151
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Huang R, Wang Y, Gao X, Liu J, Wang Z, Gao M. Nitrous oxide emission and the related denitrifier community: A short-term response to organic manure substituting chemical fertilizer. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110291. [PMID: 32061984 DOI: 10.1016/j.ecoenv.2020.110291] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Partially substituting chemical fertilizer with organic manure can aid in the disposal of agricultural wastes via recycling into agricultural land, reduce chemical fertilizer application, and influence nitrogen (N) transformation. However, relatively few studies have investigated the association between soil physicochemical properties, denitrifier communities and N2O emission after short-term substitution of organic manure in vegetable fields. We conducted a short-term vegetable field experiment which included one control treatment (CT, no fertilizer) and three fertilization treatments containing equal amount of total N, phosphorus and potassium (CF, chemical fertilizer only; CMR, chemical fertilizer plus mushroom residue; COM, chemical fertilizer plus cattle manure). The results showed that partial substitution of chemical fertilizer with organic manure greatly increased cumulative N2O emissions, N2O emission factors and yield-scaled N2O emissions by 122-203%, 238-600% and 128-181%, respectively. Compared with the CF treatment, short-term substitution with organic manure reduced the abundance of nirS- and nosZ-type denitrifiers, and increased that of nirK-type denitrifiers. Modeling indicated that nirS abundance, together with soil available N, NIR activity, nirK abundance, SOC, NH4+, and NO3- were the primary factors associated with cumulative N2O emissions. The denitrifier community composition of the CF- treated soil was separated from that of soils treated with CMR and COM, and was primarily influenced by soil NH4+ concentration. NIR activity showed a significant correlation with denitrifier community composition. Overall, short-term substitution of chemical fertilizer with cattle manure (lower C/N ratio) reduced the abundance of nirS- and nosZ-type denitrifiers, but stimulated N2O emission.
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Affiliation(s)
- Rong Huang
- College of Resources and Environment, Southwest University, Chongqing, 400715, China; College of Resources, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Yingyan Wang
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Xuesong Gao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Jiang Liu
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Zifang Wang
- College of Resources and Environment, Southwest University, Chongqing, 400715, China.
| | - Ming Gao
- College of Resources and Environment, Southwest University, Chongqing, 400715, China.
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152
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Zhong XZ, Zeng Y, Wang SP, Sun ZY, Tang YQ, Kida K. Insight into the microbiology of nitrogen cycle in the dairy manure composting process revealed by combining high-throughput sequencing and quantitative PCR. BIORESOURCE TECHNOLOGY 2020; 301:122760. [PMID: 31972401 DOI: 10.1016/j.biortech.2020.122760] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Nitrogen cycling during composting process is not yet fully understood. This study explored the key genes involved in nitrogen cycling during dairy manure composting process using high-throughput sequencing and quantitative PCR technologies. Results showed that nitrogen fixation occurred mainly during the thermophilic and cooling phases, and significantly enhanced the nitrogen content of compost. Thermoclostridium stercorarium was the main diazotroph. Ammonia oxidation occurred during the maturation phase and Nitrosomonas sp. was the most abundant ammonia oxidizing bacteria. Denitrification contributed to the greatest nitrogen loss during the composting process. The nirK community was dominated by Luteimonas sp. and Achromobacter sp., while the nirS community was dominated by Alcaligenes faecalis and Pseudomonas stutzeri. The nosZ community varied in a succession of Halomonas ilicicola, Pseudomonas flexibili and Labrenzia alba dominated communities according to different composting phases. Based on these results, nitrogen cycling models for different phases of the dairy manure composting process were established.
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Affiliation(s)
- Xiao-Zhong Zhong
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Yan Zeng
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Shi-Peng Wang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China.
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
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153
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Biocrusts Modulate Responses of Nitrous Oxide and Methane Soil Fluxes to Simulated Climate Change in a Mediterranean Dryland. Ecosystems 2020. [DOI: 10.1007/s10021-020-00497-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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154
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Chee-Sanford JC, Connor L, Krichels A, Yang WH, Sanford RA. Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications. J Microbiol Methods 2020; 172:105908. [PMID: 32234512 DOI: 10.1016/j.mimet.2020.105908] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/27/2022]
Abstract
The reduction of nitrous oxide (N2O) to N2 represents the key terminal step in canonical denitrification. Nitrous oxide reductase (NosZ), the enzyme associated with this biological step, however, is not always affiliated with denitrifying microorganisms. Such organisms were shown recently to possess a Clade II (atypical) nosZ gene, in contrast to Clade I (typical) nosZ harbored in more commonly studied denitrifiers. Subsequent phylogenetic analyses have shown that Clade II NosZ are affiliated with a much broader diversity of microorganisms than those with Clade I NosZ, the former including both non-denitrifiers and denitrifiers. Most studies attempting to characterize the nosZ gene diversity using DNA-based PCR approaches have only focused on Clade I nosZ, despite recent metagenomic sequencing studies that have demonstrated the dominance of Clade II nosZ genes in many ecosystems, particularly soil. As a result, these studies have greatly underestimated the genetic potential for N2O reduction present in ecosystems. Because the high diversity of Clade II NosZ makes it impossible to design a universal primer set that would effectively amplify all nosZ genes in this clade, we developed a suite of primer sets to specifically target seven of ten designated subclades of Clade II nosZ genes. The new primer sets yield suitable product sizes for paired end amplicon sequencing and qPCR, demonstrated here in their use for both conventional single-reaction and multiplex array platforms. In addition, we show the utility of these primers for detecting nosZ gene transcripts from mRNA extracted from soil.
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Affiliation(s)
| | | | - Alexander Krichels
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wendy H Yang
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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155
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Chee-Sanford J, Tian D, Sanford R. Consumption of N 2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27. MICROBIOLOGY-SGM 2020; 165:1345-1354. [PMID: 31580255 DOI: 10.1099/mic.0.000847] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacteria affiliated with the phylum Gemmatimonadetes are found in high abundance in many terrestrial and aquatic environments, yet little is known about their metabolic capabilities. Difficulty in their cultivation has prompted interest in identifying better growth conditions for metabolic studies, especially related to their ability to reduce N2O, a potent greenhouse gas. T-27 Gemmatimonas aurantiaca is one of few cultivated strains of Gemmatimonadetes available for physiological studies. Our objective was to test this organism's ability to use nitrite, nitrate, and N2O, and mineral forms of assimilable NH4 + at concentrations not typically used in tests for compound utilization. Cultures incubated under anaerobic conditions with nitrate, nitrite or N2O failed to grow or show depletion of these substrates. Nitrate and nitrite (1 mM) were not used even when cells were grown aerobically with the O2 allowed to deplete first. N2O reduction only commenced in the presence of O2 and continued to be depleted when refed to the culture under anaerobic, microaerobic and aerobic atmospheres. Carbon mineralization was coupled to the electron-accepting processes, with higher reducing equivalents needed for N2O utilization under aerobic atmospheres. N2O was reduced to N2 in the presence of 20% O2, however the rate of this reaction is reduced in the presence of high O2 concentration. This study demonstrated that G. aurantiaca T-27 possesses unique characteristics for assimilative and dissimilative N processes with new implications for cultivation strategies to better assess the metabolic abilities of Gemmatimonadetes.
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Affiliation(s)
| | - David Tian
- Department of Molecular and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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156
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Avşar C, Aras ES. Quantification of denitrifier genes population size and its relationship with environmental factors. Arch Microbiol 2020; 202:1181-1192. [PMID: 32076734 DOI: 10.1007/s00203-020-01826-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 108, 2.25 × 107, 2.9 × 105, 4.0 × 106 and 1.75 × 107 copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N2O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.
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Affiliation(s)
- Cumhur Avşar
- Department of Biology, Faculty of Arts and Sciences, Sinop University, Sinop, Turkey.
| | - E Sümer Aras
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
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157
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Semedo M, Song B. From Genes to Nitrogen Removal: Determining the Impacts of Poultry Industry Wastewater on Tidal Creek Denitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:146-157. [PMID: 31825200 DOI: 10.1021/acs.est.9b03560] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The intensification of the poultry industry in the last decades has led to a sharp increase in the number of animal processing plants discharging wastewater to water bodies. These discharges may have a significant effect on environmental quality and on important ecosystem functions, such as denitrification. We conducted a seasonal survey and a microcosm experiment in an impacted and a reference tidal creek to investigate the impacts of wastewater discharge from a poultry processing plant on sedimentary microbial communities, denitrification activity, and nitrate removal. Denitrification potential was measured using slurry incubations, and the microbial community was examined with 16S rDNA MiSeq sequencing and quantitative polymerase chain reaction of denitrification genes. The lowest denitrification rates were observed in the impacted creek, especially near the wastewater discharge, and denitrification inhibition by impacted creek water was clearly observed in the microcosm experiment. Denitrification rates were associated with changes in the microbial community composition and gene abundance. Estimated nitrate removal was lower in the impacted creek, and higher chlorophyll levels were observed in a downstream coastal bay through remote sensing. This study demonstrates denitrification inhibition by wastewater discharge from a poultry processing plant with potential consequences to coastal eutrophication.
