltzkowi. Folia Microbiol (Praha) 2015; 60:425-33. [PMID: 25687762 DOI: 10.1007/s12223-015-0379-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 02/06/2015] [Indexed: 11/28/2022]
Abstract
Xylophagous termites rely on nitrogen deficient foodstuff with a low C/N ratio. Most research work has focused on nitrogen fixation in termites highlighting important inflow and assimilation of atmospheric nitrogen into their bodies fundamentally geared up by their intestinal microbial symbionts. Most of termite body nitrogen is of atmospheric origin, and microbially aided nitrification is the principal source of this nitrogen acquisition, but contrarily, the information regarding potent denitrification process is very scarce and poorly known, although the termite gut is considered to carry all favorable criteria necessary for microbial denitrification. Therefore, in this study, it is hypothesized that whether nitrification and denitrification processes coexist in intestinal milieu of xylophagous termites or not, and if yes, then is there any link between the denitrification product, i.e., N2O and nitrogen content of the food substrate, and moreover where these bacterial communities are found along the length of termite gut. To answer these questions, we measured in vivo N2O emission by Nasutitermes voeltzkowi (Nasutitermitinae) maintained on different substrates with varying C/N ratio, and also, molecular techniques were applied to study the diversity (DGGE) and density (qPCR) of bacterial communities in anterior and posterior gut portions. Rersults revealed that xylophagous termites emit feeble amount of N2O and molecular studies confirmed this finding by illustrating the presence of an ample density of N2O-reductase (nosZ) gene in the intestinal tract of these termites. Furthermore, intestinal bacterial communities of these termites were found more dense and diverse in posterior than anterior portion of the gut.
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Affiliation(s)
- Muhammad Zeeshan Majeed
- Department of Agri. Entomology, University College of Agriculture, University of Sargodha, 40100, Sargodha, Pakistan,
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Response of denitrifying genes coding for nitrite (nirK or nirS) and nitrous oxide (nosZ) reductases to different physico-chemical parameters during agricultural waste composting. Appl Microbiol Biotechnol 2015; 99:4059-70. [DOI: 10.1007/s00253-014-6293-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/30/2014] [Accepted: 12/03/2014] [Indexed: 11/26/2022]
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35
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Ren LF, Liang S, Ngo HH, Guo W, Ni SQ, Liu C, Zhao YK, Hira D. Enhancement of anammox performance in a novel non-woven fabric membrane bioreactor (nMBR). RSC Adv 2015. [DOI: 10.1039/c5ra16802c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As well as a membrane separator, a non-woven fabric module could be employed as a biomass carrier to enhance microorganism proliferation and nitrogen removal.
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Affiliation(s)
- Long-Fei Ren
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- PR China
| | - Shuang Liang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- PR China
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater
- School of Civil and Environmental Engineering
- University of Technology Sydney
- Sydney
- Australia
| | - Wenshan Guo
- Centre for Technology in Water and Wastewater
- School of Civil and Environmental Engineering
- University of Technology Sydney
- Sydney
- Australia
| | - Shou-Qing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- PR China
| | - Cui Liu
- Department of Mathematics and Statistics
- Texas Tech University
- Lubbock
- USA
| | - Yuan-Kun Zhao
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- PR China
| | - Daisuke Hira
- Department of Applied Life Science
- Faculty of Biotechnology and Life Science
- Sojo University
- Kumamoto 860-0082
- Japan
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36
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Long A, Song B, Fridey K, Silva A. Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils. FEMS Microbiol Ecol 2014; 91:1-9. [PMID: 25764542 DOI: 10.1093/femsec/fiu004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.