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Affiliation(s)
- Miguel Semedo
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia 23062, United States
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia 23062, United States
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158
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Gordon BA, Lenhart C, LaPara TM. A comparison of nitrate removal and denitrifying bacteria populations among three wetland plant communities. JOURNAL OF ENVIRONMENTAL QUALITY 2020; 49:210-219. [PMID: 33016351 DOI: 10.1002/jeq2.20004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/18/2019] [Accepted: 10/21/2019] [Indexed: 06/11/2023]
Abstract
Reed canary grass (Phalaris arundinacea L.) is an invasive, cool-season grass commonly dominating wetlands with high nutrient loads. Its impact on nitrogen removal via denitrification in wetlands is unknown. Most studies of denitrification in treatment wetlands have focused on the effects of physical or chemical variables and not on the effects of plant roots on the soil environment. The purpose of this study was to measure effects of plant type on denitrification rates in typical wetland soils of the midwestern United States by comparing wet prairie mix, switchgrass-dominated, and reed canary grass plant communities. Nitrate (NO3 - ) removal and other parameters were measured in miniature wetlands, or mesocosms, containing each plant community transplanted from a small agricultural treatment wetland in southern Minnesota. Quantitative polymerase chain reaction analysis was used to quantify the total bacteria population (measured with 16S rRNA genes) and denitrifying gene abundance (measured with nosZ genes) from the rhizosphere of each plant community. The wet prairie mix mesocosms on average removed the most NO3 - in each test (p = .01 and .08). Whereas the wet prairie mix removed the most NO3 - from the surface water (p < .01), reed canary grass removed more from the subsurface (p < .01). Ratios of denitrifying to total bacteria were higher in the wet prairie mix than in the other communities' root zones (p < .05). Results suggest that reed canary grass invasion could reduce denitrification in wetlands, especially during the spring and fall when it is growing but other plants are dormant.
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Affiliation(s)
- Brad A Gordon
- Water Resources Science Graduate Program, University of Minnesota, St. Paul, MN, 55108
| | - Christian Lenhart
- Ecological Engineering Group, Department of Bioproducts and Biosystems Engineering, University of Minnesota, 303 BAE Hall, 1390 Eckles Ave., St. Paul, MN, 55108
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455
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159
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Wang S, Liu W, Zhao S, Wang C, Zhuang L, Liu L, Wang W, Lu Y, Li F, Zhu G. Denitrification is the main microbial N loss pathway on the Qinghai-Tibet Plateau above an elevation of 5000 m. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 696:133852. [PMID: 31442722 DOI: 10.1016/j.scitotenv.2019.133852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Soil nitrogen (N) deficiency is the major factor contributing to low primary productivity on the Qinghai-Tibet Plateau. However, most of our understanding of N cycling is still based on human disturbed environments, and the microbial mechanisms governing N loss in low primary productivity environment remain unclear. This study explores three microbial N loss pathways in eight wetland and dryland soil profiles from the Qinghai-Tibet Plateau, at an elevation of above 5000 m with little human activity, using 15N isotopic tracing slurry technology, quantitative PCR, and high-throughput sequencing. No denitrifying anaerobic methane oxidation was detected. Anammox occurred in two of the wetland (n = 4) and dryland (n = 4) soil profiles, while denitrification widely occurred and was the dominant N loss pathway in all samples. Where denitrification and anammox co-occurred, both abundance and activity were higher in wetland than in dryland soils and higher in surface than in subsurface soils. In comparison with non-anammox sites, nitrate levels initiate anammox-related N cycling. High-throughput sequencing and network analysis of nirK, nirS, nosZ, and hzsB gene communities showed that Bradyrhizobiaceae (a family of rhizobia) may play a dominant role in N loss pathways in this region. Given the geological evolution and relatively undisturbed habitat, these findings strongly suggest that denitrification is the dominant N loss pathway in terrestrial habitats of the Qing-Tibet Plateau with minimal anthropogenic activity.
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Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyue Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Siyan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Cheng Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Linjie Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lu Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weidong Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yonglong Lu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Sciences and Technology, Guangzhou 510650, China
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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160
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Chen S, Chee-Sanford JC, Yang WH, Sanford RA, Chen J, Yan X, Shan J. Effects of triclosan and triclocarban on denitrification and N 2O emissions in paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133782. [PMID: 31416034 DOI: 10.1016/j.scitotenv.2019.133782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/01/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
Triclosan (TCS) and triclocarban (TCC) are two common antimicrobial compounds, which are widely used as ingredients in pharmaceuticals and personal care products. They occur ubiquitously in soil due to biosolid application as agricultural fertilizers, but their influence on microbially mediated soil biogeochemical processes is poorly understood. We tested the effects of varying concentrations of TCS and TCC applied both individually and together on denitrification and N2O emissions in paddy soil. We also quantified denitrification functional gene abundances by q-PCR to elucidate the microbial mechanisms of TCS and TCC's effects. Our results showed that TCS and TCC exposure both individually and together significantly (p < 0.05) inhibited denitrification (7.0-36.7%) and N2O emissions (15.4-86.4%) except for the 0.01 mg kg-1 TCC treatment in which denitrification was slightly but significantly (p < 0.05) stimulated. The inhibitory effects of TCS and TCC exposure were mainly attributed to their negative net effects on denitrifying bacteria as suggested by the decrease in abundances of 16S rRNA, narG, nirK and clade I nosZ genes in the TCS and TCC treatments. Overall, we found that TCS and TCC exposure in paddy soil could substantially alter nitrogen cycling in rice paddy ecosystems by inhibiting denitrification and N2O emissions. These effects should be taken into consideration when evaluating the environmental impacts of TCS and TCC.
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Affiliation(s)
- Shuntao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Joanne C Chee-Sanford
- United States Department of Agriculture, Agricultural Research Service, Urbana, IL 61801, USA
| | - Wendy H Yang
- Departments of Plant Biology, University of Illinois, Urbana, IL 61801, USA; Department of Geology, University of Illinois, Urbana, IL 61801, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois, Urbana, IL 61801, USA
| | - Jianqiu Chen
- College of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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161
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Chen H, Yin C, Fan X, Ye M, Peng H, Li T, Zhao Y, Wakelin SA, Chu G, Liang Y. Reduction of N 2O emission by biochar and/or 3,4-dimethylpyrazole phosphate (DMPP) is closely linked to soil ammonia oxidizing bacteria and nosZI-N 2O reducer populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133658. [PMID: 31398644 DOI: 10.1016/j.scitotenv.2019.133658] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/25/2019] [Accepted: 07/28/2019] [Indexed: 04/14/2023]
Abstract
Biochar has been demonstrated to reduce nitrous oxide (N2O) emissions from soils, but its effect is highly soil-dependent. In particular, in soils with strong nitrification potential, biochar addition may increase N2O emissions. Thus, in soils with strong nitrification potential, the combination of biochar with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) may be more effective in reducing N2O emissions than biochar alone. However, the combined use of biochar and DMPP on soil N2O emissions is relatively unexplored, and underlying microbial mechanisms of how biochar and/or DMPP amendment affect N2O emissions is still largely unknown. Here, a 30-day incubation experiment was established with four treatments: CK (control), BC (biochar), DMPP, and BD (biochar and DMPP), all at agronomically recommended rates, and N cycling assessed following addition of urea. Treatment of soil with BC, DMPP and BD reduced N2O emissions (compared with urea alone) by 59.1%, 95.5% and 74.1%, respectively. Quantification of N cycling genes (amoA, nirS, nirK, and nosZ) indicated that biochar stimulated growth of ammonia oxidizing archaea (AOA) and bacteria (AOB), while DMPP alone inhibited the activity and growth of AOB. In the BD treatment, DMPP was absorbed onto biochar reducing its efficacy in inhibiting AOB growth. The response patterns of nirS/nirK nitrite-reducing denitrifiers to biochar and/or DMPP addition varied among clades. Notably, biochar and/or DMPP increased the abundance of nosZI and nosZII-N2O reducers, but nosZI-clade taxa were more closely associated with reducing N2O emission than nosZII taxa. Overall, our findings proved that the dynamics of AOB and nosZI-N2O reducers resulting from the addition of biochar and/or DMPP played a key role in governing soil N2O emissions.
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Affiliation(s)
- Hao Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chang Yin
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoping Fan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mujun Ye
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongyun Peng
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuhua Zhao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Guixin Chu
- College of Life Sciences, Shaoxing University, Shaoxing 312000, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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162
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Huang S, Zheng Z, Wei Q, Han I, Jaffé PR. Performance of sulfur-based autotrophic denitrification and denitrifiers for wastewater treatment under acidic conditions. BIORESOURCE TECHNOLOGY 2019; 294:122176. [PMID: 31574366 DOI: 10.1016/j.biortech.2019.122176] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/14/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Autotrophic denitrification under acidic conditions using sulfide (S2-), elemental sulfur (S0), and thiosulfate (S2O32-) as electron donors are evaluated. Results from batch and column experiments show that when different S species were supplied, different pH conditions and denitrifier communities were required for denitrification to occur. Nitrate and nitrite were removed via autotrophic denitrification at pH ranging from 4 to 8, when S2- or S2O32- was the electron donor, while with S0 denitrification was only observed at pH > 6. When S2- was used as electron donor, it was converted to S0, and S0 was not used while S2- was available. When addition of S2- was discontinued, or S2- depleted, S0 that had accumulated was used as electron donor for denitrification. These findings demonstrate that sulfur-based autotrophic denitrification can proceed under acidic conditions, but that the addition of appropriate S species and the presence of an effective denitrifier community are required.
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Affiliation(s)
- Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Zhaoming Zheng
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Qingqing Wei
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Il Han
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Peter R Jaffé
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA.
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163
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Community structures and comparison of nosZ and 16S rRNA genes from culturable denitrifying bacteria. Folia Microbiol (Praha) 2019; 65:497-510. [DOI: 10.1007/s12223-019-00754-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 10/14/2019] [Indexed: 10/25/2022]
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164
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Suenaga T, Hori T, Riya S, Hosomi M, Smets BF, Terada A. Enrichment, Isolation, and Characterization of High-Affinity N 2O-Reducing Bacteria in a Gas-Permeable Membrane Reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:12101-12112. [PMID: 31517481 DOI: 10.1021/acs.est.9b02237] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The recent discovery of nitrous oxide (N2O)-reducing bacteria suggests a potential biological sink for the potent greenhouse gas N2O. For an application toward N2O mitigation, characterization of more isolates will be required. Here, we describe the successful enrichment and isolation of high-affinity N2O-reducing bacteria using a N2O-fed reactor (N2OFR). Two N2OFRs, where N2O was continuously and directly supplied as the sole electron acceptor to a biofilm grown on a gas-permeable membrane, were operated with acetate or a mixture of peptone-based organic substrates as an electron donor. In parallel, a NO3- -fed reactor (NO3FR), filled with a nonwoven sheet substratum, was operated using the same inoculum. We hypothesized that supplying N2O vs NO3- would enhance the dominance of distinct N2O-reducing bacteria. Clade II type nosZ bacteria became rapidly enriched over clade I type nosZ bacteria in the N2OFRs, whereas the opposite held in the NO3FR. High-throughput sequencing of 16S rRNA gene amplicons revealed the dominance of Rhodocyclaceae in the N2OFRs. Strains of the Azospira and Dechloromonas genera, canonical denitrifiers harboring clade II type nosZ, were isolated with high frequency from the N2OFRs (132 out of 152 isolates). The isolates from the N2OFR demonstrated higher N2O uptake rates (Vmax: 4.23 × 10-3-1.80 × 10-2 pmol/h/cell) and lower N2O half-saturation coefficients (Km,N2O: 1.55-2.10 μM) than a clade I type nosZ isolate from the NO3FR. Furthermore, the clade II type nosZ isolates had higher specific growth rates on N2O than nitrite as an electron acceptor. Hence, continuously and exclusively supplying N2O in an N2OFR allows the enrichment and isolation of high-affinity N2O-reducing strains, which may be used as N2O sinks in bioaugmentation efforts.
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Affiliation(s)
- Toshikazu Suenaga
- Department of Chemical Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
- Institute of Global Innovation Research , Tokyo University of Agriculture and Technology , 3-8-1 Harumi-cho , Fuchu , Tokyo 185-8538 , Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Onogawa 16-1 , Tsukuba , Ibaraki 305-8569 , Japan
| | - Shohei Riya
- Department of Chemical Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
- Institute of Global Innovation Research , Tokyo University of Agriculture and Technology , 3-8-1 Harumi-cho , Fuchu , Tokyo 185-8538 , Japan
| | - Masaaki Hosomi
- Department of Chemical Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
| | - Barth F Smets
- Institute of Global Innovation Research , Tokyo University of Agriculture and Technology , 3-8-1 Harumi-cho , Fuchu , Tokyo 185-8538 , Japan
- Department of Environmental Engineering , Technical University of Denmark , Miljoevej, Lyngby 2800 , Denmark
| | - Akihiko Terada
- Department of Chemical Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
- Institute of Global Innovation Research , Tokyo University of Agriculture and Technology , 3-8-1 Harumi-cho , Fuchu , Tokyo 185-8538 , Japan
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165
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Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions. Adv Microb Physiol 2019; 75:137-175. [PMID: 31655736 DOI: 10.1016/bs.ampbs.2019.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biologically catalyzed nitrous oxide (N2O, laughing gas) reduction to dinitrogen gas (N2) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N2O reductase (NosZ), which is the only known enzyme that converts N2O to N2. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N2O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N2O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N2O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N2O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N2O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.
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166
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Gaimster H, Alston M, Richardson DJ, Gates AJ, Rowley G. Transcriptional and environmental control of bacterial denitrification and N2O emissions. FEMS Microbiol Lett 2019; 365:4768087. [PMID: 29272423 DOI: 10.1093/femsle/fnx277] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/18/2017] [Indexed: 12/18/2022] Open
Abstract
In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3-) respiration in which the NO3- is sequentially reduced via nitrite (NO2-), nitric oxide (NO) and nitrous oxide (N2O) to dinitrogen (N2). However, atmospheric N2O continues to rise, a significant proportion of which is microbial in origin. This implies that the enzyme responsible for N2O reduction, nitrous oxide reductase (NosZ), does not always carry out the final step of denitrification either efficiently or in synchrony with the rest of the pathway. Despite a solid understanding of the biochemistry underpinning denitrification, there is a relatively poor understanding of how environmental signals and respective transcriptional regulators control expression of the denitrification apparatus. This minireview describes the current picture for transcriptional regulation of denitrification in the model bacterium, Paracoccus denitrificans, highlighting differences in other denitrifying bacteria where appropriate, as well as gaps in our understanding. Alongside this, the emerging role of small regulatory RNAs in regulation of denitrification is discussed. We conclude by speculating how this information, aside from providing a better understanding of the denitrification process, can be translated into development of novel greenhouse gas mitigation strategies.
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Affiliation(s)
- Hannah Gaimster
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Mark Alston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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167
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Bai Y, Huang X, Zhou X, Xiang Q, Zhao K, Yu X, Chen Q, Jiang H, Nyima T, Gao X, Gu Y. Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China. PeerJ 2019; 7:e7356. [PMID: 31428538 PMCID: PMC6698129 DOI: 10.7717/peerj.7356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/26/2019] [Indexed: 11/20/2022] Open
Abstract
Background The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).
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Affiliation(s)
- Yan Bai
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiying Huang
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiangrui Zhou
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Quanju Xiang
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ke Zhao
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiumei Yu
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiang Chen
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hao Jiang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Tashi Nyima
- Institute of Agricultural Resources and Environmental Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Xue Gao
- Institute of Agricultural Resources and Environmental Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Yunfu Gu
- Department of Microbiology/ College of Resources/Sichuan Agricultural University, Sichuan Agricultural University, Chengdu, Sichuan, China
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168
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Ding X, Wei D, Guo W, Wang B, Meng Z, Feng R, Du B, Wei Q. Biological denitrification in an anoxic sequencing batch biofilm reactor: Performance evaluation, nitrous oxide emission and microbial community. BIORESOURCE TECHNOLOGY 2019; 285:121359. [PMID: 31015181 DOI: 10.1016/j.biortech.2019.121359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/14/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
The present study evaluated the performance of biological denitrification in an anoxic sequencing batch biofilm reactor (ASBBR) and its nitrous oxide (N2O) emission. After 90 days operation, the effluent chemical oxygen demand and total nitrogen removal efficiencies high of 94.8% and 95.0%, respectively. Both polysaccharides and protein contents were reduced in bound EPS (TB-EPS) and loosely bound EPS (LB-EPS) after biofilm formation. According to typical cycle, N2O release rate was related to the free nitrous acid (FNA) concentration with the maximum value of 3.88 μg/min and total conversion rate of 1.27%. Two components were identified from EEM-PARAFAC model in soluble microbial products (SMP). Protein-like substances for component 1 changed significantly in denitrification process, whereas humic-like and fulvic acid-like substances for component 2 remained relatively stable. High-throughput sequencing results showed that Lysobacter, Tolumonas and Thauera were the dominant genera, indicating the co-existence of autotrophic and heterotrophic denitrifiers in ASBBR.
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Affiliation(s)
- Xiangwei Ding
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, PR China
| | - Dong Wei
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, PR China.
| | - Wenshan Guo
- School of Civil and Environmental Engineering, University of Technology Sydney, Broadway, NSW 2007, Australia
| | - Ben Wang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, PR China
| | - Zijun Meng
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, PR China
| | - Rui Feng
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, PR China
| | - Bin Du
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, PR China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
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169
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Otte JM, Blackwell N, Ruser R, Kappler A, Kleindienst S, Schmidt C. N 2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment. Sci Rep 2019; 9:10691. [PMID: 31366952 PMCID: PMC6668465 DOI: 10.1038/s41598-019-47172-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 07/12/2019] [Indexed: 11/08/2022] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas that also contributes to stratospheric ozone depletion. Besides microbial denitrification, abiotic nitrite reduction by Fe(II) (chemodenitrification) has the potential to be an important source of N2O. Here, using microcosms, we quantified N2O formation in coastal marine sediments under typical summer temperatures. Comparison between gamma-radiated and microbially-active microcosm experiments revealed that at least 15-25% of total N2O formation was caused by chemodenitrification, whereas 75-85% of total N2O was potentially produced by microbial N-transformation processes. An increase in (chemo)denitrification-based N2O formation and associated Fe(II) oxidation caused an upregulation of N2O reductase (typical nosZ) genes and a distinct community shift to potential Fe(III)-reducers (Arcobacter), Fe(II)-oxidizers (Sulfurimonas), and nitrate/nitrite-reducing microorganisms (Marinobacter). Our study suggests that chemodenitrification contributes substantially to N2O formation from marine sediments and significantly influences the N- and Fe-cycling microbial community.