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Affiliation(s)
- Andrew Long
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Bongkeun Song
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403 Department of Biological Sciences, Virginia Institute of Marine Sciences, Gloucester Point, VA 23062, USA Department of Life Science, Dongguk University-Seoul, Seoul 100-715, South Korea
| | - Kelly Fridey
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Amy Silva
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
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Lee KH, Wang YF, Zhang GX, Gu JD. Distribution patterns of ammonia-oxidizing bacteria and anammox bacteria in the freshwater marsh of Honghe wetland in Northeast China. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:1930-1942. [PMID: 25139035 DOI: 10.1007/s10646-014-1333-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/09/2014] [Indexed: 06/03/2023]
Abstract
Community characteristics of aerobic ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria in Honghe freshwater marsh, a Ramsar-designated wetland in Northeast China, were analyzed in this study. Samples were collected from surface and low layers of sediments in the Experimental, Buffer, and Core Zones in the reserve. Community structures of AOB were investigated using both 16S rRNA and amoA (encoding for the α-subunit of the ammonia monooxygenase) genes. Majority of both 16S rRNA and amoA gene-PCR amplified sequences obtained from the samples in the three zones affiliated with Nitrosospira, which agreed with other wetland studies. A relatively high richness of β-AOB amoA gene detected in the freshwater marsh might suggest minimal external pressure was experienced, providing a suitable habitat for β-AOB communities. Anammox bacteria communities were assessed using both 16S rRNA and hzo (encoding for hydrazine oxidoreductase) genes. However, PCR amplification of the hzo gene in all samples failed, suggesting that the utilization of hzo biomarker for detecting anammox bacteria in freshwater marsh might have serious limitations. Results with 16S rRNA gene showed that Candidatus Kuenenia was detected in only the Experimental Zone, whereas Ca. Scalindua including different lineages was observed in both the Buffer and Experimental Zones but not the Core Zone. These results indicated that both AOB and anammox bacteria have specific distribution patterns in the ecosystem corresponding to the extent of anthropogenic impact.
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Affiliation(s)
- Kwok-Ho Lee
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
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38
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Lee KH, Wang YF, Li H, Gu JD. Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:2081-2091. [PMID: 25163821 DOI: 10.1007/s10646-014-1334-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/09/2014] [Indexed: 06/03/2023]
Abstract
Ecophysiological differences between ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) enable them to adapt to different niches in complex freshwater wetland ecosystems. The community characters of AOA and AOB in the different niches in a freshwater wetland receiving municipal wastewater, as well as the physicochemical parameters of sediment/soil samples, were investigated in this study. AOA community structures varied and separated from each other among four different niches. Wetland vegetation including aquatic macrophytes and terrestrial plants affected the AOA community composition but less for AOB, whereas sediment depths might contribute to the AOB community shift. The diversity of AOA communities was higher than that of AOB across all four niches. Archaeal and bacterial amoA genes (encoding for the alpha-subunit of ammonia monooxygenases) were most diverse in the dry-land niche, indicating O2 availability might favor ammonia oxidation. The majority of AOA amoA sequences belonged to the Soil/sediment Cluster B in the freshwater wetland ecosystems, while the dominant AOB amoA sequences were affiliated with Nitrosospira-like cluster. In the Nitrosospira-like cluster, AOB amoA gene sequences affiliated with the uncultured ammonia-oxidizing beta-proteobacteria constituted the largest portion (99%). Moreover, independent methods for phylogenetic tree analysis supported high parsimony bootstrap values. As a consequence, it is proposed that Nitrosospira-like amoA gene sequences recovered in this study represent a potentially novel cluster, grouping with the sequences from Gulf of Mexico deposited in the public databases.
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Affiliation(s)
- Kwok-Ho Lee
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
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39
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Wang L, Zheng B, Nan B, Hu P. Diversity of bacterial community and detection of nirS- and nirK-encoding denitrifying bacteria in sandy intertidal sediments along Laizhou Bay of Bohai Sea, China. MARINE POLLUTION BULLETIN 2014; 88:215-223. [PMID: 25256298 DOI: 10.1016/j.marpolbul.2014.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/29/2014] [Accepted: 09/06/2014] [Indexed: 06/03/2023]
Abstract
The microbial community and the nirS- and nirK-encoding denitrifiers in the intertidal sediments along Laizhou Bay in China were studied using pyrosequencing and real-time quantitative PCR (qPCR), respectively. There were three primary intertidal zones: Laizhou (La), Weifang Harbor (We), and Dongying (Do). Significant differences in composition and abundances at the different taxonomic levels were observed among the three bacterial communities. The qPCR results indicated that the nirS gene abundance varied from 8.67 × 10(5) to 5.68 × 10(6)copies/gwet weight (ww), whereas the nirK gene abundance varied from 1.26 × 10(5) to 1.89 × 10(6)copies/gww. The canonical correlation analysis (CCA) indicated that the sand percentage was the most important factor in shaping the bacterial community followed by silt percentage, NO2(-), TOC, DO, pH, and clay percentage, whereas the clay percentage, pH, NO3(-), DO, NO2(-), TOC, silt percentage, and sand percentage were the most important factors associated with regulating the abundance of nirS- and nirK-encoding denitrifiers.
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Affiliation(s)
- Liping Wang
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| | - Binghui Zheng
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Bingxu Nan
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Peilong Hu
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
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40
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Shrestha RK, Strahm BD, Sucre EB. Nitrous Oxide Fluxes in Fertilized L. Plantations across a Gradient of Soil Drainage Classes. JOURNAL OF ENVIRONMENTAL QUALITY 2014; 43:1823-1832. [PMID: 25602199 DOI: 10.2134/jeq2014.03.0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The effect of fertilizer management on nitrous oxide (NO) fluxes in agricultural ecosystems is well documented; however, our knowledge of these effects in managed forests is minimal. We established a comprehensive research study to address this knowledge gap across a range of soil drainage classes (poorly, moderately, and well drained) common in southern pine plantation management. Fertilizer treatments in each drainage class comprised of control (no fertilizer), urea + phosphorus (P), and P-coated urea fertilizer (CUF). Fertilization (168 kg N ha) occurred independently during the spring, summer, and fall to assess the effects of application timing. Nitrous oxide sampling, using vented static chambers, started immediately after seasonal fertilizer application and was performed every 6 wk for more than 1 yr. Time-integrated net annual NO emissions increased with urea (1.15 kg NO-N ha) and CUF (0.88 kg NO-N ha) application compared with unfertilized control (0.22 kg NO-N ha). Mean annual NO flux was significantly increased with fall fertilization (1.17 kg NO-N ha) relative to spring (0.73 kg NO-N ha) or summer (0.33 kg NO-N ha). Similarly, average annual NO flux was higher in poorly drained soils (1.40 kg NO-N ha) than in moderately drained (0.46 kg NO-N ha) and well-drained soils (0.39 kg NO-N ha). This study suggests that NO emissions after fertilization can be minimized by avoiding fall fertilization and poorly drained soils and by selecting enhanced-efficiency N fertilizers over urea.
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41
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Gómez-Silván C, Vílchez-Vargas R, Arévalo J, Gómez MA, González-López J, Pieper DH, Rodelas B. Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor. BIORESOURCE TECHNOLOGY 2014; 169:126-133. [PMID: 25043345 DOI: 10.1016/j.biortech.2014.06.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 05/15/2023]
Abstract
The abundance and transcription levels of specific gene markers of total bacteria, ammonia-oxidizing Betaproteobacteria, nitrite-oxidizing bacteria (Nitrospira-like) and denitrifiers (N2O-reducers) were analyzed using quantitative PCR (qPCR) and reverse-transcription qPCR during 9 months in a full-scale membrane bioreactor treating urban wastewater. A stable community of N-removal key players was developed; however, the abundance of active populations experienced sharper shifts, demonstrating their fast adaptation to changing conditions. Despite constituting a small percentage of the total bacterial community, the larger abundances of active populations of nitrifiers explained the high N-removal accomplished by the MBR. Multivariate analyses revealed that temperature, accumulation of volatile suspended solids in the sludge, BOD5, NH4(+) concentration and C/N ratio of the wastewater contributed significantly (23-38%) to explain changes in the abundance of nitrifiers and denitrifiers. However, each targeted group showed different responses to shifts in these parameters, evidencing the complexity of the balance among them for successful biological N-removal.
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Affiliation(s)
- C Gómez-Silván
- Departamento de Microbiología, Facultad de Farmacia, University of Granada, Granada, Spain.