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Affiliation(s)
- Julia M Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Nia Blackwell
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Reiner Ruser
- Fertilization and Soil Matter Dynamics, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany.
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark.
| | - Sara Kleindienst
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
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170
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Romdhane S, Spor A, Busset H, Falchetto L, Martin J, Bizouard F, Bru D, Breuil MC, Philippot L, Cordeau S. Cover Crop Management Practices Rather Than Composition of Cover Crop Mixtures Affect Bacterial Communities in No-Till Agroecosystems. Front Microbiol 2019; 10:1618. [PMID: 31338089 PMCID: PMC6629898 DOI: 10.3389/fmicb.2019.01618] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 06/28/2019] [Indexed: 12/21/2022] Open
Abstract
Cover cropping plays a key role in the maintenance of arable soil health and the enhancement of agroecosystem services. However, our understanding of how cover crop management impacts soil microbial communities and how these interactions might affect soil nutrient cycling is still limited. Here, we studied the impact of four cover crop mixtures varying in species richness and functional diversity, three cover crop termination strategies (i.e., frost, rolling, and glyphosate) and two levels of irrigation at the cover crop sowing on soil nitrogen and carbon dynamics, soil microbial diversity, and structure as well as the abundance of total bacteria, archaea, and N-cycling microbial guilds. We found that total nitrogen and soil organic carbon were higher when cover crops were killed by frost compared to rolling and glyphosate termination treatments, while cover crop biomass was positively correlated to soil carbon and C:N ratio. Modifications of soil properties due to cover crop management rather than the composition of cover crop mixtures were related to changes in the abundance of ammonia oxidizers and denitrifiers, while there was no effect on the total bacterial abundance. Unraveling the underlying processes by which cover crop management shapes soil physico-chemical properties and bacterial communities is of importance to help selecting optimized agricultural practices for sustainable farming systems.
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Affiliation(s)
- Sana Romdhane
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - Aymé Spor
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - Hugues Busset
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | | | | | - Florian Bizouard
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - David Bru
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | | | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
| | - Stéphane Cordeau
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, Dijon, France
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Hellman M, Bonilla-Rosso G, Widerlund A, Juhanson J, Hallin S. External carbon addition for enhancing denitrification modifies bacterial community composition and affects CH 4 and N 2O production in sub-arctic mining pond sediments. WATER RESEARCH 2019; 158:22-33. [PMID: 31009831 DOI: 10.1016/j.watres.2019.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/04/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
Explosives used in mining operations release reactive nitrogen (N) that discharge into surrounding waters. Existing pond systems at mine sites could be used for N removal through denitrification and we investigated capacity in tailings and clarification pond sediments at an iron-ore mine site. Despite differences in microbial community structure in the two ponds, the potential denitrification rates were similar, although carbon limited. Therefore, a microcosm experiment in which we amended sediment from the clarification pond with acetate, cellulose or green algae as possible carbon sources was conducted during 10 weeks under denitrifying conditions. Algae and acetate treatments showed efficient nitrate removal and increased potential denitrification rates, whereas cellulose was not different from the control. Denitrifiers were overall more abundant than bacteria performing dissimilatory nitrate reduction to ammonium (DNRA) or anaerobic ammonium oxidation, although DNRA bacteria increased in the algae treatment and this coincided with accumulation of ammonium. The algae addition also caused higher emissions of methane (CH4) and nitrous oxide (N2O). The bacterial community in this treatment had a large proportion of Bacteroidia, sulfate reducing taxa and bacteria known as fermenters. Functional gene abundances indicated an imbalance between organisms that produce N2O in relation to those that can reduce it, with the algae treatment showing the lowest relative capacity for N2O reduction. These findings show that pond sediments have the potential to contribute to mitigating nitrate levels in water from mining industry, but it is important to consider the type of carbon supply as it affects the community composition, which in turn can lead to unwanted processes and increased greenhouse gas emissions.
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Affiliation(s)
- Maria Hellman
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Germán Bonilla-Rosso
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Anders Widerlund
- Luleå University of Technology, Division of Geosciences and Environmental Engineering, 97187, Luleå, Sweden.
| | - Jaanis Juhanson
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
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Beule L, Corre MD, Schmidt M, Göbel L, Veldkamp E, Karlovsky P. Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes. PLoS One 2019; 14:e0218779. [PMID: 31246995 PMCID: PMC6597161 DOI: 10.1371/journal.pone.0218779] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 06/10/2019] [Indexed: 01/15/2023] Open
Abstract
Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in paired monoculture and agroforestry cropland in a Phaeozem soil, and paired open grassland and agroforestry grassland in Histosol and Anthrosol soils. The soil fungi-to-bacteria ratio was greater in the tree row than in the crop or grass rows of the monoculture cropland and open grassland in all soil types, possibly due to increased input of tree residues and the absence of tillage in the Phaeozem (cropland) soil. In the Phaeozem (cropland) soil, gene abundances of amoA indicated a niche differentiation between archaeal and bacterial ammonia oxidizers that distinctly separated the influence of the tree row from the crop row and monoculture system. Abundances of nitrate (napA and narG), nitrite (nirK and nirS) and nitrous oxide reductase genes (nosZ clade I) were largely influenced by soil type rather than management system. The soil types’ effects were associated with their differences in soil organic C, total N and pH. Our findings show that in temperate regions, conversion of monoculture cropland and open grassland to agroforestry systems can alter the abundance of soil bacteria and fungi and soil-N-cycling genes, particularly genes involved in ammonium oxidation.
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Affiliation(s)
- Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, Goettingen, Germany
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
- * E-mail:
| | - Marife D. Corre
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Marcus Schmidt
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Leonie Göbel
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, Goettingen, Germany
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Palacin-Lizarbe C, Camarero L, Hallin S, Jones CM, Cáliz J, Casamayor EO, Catalan J. The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats. Front Microbiol 2019; 10:1229. [PMID: 31214153 PMCID: PMC6558203 DOI: 10.3389/fmicb.2019.01229] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/16/2019] [Indexed: 01/04/2023] Open
Abstract
Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N2O release. Loss as N2 was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N2O emissions from productive lakes.
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Affiliation(s)
- Carlos Palacin-Lizarbe
- Centro de Investigación Ecológica y Aplicaciones Forestales, Cerdanyola del Vallès, Spain
| | - Lluís Camarero
- Center for Advanced Studies of Blanes, (CEAB-CSIC), Girona, Spain
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Joan Cáliz
- Center for Advanced Studies of Blanes, (CEAB-CSIC), Girona, Spain
| | | | - Jordi Catalan
- Centro de Investigación Ecológica y Aplicaciones Forestales, Cerdanyola del Vallès, Spain.,Consejo Superior de Investigaciones Científicas, Cerdanyola del Vallès, Spain
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Altering N 2O emissions by manipulating wheat root bacterial community. Sci Rep 2019; 9:7613. [PMID: 31110207 PMCID: PMC6527579 DOI: 10.1038/s41598-019-44124-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/09/2019] [Indexed: 11/29/2022] Open
Abstract
Nitrous oxide (N2O) is a greenhouse gas and a potent ozone-depleting substance in the stratosphere. Agricultural soils are one of the main global sources of N2O emissions, particularly from cereal fields due to their high areal coverage. The aim of this study was to isolate N2O-reducing bacteria able to mitigate N2O emissions from the soil after inoculation. We isolated several bacteria from wheat roots that were capable of N2O reduction in vitro and studied their genetic potential and activity under different environmental conditions. Three of these isolates- all carrying the nitrous oxide reductase-encoding clade I nosZ, able to reduce N2O in vitro, and efficient colonizers of wheat roots- presented different N2O-reduction strategies when growing in the root zone, possibly due to the different conditions in situ and their metabolic preferences. Each isolate seemed to prefer to operate at different altered oxygen levels. Isolate AU243 (related to Agrobacterium/Rhizobium) could reduce both nitrate and N2O and operated better at lower oxygen levels. Isolate AU14 (related to Alcaligenes faecalis), lacking nitrate reductases, operated better under less anoxic conditions. Isolate NT128 (related to Pseudomonas stutzeri) caused slightly increased N2O emissions under both anoxic and ambient conditions. These results therefore emphasize the importance of a deep understanding of soil–plant–microbe interactions when environmental application is being considered.