| | - R Vílchez-Vargas
- Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - J Arévalo
- Departamento de Ingeniería Civil, University of Granada, Granada, Spain
| | - M A Gómez
- Departamento de Ingeniería Civil, University of Granada, Granada, Spain
| | - J González-López
- Departamento de Microbiología, Facultad de Farmacia, University of Granada, Granada, Spain
| | - D H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - B Rodelas
- Departamento de Microbiología, Facultad de Farmacia, University of Granada, Granada, Spain
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42
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Denitrification in agriculturally impacted streams: seasonal changes in structure and function of the bacterial community. PLoS One 2014; 9:e105149. [PMID: 25171209 PMCID: PMC4149370 DOI: 10.1371/journal.pone.0105149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/21/2014] [Indexed: 11/19/2022] Open
Abstract
Denitrifiers remove fixed nitrogen from aquatic environments and hydrologic conditions are one potential driver of denitrification rate and denitrifier community composition. In this study, two agriculturally impacted streams in the Sugar Creek watershed in Indiana, USA with different hydrologic regimes were examined; one stream is seasonally ephemeral because of its source (tile drainage), whereas the other stream has permanent flow. Additionally, a simulated flooding experiment was performed on the riparian benches of the ephemeral stream during a dry period. Denitrification activity was assayed using the chloramphenicol amended acetylene block method and bacterial communities were examined based on quantitative PCR and terminal restriction length polymorphisms of the nitrous oxide reductase (nosZ) and 16S rRNA genes. In the stream channel, hydrology had a substantial impact on denitrification rates, likely by significantly lowering water potential in sediments. Clear patterns in denitrification rates were observed among pre-drying, dry, and post-drying dates; however, a less clear scenario was apparent when analyzing bacterial community structure suggesting that denitrifier community structure and denitrification rate were not strongly coupled. This implies that the nature of the response to short-term hydrologic changes was physiological rather than increases in abundance of denitrifiers or changes in composition of the denitrifier community. Flooding of riparian bench soils had a short-term, transient effect on denitrification rate. Our results imply that brief flooding of riparian zones is unlikely to contribute substantially to removal of nitrate (NO3-) and that seasonal drying of stream channels has a negative impact on NO3- removal, particularly because of the time lag required for denitrification to rebound. This time lag is presumably attributable to the time required for the denitrifiers to respond physiologically rather than a change in abundance or community composition.
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43
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Brown SM, Jenkins BD. Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments. Environ Microbiol 2014; 16:3128-42. [PMID: 24447468 PMCID: PMC4231279 DOI: 10.1111/1462-2920.12403] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 01/12/2014] [Indexed: 11/29/2022]
Abstract
Nitrogen (N) cycling microbial communities in marine sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed genes for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site. Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes. Quantitative polymerase chain reaction (qPCR) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) data shows the highest abundance of both groups at a mid bay site, and the highest nifH expression at the head of the estuary, regardless of season. Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.
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Affiliation(s)
- S M Brown
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
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Liu J, Shan J, Jiang B, Wang L, Yu B, Chen J, Guo H, Ji R. Degradation and bound-residue formation of nonylphenol in red soil and the effects of ammonium. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2014; 186:83-89. [PMID: 24368312 DOI: 10.1016/j.envpol.2013.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 06/03/2023]
Abstract
Fate of nonylphenol (NP) in soils and the effects of nitrogen fertilizers are unclear. Using (14)C-tracer, we studied the aerobic and anaerobic degradation of 4-NP111 in a paddy red soil amended without and with ammonium chloride. Under oxic conditions, 4-NP111 had a half-life of 16.1 ± 1.6 days and minor mineralization (3.84 ± 0.02%), forming no extractable metabolite but abundant bound residues (60.9 ± 1.7%, mostly bound to humin) after 49 days of incubation. The ammonium amendment (8 mmol/kg soil) significantly inhibited the degradation (half-life of 68.0 ± 7.7 days), mineralization (2.0 ± 1.1%), and bound-residue formation (23.7 ± 0.2%). Under anoxic conditions, 4-NP111 did not degrade during 49 days of incubation and the ammonium amendment (40 mmol/kg soil) did not affect its persistence. Our results demonstrate that bound-residue formation was a major mechanism for NP dissipation in the red soil under oxic conditions and that chemical nitrogen fertilizer at average field application rate may already considerably increase NP recalcitrance in agricultural soils.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue 163, 210023 Nanjing, China
| | - Jun Shan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue 163, 210023 Nanjing, China
| | - Bingqi Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue 163, 210023 Nanjing, China
| | - Lianhong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue 163, 210023 Nanjing, China
| | - Bin Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue 163, 210023 Nanjing, China
| | - Jianqiu Chen
- Department of Environmental Science, China Pharmaceutical University, Tongjia Alley 24, 210009 Nanjing, China
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue 163, 210023 Nanjing, China; Institute for Climate and Global Change Research, Nanjing University, Hankou Road 22, 210093 Nanjing, China
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue 163, 210023 Nanjing, China; Institute for Climate and Global Change Research, Nanjing University, Hankou Road 22, 210093 Nanjing, China.