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175
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Gao H, Mao Y, Zhao X, Liu WT, Zhang T, Wells G. Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess. WATER RESEARCH 2019; 155:275-287. [PMID: 30852315 DOI: 10.1016/j.watres.2019.02.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Denitrification is the stepwise microbial reduction of nitrate or nitrite (NO2-) to nitrogen gas via the obligate intermediates nitric oxide (NO) and nitrous oxide (N2O). Substantial N2O accumulation has been reported in denitrifying enhanced biological phosphorus removal (EBPR) bioreactors enriched in denitrifying polyphosphate accumulating organisms (DPAOs), but little is known about underlying mechanisms for N2O generation, prevalence of complete versus truncated denitrification pathways, or the impact of NO2- feed on DPAO-enriched consortia. To address this knowledge gap, we employed genome-resolved metagenomics to investigate nitrogen transformation potential in a NO2- fed denitrifying EBPR bioreactor enriched in Candidatus Accumulibacter and prone to N2O accumulation. Our analysis yielded 41 near-complete metagenome-assembled genomes (MAGs), including two co-occurring Accumulibacter strains affiliated with clades IA and IC (the first published genome from this clade) and 39 non-PAO flanking bacterial genomes. The dominant Accumulibacter clade IA encoded genes for complete denitrification, while the lower abundance Accumulibacter clade IC harbored all denitrification genes except for a canonical respiratory NO reductase. Analysis of the 39 non-PAO MAGs revealed a high prevalence of taxa harboring an incomplete denitrification pathway. Of the 27 MAGs harboring capacity for at least one step in the denitrification pathway, 10 were putative N2O producers lacking N2O reductase, 16 were putative N2O reducers that lacked at least one upstream denitrification gene, and only one harbored a complete denitrification pathway. We also documented increasing abundance over the course of reactor operation of putative N2O producers. Our results suggest that the unusually high levels of N2O production observed in this Accumulibacter-enriched consortium are linked in part to the selection for non-PAO flanking microorganisms with truncated denitrification pathways.
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Affiliation(s)
- Han Gao
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, United States
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, Shenzhen University, Shenzhen, 518060, PR China; Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong.
| | - Xiaotian Zhao
- Master of Science in Biotechnology Program, McCormick School of Engineering, Northwestern University, Evanston, IL, 60208, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - George Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, United States.
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176
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Yoon S, Song B, Phillips RL, Chang J, Song MJ. Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems. FEMS Microbiol Ecol 2019; 95:5488431. [DOI: 10.1093/femsec/fiz066] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/10/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.
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Affiliation(s)
- Sukhwan Yoon
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Sciences, College of William and Mary, 1375 Greate Rd, Gloucester Point, VA 23062, USA
| | - Rebecca L Phillips
- Ecological Insights Corporation, 130 69th Street SE, Hazelton, ND 58544, USA
| | - Jin Chang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
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177
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Wang M, Xiong W, Zou Y, Lin M, Zhou Q, Xie X, Sun Y. Evaluating the net effect of sulfadimidine on nitrogen removal in an aquatic microcosm environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:1010-1019. [PMID: 31091633 DOI: 10.1016/j.envpol.2019.02.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/22/2019] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
Antibiotics enter into aquatic pond sediments by wastewater and could make detrimental effects on microbial communities. In this study, we examined the effects of sulfadimidine on nitrogen removal when added to experimental pond sediments. We found that sulfadimidine increased the number of sulfadimidine resistant bacteria and significantly increased the abundance of sul2 at the end of the incubation time (ANOVA test at Tukey HSD, P < 0.05). In addition, sulfadimidine decreased the N2O reduction rate as well as the amount of nitrate reduction. Pearson correlation analysis revealed that the N2O reduction rate was significantly and negatively correlated with narG (r = -0.679, P < 0.05). In contrast, we found a significant positive correlation between the amount of nitrate reduction and the abundance of narG (r = 0.609, P < 0.05) and nirK (r = 0.611, P < 0.05). High-throughput sequencing demonstrated that Actinobacteria, Euryarchaeota, Gemmatimonadetes, Nitrospirae, Burkholderiaceae (a family of Proteobacteria), and Thermoanaerobaculaceae (a family of Firmicutes) decreased with sulfadimidine exposure. In sediments, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonbacteraeota, Euryarchaeota, Firmicutes, Gemmatimonadetes, and Spirochaetesat may play key roles in nitrogen transformation. Overall, the study exhibited a net effect of antibiotic exposure regarding nitrogen removal in an aquatic microcosm environment through a combination of biochemical pathways and molecular pathways, and draws attention to controlling antibiotic pollution in aquatic ecosystems.
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Affiliation(s)
- Mei Wang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yong Zou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Manxia Lin
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Qin Zhou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Xiying Xie
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
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178
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Wang H, Sun Y, Wu G, Guan Y. Effect of anoxic to aerobic duration ratios on nitrogen removal and nitrous oxide emission in the multiple anoxic/aerobic process. ENVIRONMENTAL TECHNOLOGY 2019; 40:1676-1685. [PMID: 29333979 DOI: 10.1080/09593330.2018.1427801] [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: 09/07/2017] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
Characteristics of nitrogen removal and nitrous oxide (N2O) emission in the multiple anoxic/aerobic (AO) process were examined in three sequencing batch reactors (SBRs) with different anoxic durations (50 min, SBRH; 40 min, SBRM; 30 min, SBRL) and a fixed aerobic duration of 30 min. The highest total inorganic nitrogen removal percentage of 85.8% was obtained in SBRH, while a minimum N2O emission factor of 1.9% was obtained in SBRL. During nitrification batch experiments, the N2O emission factor and emission rate were both lower in SBRH than SBRL. More N2O production was obtained during denitrification in SBRH when denitrifiers utilized intracellular organic carbon. Nitrite reduction by heterotrophs was the main N2O production pathway during simultaneous nitrification and denitrification in SBRH and SBRL, with the N2O emission factor of 31.3% and 36.3%, respectively. Adequate anoxic duration and lowering aerobic nitrite concentrations could be adopted to mitigate N2O emission in the multiple AO process. The dominant microorganisms at the phylum level in all reactors were Proteobacteria and Bacteroidetes, while the abundance of Nitrospira was the highest in SBRH with relatively lowest dissolved oxygen concentrations.
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Affiliation(s)
- Huoqing Wang
- a Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen , Tsinghua University , Shenzhen , People's Republic of China
| | - Yuepeng Sun
- a Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen , Tsinghua University , Shenzhen , People's Republic of China
| | - Guangxue Wu
- a Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen , Tsinghua University , Shenzhen , People's Republic of China
| | - Yuntao Guan
- a Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen , Tsinghua University , Shenzhen , People's Republic of China
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179
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Bennett SP, Soriano-Laguna MJ, Bradley JM, Svistunenko DA, Richardson DJ, Gates AJ, Le Brun NE. NosL is a dedicated copper chaperone for assembly of the Cu Z center of nitrous oxide reductase. Chem Sci 2019; 10:4985-4993. [PMID: 31183047 PMCID: PMC6530538 DOI: 10.1039/c9sc01053j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the terminal enzyme of the denitrification pathway of soil bacteria that reduces the greenhouse gas nitrous oxide (N2O) to dinitrogen. In addition to a binuclear CuA site that functions in electron transfer, the active site of N2OR features a unique tetranuclear copper cluster bridged by inorganic sulfide, termed CuZ. In copper-limited environments, N2OR fails to function, resulting in truncation of denitrification and rising levels of N2O released by cells to the atmosphere, presenting a major environmental challenge. Here we report studies of nosL from Paracoccus denitrificans, which is part of the nos gene cluster, and encodes a putative copper binding protein. A Paracoccus denitrificans ΔnosL mutant strain had no denitrification phenotype under copper-sufficient conditions but failed to reduce N2O under copper-limited conditions. N2OR isolated from ΔnosL cells was found to be deficient in copper and to exhibit attenuated activity. UV-visible absorbance spectroscopy revealed that bands due to the CuA center were unaffected, while those corresponding to the CuZ center were significantly reduced in intensity. In vitro studies of a soluble form of NosL without its predicted membrane anchor showed that it binds one Cu(i) ion per protein with attomolar affinity, but does not bind Cu(ii). Together, the data demonstrate that NosL is a copper-binding protein specifically required for assembly of the CuZ center of N2OR, and thus represents the first characterised assembly factor for the CuZ active site of this key environmental enzyme, which is globally responsible for the destruction of a potent greenhouse gas.
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Affiliation(s)
- Sophie P Bennett
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Manuel J Soriano-Laguna
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Justin M Bradley
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Dimitri A Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester CO4 3SQ , UK
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
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180
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Cannon J, Sanford RA, Connor L, Yang WH, Chee-Sanford J. Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification. J Microbiol Methods 2019; 160:49-59. [PMID: 30905502 DOI: 10.1016/j.mimet.2019.03.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) is now known to be a more prevalent process in terrestrial ecosystems than previously thought. The key enzyme, a pentaheme cytochrome c nitrite reductase NrfA associated with respiratory nitrite ammonification, is encoded by the nrfA gene in a broad phylogeny of bacteria. The lack of reliable and comprehensive molecular tools to detect diverse nrfA from environmental samples has hampered efforts to meaningfully characterize the genetic potential for DNRA in environmental systems. In this study, modifications were made to optimize the amplification efficiency of previously-designed PCR primers, targeting the diagnostic region of NrfA between the conserved third- and fourth heme binding domains, and to increase coverage to include detection of environmentally relevant Geobacteraceae-like nrfA. Using an alignment of the primers to >270 bacterial nrfA genes affiliated with 18 distinct clades, modifications to the primer sequences improved coverage, minimized amplification artifacts, and yielded the predicted product sizes from reference-, soil-, and groundwater DNA. Illumina sequencing of amplicons showed the successful recovery of nrfA gene fragments from environmental DNA based on alignments of the translated sequences. The new primers developed in this study are more efficient in PCR reactions, although gene targets with high GC content affect efficiency. Furthermore, the primers have a broader spectrum of detection and were validated rigorously for use in detecting nrfA from natural environments. These are suitable for conventional PCR, qPCR, and use in PCR access array technologies that allow multiplex gene amplification for downstream high throughput sequencing platforms.
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Affiliation(s)
- Jordan Cannon
- Dept. of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Dept. of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Wendy H Yang
- Dept. of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Dept. of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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181
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Ma Y, Zilles JL, Kent AD. An evaluation of primers for detecting denitrifiers via their functional genes. Environ Microbiol 2019; 21:1196-1210. [PMID: 30724437 DOI: 10.1111/1462-2920.14555] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022]
Abstract
Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.
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Affiliation(s)
- Yanjun Ma
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julie L Zilles
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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182
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Hammerl V, Kastl EM, Schloter M, Kublik S, Schmidt H, Welzl G, Jentsch A, Beierkuhnlein C, Gschwendtner S. Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. Sci Rep 2019; 9:2280. [PMID: 30783152 PMCID: PMC6381133 DOI: 10.1038/s41598-018-38147-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022] Open
Abstract
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
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Affiliation(s)
- Verena Hammerl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Chair for Soil Ecology - Technische Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Eva-Maria Kastl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Schmidt
- Institute of Natural Sciences - Universität Koblenz Landau, Campus Koblenz, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Gerhard Welzl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anke Jentsch
- Disturbance Ecology - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Carl Beierkuhnlein
- Chair of Biogeography - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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183
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Romdhane S, Devers-Lamrani M, Beguet J, Bertrand C, Calvayrac C, Salvia MV, Jrad AB, Dayan FE, Spor A, Barthelmebs L, Martin-Laurent F. Assessment of the ecotoxicological impact of natural and synthetic β-triketone herbicides on the diversity and activity of the soil bacterial community using omic approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:241-249. [PMID: 30236841 DOI: 10.1016/j.scitotenv.2018.09.159] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The emergence of pesticides of natural origin appears as an environmental-friendly alternative to synthetic pesticides for managing weeds. To verify this assumption, leptospermone, a natural β-triketone herbicide, and sulcotrione, a synthetic one, were applied to soil microcosms at 0× (control), 1× or 10× recommended field dose. The fate of these two herbicides (i.e. dissipation and formation of transformation products) was monitored to assess the scenario of exposure of soil microorganisms to natural and synthetic herbicides. Ecotoxicological impact of both herbicides was explored by monitoring soil bacterial diversity and activity using next-generation sequencing of 16S rRNA gene amplicons and soil metabolomics. Both leptospermone and sulcotrione fully dissipated over the incubation period. During their dissipation, transformation products of natural and synthetic β-triketone were detected. Hydroxy-leptospermone was almost completely dissipated by the end of the experiment, while CMBA, the major metabolite of sulcotrione, remained in soil microcosms. After 8 days of exposure, the diversity and structure of the soil bacterial community treated with leptospermone was significantly modified, while less significant changes were observed for sulcotrione. For both herbicides, the diversity of the soil bacterial community was still not completely recovered by the end of the experiment (45 days). The combined use of next-generation sequencing and metabolomic approaches allowed us to assess the ecotoxicological impact of natural and synthetic pesticides on non-target soil microorganisms and to detect potential biomarkers of soil exposure to β-triketones.
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Affiliation(s)
- Sana Romdhane
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté Dijon, Agroécologie, France; Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia, Perpignan, France.
| | | | - Jérémie Beguet
- AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté Dijon, Agroécologie, France
| | - Cédric Bertrand
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia, Perpignan, France
| | - Christophe Calvayrac
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, 66650 Banyuls sur Mer, France
| | - Marie-Virginie Salvia
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia, Perpignan, France
| | - Amani Ben Jrad
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, 66650 Banyuls sur Mer, France
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management Department, Colorado State University, Fort Collins, CO, USA
| | - Aymé Spor
- AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté Dijon, Agroécologie, France
| | - Lise Barthelmebs
- Biocapteurs Analyse Environment, University of Perpignan via Domitia, Perpignan, France; Sorbonne Universités, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, 66650 Banyuls sur Mer, France
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184
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Vieira A, Galinha CF, Oehmen A, Carvalho G. The link between nitrous oxide emissions, microbial community profile and function from three full-scale WWTPs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:2460-2472. [PMID: 30336436 DOI: 10.1016/j.scitotenv.2018.10.132] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 09/28/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Few attempts have been made in previous studies to link the microbial community structure and function with nitrous oxide (N2O) emissions at full-scale wastewater treatment plants (WWTPs). In this work, high-throughput sequencing and reverse transcriptase-qPCR (RT-qPCR) was applied to activated sludge samples from three WWTPs for two seasonal periods (winter and summer) and linked with the N2O emissions and wastewater characteristics. The total N2O emissions ranged from 7.2 to 937.0 g N-N2O/day, which corresponds to an emission factor of 0.001 to 0.280% of the influent NH4-N being emitted as N2O. Those emissions were related to the abundance of Nitrotoga, Candidatus Microthrix and Rhodobacter genera, which were favored by higher dissolved oxygen (DO) and nitrate (NO3-) concentrations in the activated sludge tanks. Furthermore, a relationship between the nirK gene expression and N2O emissions was verified. Detected N2O emission peaks were associated with different process events, related to aeration transition periods, that occurred during the regular operation of the plants, which could be potentially associated to increased emissions of the WWTP. The design of mitigation strategies, such as optimizing the aeration regime, is therefore important to avoid process events that lead to those N2O emissions peaks. Furthermore, this study also demonstrates the importance of assessing the gene expression of nosZ clade II, since its high abundance in WWTPs could be an important key to reduce the N2O emissions.
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Affiliation(s)
- A Vieira
- iBET - Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal; ITQB - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - C F Galinha
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Portugal
| | - A Oehmen
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Portugal; School of Chemical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia
| | - G Carvalho
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Portugal; Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, QLD 4072, Australia.
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185
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Xu HJ, Yang XR, Li S, Xue XM, Chang S, Li H, Singh BK, Su JQ, Zhu YG. Nitrogen inputs are more important than denitrifier abundances in controlling denitrification-derived N 2O emission from both urban and agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:2807-2817. [PMID: 30373058 DOI: 10.1016/j.scitotenv.2018.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Cities are increasingly being recognized as important contributors in global warming, for example by increasing atmospheric nitrous oxide (N2O). However, urban ecosystems remain poorly understood due to their functional complexity. Further, few studies have documented the microbial processes governing the N2O emissions from urban soils. Here, a field study was performed to assess in situ N2O emissions in an urban and agricultural soil located in Xiamen, China. The mechanisms underlying the difference in N2O emission patterns in both soils were further explored in an incubation experiment. Field investigations showed that N2O emission (3.5-19.0 μg N2O-N m-2 h-1) from the urban soil was significantly lower than that from the agricultural soil (25.4-18,502.3 μg N2O-N m-2 h-1). Incubation experiments showed that the urban soil initially emitted lower denitrification-derived N2O because of the lower nirS (encoding nitrite reductases) abundances, whereas overall N2O accumulation during the incubation was mainly controlled by the initial nitrate content in soil. Nitrate addition in a short period (5 days) did not change the total bacterial and denitrifier abundances or the soil bacterial community composition, but significantly altered the relative distribution of some key genera capable of denitrification. Although the urban soil exhibited lower N2O emission than its agricultural counterpart in this study, the expanding urban green areas should be taken into account when building N2O emission reduction targets.
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Affiliation(s)
- Hui-Juan Xu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shun Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Applied Geosciences, University of Tübingen, Tübingen 72074, Germany
| | - Xi-Mei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shuai Chang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrih 2751, New South Wales, Australia; Global Centre for Land-Based Innovation, University of Western Sydney, Penrith 2751, New South Wales, Australia
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Beijing 100085, China
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186
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Anderson CR, Peterson ME, Frampton RA, Bulman SR, Keenan S, Curtin D. Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum. PeerJ 2018; 6:e6090. [PMID: 30581677 PMCID: PMC6295159 DOI: 10.7717/peerj.6090] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/08/2018] [Indexed: 01/13/2023] Open
Abstract
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO2 respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N2-N g-1 h-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.
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Affiliation(s)
- Craig R Anderson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Michelle E Peterson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Rebekah A Frampton
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Simon R Bulman
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Sandi Keenan
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Denis Curtin
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
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187
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Brenzinger K, Drost SM, Korthals G, Bodelier PLE. Organic Residue Amendments to Modulate Greenhouse Gas Emissions From Agricultural Soils. Front Microbiol 2018; 9:3035. [PMID: 30581429 PMCID: PMC6292959 DOI: 10.3389/fmicb.2018.03035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/23/2018] [Indexed: 01/08/2023] Open
Abstract
Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH4 oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO2 and N2O differed considerably between the treatments, CH4 fluxes remained stable. In contrast, in vitro CH4 oxidation showed a clear increase for all amendments over time. CO2 fluxes were mostly dependent on the amount of organic residue that was used, while N2O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO2, CH4, and/or N2O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.
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Affiliation(s)
- Kristof Brenzinger
- Department of Microbial Ecology Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Sytske M Drost
- Department of Microbial Ecology Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Gerard Korthals
- Department of Microbial Ecology Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Paul L E Bodelier
- Department of Microbial Ecology Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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188
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Nakagawa T, Tsuchiya Y, Ueda S, Fukui M, Takahashi R. Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan. Microbes Environ 2018; 34:13-22. [PMID: 30504642 PMCID: PMC6440730 DOI: 10.1264/jsme2.me18103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.