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Impacts of edaphic factors on communities of ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrification in tropical soils. PLoS One 2014; 9:e89568. [PMID: 24586878 PMCID: PMC3938500 DOI: 10.1371/journal.pone.0089568] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 105 to 106 copies archaeal amoA g−1 soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity.
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46
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Jiang Y, Jin C, Sun B. Soil aggregate stratification of nematodes and ammonia oxidizers affects nitrification in an acid soil. Environ Microbiol 2013; 16:3083-94. [DOI: 10.1111/1462-2920.12339] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 11/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; No. 71 East Beijing Road Nanjing 210008 China
| | - Chen Jin
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; No. 71 East Beijing Road Nanjing 210008 China
- College of Resources and Environmental Sciences; Nanjing Agricultural University; Nanjing 210095 China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; No. 71 East Beijing Road Nanjing 210008 China
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47
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Murdoch RW, Costello Staniec A. Diversity and community analysis of ammonia oxidizing bacteria in a streambed surrounding an artificial dam. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2013; 127:237-243. [PMID: 23764474 DOI: 10.1016/j.jenvman.2013.05.032] [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: 11/28/2012] [Revised: 04/29/2013] [Accepted: 05/08/2013] [Indexed: 06/02/2023]
Abstract
The degree to which small natural dams affect the native bacterial nitrogen cycling community was explored by molecular methods. The identities and relative abundances of ammonia oxidizing bacteria in the sediment surrounding an artificial dam both at the surface and in the hyporheic zone were characterized. Analyses were performed using tRFLP of the conserved amoA gene using a semi-nested degenerate PCR approach. Additionally, an amoA gene library was constructed to characterize the most dominant sediment genotypes. The results of the tRFLP analyses showed clear differences between the upstream and downstream communities at different depths in the sediment column. Non-metric multidimensional scaling ordination of the tRFLP data set produced a stable one-dimensional solution with significant correlations to oxygen, pH, nitrate, and dissolved organic nitrogen levels. The sample corresponding to the hyporheic zone downstream of the dam showed 28-50% higher amoA richness and higher diversity than the other samples. All gene fragments sequenced from the samples grouped with sequences of the Nitrosospira type. Ordination of 16S rDNA tRFLP data revealed a two dimensional data structure, one axis of which had similar chemical correlation characteristics as the amoA model axis. Taken together, the results from this study suggest that the presence of the dam creates physical and chemical heterogeneity that may foster genetic diversity and community changes amongst ammonia oxidizing bacteria.
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Affiliation(s)
- Robert W Murdoch
- Department of Civil and Environmental Engineering, Link Hall, Syracuse University, Syracuse, NY 13244, USA.
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48
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Sher Y, Zaady E, Nejidat A. Spatial and temporal diversity and abundance of ammonia oxidizers in semi-arid and arid soils: indications for a differential seasonal effect on archaeal and bacterial ammonia oxidizers. FEMS Microbiol Ecol 2013; 86:544-56. [DOI: 10.1111/1574-6941.12180] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 07/02/2013] [Accepted: 07/11/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yonatan Sher
- Department of Environmental Hydrology and Microbiology; Zuckerberg Institute for Water Research; Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Sede Boqer Israel
| | - Eli Zaady
- Department of Natural Resources; Gilat Research Center; Agriculture Research Organization; Mobile Post Negev Israel
| | - Ali Nejidat
- Department of Environmental Hydrology and Microbiology; Zuckerberg Institute for Water Research; Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Sede Boqer Israel
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Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China. J Basic Microbiol 2013; 54:180-9. [DOI: 10.1002/jobm.201300217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/13/2013] [Indexed: 11/07/2022]
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Yao H, Campbell CD, Chapman SJ, Freitag TE, Nicol GW, Singh BK. Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey. Environ Microbiol 2013; 15:2545-56. [PMID: 23635043 DOI: 10.1111/1462-2920.12141] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/18/2013] [Accepted: 04/05/2013] [Indexed: 11/27/2022]
Abstract
The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different ammonia oxidizers, we used samples (n = 713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40-45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13-16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main ammonia oxidizers in acidic soils. However, for AOB, soil pH and substrate (ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning.
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Affiliation(s)
- Huaiying Yao
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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