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Affiliation(s)
| | | | - Shingo Ueda
- College of Bioresource Sciences, Nihon University
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University
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189
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Storer K, Coggan A, Ineson P, Hodge A. Arbuscular mycorrhizal fungi reduce nitrous oxide emissions from N 2 O hotspots. THE NEW PHYTOLOGIST 2018; 220:1285-1295. [PMID: 29206293 PMCID: PMC6282961 DOI: 10.1111/nph.14931] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/26/2017] [Indexed: 05/05/2023]
Abstract
Nitrous oxide (N2 O) is a potent, globally important, greenhouse gas, predominantly released from agricultural soils during nitrogen (N) cycling. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with two-thirds of land plants, providing phosphorus and/or N in exchange for carbon. As AMF acquire N, it was hypothesized that AMF hyphae may reduce N2 O production. AMF hyphae were either allowed (AMF) or prevented (nonAMF) access to a compartment containing an organic matter and soil patch in two independent microcosm experiments. Compartment and patch N2 O production was measured both before and after addition of ammonium and nitrate. In both experiments, N2 O production decreased when AMF hyphae were present before inorganic N addition. In the presence of AMF hyphae, N2 O production remained low following ammonium application, but increased in the nonAMF controls. By contrast, negligible N2 O was produced following nitrate application to either AMF treatment. Thus, the main N2 O source in this system appeared to be via nitrification, and the production of N2 O was reduced in the presence of AMF hyphae. It is hypothesized that AMF hyphae may be outcompeting slow-growing nitrifiers for ammonium. This has significant global implications for our understanding of soil N cycling pathways and N2 O production.
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Affiliation(s)
- Kate Storer
- Department of BiologyUniversity of YorkWentworth WayYorkYO10 5DDUK
- Present address:
ADAS High MowthorpeDuggleby, MaltonNorth YorkshireYO17 8BPUK
| | - Aisha Coggan
- Department of BiologyUniversity of YorkWentworth WayYorkYO10 5DDUK
| | - Phil Ineson
- Department of BiologyUniversity of YorkWentworth WayYorkYO10 5DDUK
| | - Angela Hodge
- Department of BiologyUniversity of YorkWentworth WayYorkYO10 5DDUK
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190
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Calderoli PA, Espínola FJ, Dionisi HM, Gil MN, Jansson JK, Lozada M. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. PLoS One 2018; 13:e0207606. [PMID: 30496195 PMCID: PMC6264515 DOI: 10.1371/journal.pone.0207606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.
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Affiliation(s)
- Priscila A Calderoli
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Fernando J Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Mónica N Gil
- Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina.,Laboratorio de Química General y Análisis de Elementos, CCT CONICET CENPAT, Puerto Madryn, Chubut Province, Argentina
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
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191
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Mino S, Yoneyama N, Nakagawa S, Takai K, Sawabe T. Enrichment and Genomic Characterization of a N 2O-Reducing Chemolithoautotroph From a Deep-Sea Hydrothermal Vent. Front Bioeng Biotechnol 2018; 6:184. [PMID: 30547029 PMCID: PMC6279868 DOI: 10.3389/fbioe.2018.00184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/13/2018] [Indexed: 01/24/2023] Open
Abstract
Nitrous oxide (N2O) is a greenhouse gas and also leads to stratospheric ozone depletion. In natural environments, only a single N2O sink process is the microbial reduction of N2O to N2, which is mediated by nitrous oxide reductase (NosZ) encoded by nosZ gene. The nosZ phylogeny has two distinct clades, clade I and formerly overlooked clade II. In deep-sea hydrothermal environments, several members of the class Campylobacteria are shown to harbor clade II nosZ gene and perform the complete denitrification of nitrate to N2; however, little is known about their ability to grow on exogenous N2O as the sole electron acceptor. Here, we obtained an enrichment culture from a deep-sea hydrothermal vent in the Southern Mariana Trough, which showed a respiratory N2O reduction with H2 as an electron donor. The single amplicon sequence variant (ASV) presenting 90% similarity to Hydrogenimonas species within the class Campylobacteria was predominant throughout the cultivation period. Metagenomic analyses using a combination of short-read and long-read sequence data succeeded in reconstructing a complete genome of the dominant ASV, which encoded clade II nosZ gene. This study represents the first cultivation analysis that shows the occurrence of N2O-respiring microorganisms in a deep-sea hydrothermal vent and provides the opportunity to assess their capability to reduce N2O emission from the environments.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Naoki Yoneyama
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.,Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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192
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Duan P, Zhang X, Zhang Q, Wu Z, Xiong Z. Field-aged biochar stimulated N 2O production from greenhouse vegetable production soils by nitrification and denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1303-1310. [PMID: 30045510 DOI: 10.1016/j.scitotenv.2018.06.166] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Evidence suggests that biochar is among ideal strategies for climate change mitigation and sustainable agriculture. However, the effects of soil aging on the physicochemical characteristics of biochar and nitrous oxide (N2O) production remain elusive. We set up a microcosm experiment with two greenhouse vegetable production (GVP) (alkaline and acid) soils by using the 15N tracing technique and quantitative polymerase chain reaction (qPCR) to investigate the mechanisms of N2O production as affected by fresh (FB) and aged biochar (AB) amendment. The results showed that AB increased the specific surface area, organic C, ammonium sorption capacity and cation exchange capacity, whereas decreased the pore size and pH relative to the FB. Results also demonstrated that FB effectively decreased N2O emissions from both soils while it enhanced the abundance of nirK and nosZI genes in alkaline soil and reduced the abundance of ammonia-oxidizing bacteria (AOB) amoA and increased nirK and nosZII genes in acid soil. In contrast, AB significantly stimulated nitrification and denitrification in both soils and thus significantly increased the N2O emissions by 43-78%. Furthermore, AB induced increases in ammonia-oxidizing archaeal (AOA) amoA and nirK gene abundances in alkaline soil and fungal nirK gene abundances in acid soil. These results suggest that AB may not be suitable for the mitigation of soil N2O emissions in GVP soils thus improving our understanding of the potential mechanism of biochar in N2O emissions.
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Affiliation(s)
- Pengpeng Duan
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qianqian Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Wu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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193
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Calderón K, Philippot L, Bizouard F, Breuil MC, Bru D, Spor A. Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions. Front Microbiol 2018; 9:2721. [PMID: 30459749 PMCID: PMC6232425 DOI: 10.3389/fmicb.2018.02721] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/24/2018] [Indexed: 11/13/2022] Open
Abstract
There is a growing interest of overcoming the uncertainty related to the cumulative impacts of multiple disturbances of different nature in all ecosystems. With global change leading to acute environmental disturbances, recent studies demonstrated a significant increase in the possible number of interactions between disturbances that can generate complex, non-additive effects on ecosystems functioning. However, how the chronology of disturbances can affect ecosystems functioning is unknown even though there is increasing evidence that community assembly history dictates ecosystems functioning. Here, we experimentally examined the importance of the disturbances chronology in modulating the resilience of soil microbial communities and N-cycle related functions. We studied the impact of 3-way combinations of global change related disturbances on total bacterial diversity and composition, on the abundance of N-cycle related guilds and on N-cycle related activities in soil microcosms. The model pulse disturbances, i.e., short-term ceasing disturbances studied were heat, freeze-thaw and anaerobic cycles. We determined that repeated disturbances of the same nature can either lead to the resilience or to shifts in N-cycle related functions concomitant with diversity loss. When considering disturbances of different nature, we demonstrated that the chronology of compounded disturbances impacting an ecosystem determines the aggregated impact on ecosystem properties and functions. Thus, after 3 weeks the impact of the 'anoxia/heat/freeze-thaw' sequence was almost two times stronger than that of the 'heat/anoxia/freeze-thaw' sequence. Finally, we showed that about 29% of the observed variance in ecosystem aggregated impact caused by series of disturbances could be attributed to changes in the microbial community composition measured by weighted UniFrac distances. This indicates that surveying changes in bacterial community composition can help predict the strength of the impact of compounded disturbances on N-related functions and properties.
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Affiliation(s)
- Kadiya Calderón
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
- Departamento de Investigaciones Científicas y Tecnológicas Universidad de Sonora, Hermosillo, Mexico
| | - Laurent Philippot
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Florian Bizouard
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | | | - David Bru
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Aymé Spor
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
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194
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Duan YF, Hallin S, Jones CM, Priemé A, Labouriau R, Petersen SO. Catch Crop Residues Stimulate N 2O Emissions During Spring, Without Affecting the Genetic Potential for Nitrite and N 2O Reduction. Front Microbiol 2018; 9:2629. [PMID: 30450089 PMCID: PMC6225543 DOI: 10.3389/fmicb.2018.02629] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/15/2018] [Indexed: 01/27/2023] Open
Abstract
Agricultural soils are a significant source of anthropogenic nitrous oxide (N2O) emissions, because of fertilizer application and decomposition of crop residues. We studied interactions between nitrogen (N) amendments and soil conditions in a 2-year field experiment with or without catch crop incorporation before seeding of spring barley, and with or without application of N in the form of digested liquid manure or mineral N fertilizer. Weather conditions, soil inorganic N dynamics, and N2O emissions were monitored during spring, and soil samples were analyzed for abundances of nitrite reduction (nirK and nirS) and N2O reduction genes (nosZ clade I and II), and structure of nitrite- and N2O-reducing communities. Fertilization significantly enhanced soil mineral N accumulation compared to treatments with catch crop residues as the only N source. Nitrous oxide emissions, in contrast, were stimulated in rotations with catch crop residue incorporation, probably as a result of concurrent net N mineralization, and O2 depletion associated with residue degradation in organic hotspots. Emissions of N2O from digested manure were low in both years, while emissions from mineral N fertilizer were nearly absent in the first year, but comparable to emissions from catch crop residues in the second year with higher precipitation and delayed plant N uptake. Higher gene abundances, as well as shifts in community structure, were also observed in the second year, which were significantly correlated to NO3- availability. Both the size and structure of the nitrite- and N2O-reducing communities correlated to the difference in N2O emissions between years, while there were no consistent effects of management as represented by catch crops or fertilization. It is concluded that N2O emissions were constrained by environmental, rather than the genetic potential for nitrite and N2O reduction.
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Affiliation(s)
- Yun-Feng Duan
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Priemé
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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195
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Marchant HK, Tegetmeyer HE, Ahmerkamp S, Holtappels M, Lavik G, Graf J, Schreiber F, Mussmann M, Strous M, Kuypers MMM. Metabolic specialization of denitrifiers in permeable sediments controls N 2 O emissions. Environ Microbiol 2018; 20:4486-4502. [PMID: 30117262 DOI: 10.1111/1462-2920.14385] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 11/28/2022]
Abstract
Coastal oceans receive large amounts of anthropogenic fixed nitrogen (N), most of which is denitrified in the sediment before reaching the open ocean. Sandy sediments, which are common in coastal regions, seem to play an important role in catalysing this N-loss. Permeable sediments are characterized by advective porewater transport, which supplies high fluxes of organic matter into the sediment, but also leads to fluctuations in oxygen and nitrate concentrations. Little is known about how the denitrifying communities in these sediments are adapted to such fluctuations. Our combined results indicate that denitrification in eutrophied sandy sediments from the world's largest tidal flat system, the Wadden Sea, is carried out by different groups of microorganisms. This segregation leads to the formation of N2 O which is advectively transported to the overlying waters and thereby emitted to the atmosphere. At the same time, the production of N2 O within the sediment supports a subset of Flavobacteriia which appear to be specialized on N2 O reduction. If the mechanisms shown here are active in other coastal zones, then denitrification in eutrophied sandy sediments may substantially contribute to current marine N2 O emissions.
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Affiliation(s)
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jon Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frank Schreiber
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,ETH Zurich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Microbiology, Dübendorf, Switzerland.,Division of Biodeterioration and Reference Organisms, Department of Materials and Environment, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Marc Mussmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Strous
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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196
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Pelissari C, Guivernau M, Viñas M, García J, Velasco-Galilea M, Souza SS, Sezerino PH, Ávila C. Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands. WATER RESEARCH 2018; 141:185-195. [PMID: 29787952 DOI: 10.1016/j.watres.2018.05.002] [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: 12/11/2017] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 06/08/2023]
Abstract
Nitrogen dynamics and its association to metabolically active microbial populations were assessed in two vertical subsurface vertical flow (VF) wetlands treating urban wastewater. These VF wetlands were operated in parallel with unsaturated (UVF) and partially saturated (SVF) configurations. The SVF wetland exhibited almost 2-fold higher total nitrogen removal rate (5 g TN m-2 d-1) in relation to the UVF wetland (3 g TN m-2 d-1), as well as a low NOx-N accumulation (1 mg L-1 vs. 26 mg L-1 in SVF and UVF wetland effluents, respectively). After 6 months of operation, ammonia oxidizing prokaryotes (AOP) and nitrite oxidizing bacteria (NOB) displayed an important role in both wetlands. Oxygen availability and ammonia limiting conditions promoted shifts on the metabolically active nitrifying community within 'nitrification aggregates' of wetland biofilms. Ammonia oxidizing archaea (AOA) and Nitrospira spp. overcame ammonia oxidizing bacteria (AOB) in the oxic layers of both wetlands. Microbial quantitative and diversity assessments revealed a positive correlation between Nitrobacter and AOA, whereas Nitrospira resulted negatively correlated with Nitrobacter and AOB populations. The denitrifying gene expression was enhanced mainly in the bottom layer of the SVF wetland, in concomitance with the depletion of NOx-N from wastewater. Functional gene expression of nitrifying and denitrifying populations combined with the active microbiome diversity brought new insights on the microbial nitrogen-cycling occurring within VF wetland biofilms under different operational conditions.
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Affiliation(s)
- Catiane Pelissari
- GESAD - Decentralized Sanitation Research Group, Department of Sanitary and Environmental Engineering, Federal University of Santa Catarina, Trindade, Florianópolis, Santa Catarina, 88040-900, Brazil.
| | - Miriam Guivernau
- GIRO - Program of Integrated Management of Organic Waste, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, E-08140, Caldes de Montbui, Barcelona, Spain
| | - Marc Viñas
- GIRO - Program of Integrated Management of Organic Waste, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, E-08140, Caldes de Montbui, Barcelona, Spain
| | - Joan García
- GEMMA - Environmental Engineering and Microbiology Research Group, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya-BarcelonaTech, c/ Jordi Girona, 1-3, Building D1, E-08034, Barcelona, Spain
| | - María Velasco-Galilea
- GMA - Program of Genetics and Animal Breeding, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, E-08140, Caldes de Montbui, Barcelona, Spain
| | - Samara Silva Souza
- INTELAB - Integrated Technologies Laboratory, Chemical and Food Engineering Department, Federal University of Santa Catarina, Trindade, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - Pablo Heleno Sezerino
- GESAD - Decentralized Sanitation Research Group, Department of Sanitary and Environmental Engineering, Federal University of Santa Catarina, Trindade, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - Cristina Ávila
- ICRA - Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, Emili Grahit, 101, E-17003, Girona, Spain; AIMEN Technology Center, c/ Relva, 27 A, Torneiros, E-36410, Porriño, Pontevedra, Spain
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197
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Semedo M, Song B, Sparrer T, Phillips RL. Antibiotic Effects on Microbial Communities Responsible for Denitrification and N 2O Production in Grassland Soils. Front Microbiol 2018; 9:2121. [PMID: 30254616 PMCID: PMC6141661 DOI: 10.3389/fmicb.2018.02121] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N2O) and dinitrogen (N2) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N2O and N2 production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N2O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference. Soil samples treated with tetracycline generated 12 times more N2O, but N2 production was reduced by 84% compared to the control. In parallel with greater N2O production, we observed an increase in the fungi:bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected. NosZ-II-carrying Bacillus spp. (Firmicutes) and Anaeromyxobacter spp. (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N2O sink in grassland soils. Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N2O production due to the inhibitory effects on nosZ-II-carrying communities.
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Affiliation(s)
- Miguel Semedo
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA, United States
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA, United States
| | - Tavis Sparrer
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA, United States
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198
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Sabba F, Terada A, Wells G, Smets BF, Nerenberg R. Nitrous oxide emissions from biofilm processes for wastewater treatment. Appl Microbiol Biotechnol 2018; 102:9815-9829. [DOI: 10.1007/s00253-018-9332-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 01/21/2023]
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199
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Wigginton S, Brannon E, Kearns PJ, Lancellotti B, Cox A, Loomis GW, Amador JA. Nitrifying and Denitrifying Bacterial Communities in Advanced Nitrogen-Removal Onsite Wastewater Treatment Systems. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1163-1171. [PMID: 30272776 DOI: 10.2134/jeq2018.03.0116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Advanced N-removal onsite wastewater treatment systems (OWTS) rely on nitrification and denitrification to remove N from wastewater. Despite their use to reduce N contamination, we know little about microbial communities controlling N removal in these systems. We used quantitative polymerase chain reaction and high-throughput sequencing targeting nitrous oxide reductase () and bacterial ammonia monooxygenase () to determine the size, structure, and composition of communities containing these genes. We analyzed water samples from three advanced N-removal technologies in 38 systems in five towns in Rhode Island in August 2016, and in nine systems from one town in June, August, and October 2016. Abundance of ranged from 9.1 × 10 to 9 × 10 copies L and differed among technologies and over time, whereas bacterial abundance ranged from 0 to 1.9 × 10 copies L and was not different among technologies or over time. Richness and diversity of -but not -differed over time, with median Shannon diversity indices ranging from 2.61 in October to 4.53 in August. We observed weak community similarity patterns driven by geography and technology in The most abundant and containing bacteria were associated with water distribution and municipal wastewater treatment plants, such as and species. Our results show that communities in N-removal OWTS technologies differ slightly in terms of size and diversity as a function of time, but not geography, whereas communities are similar across time, technology, and geography. Furthermore, community composition appears to be stable across technologies, geography, and time for .
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200
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Pandey A, Suter H, He JZ, Hu HW, Chen D. Nitrogen Addition Decreases Dissimilatory Nitrate Reduction to Ammonium in Rice Paddies. Appl Environ Microbiol 2018; 84:e00870-18. [PMID: 29934331 PMCID: PMC6102975 DOI: 10.1128/aem.00870-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/13/2018] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox), and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. While the effect of N application on BNF is known, little is known about its effect on NO3- partitioning between DNRA, denitrification, and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox, and BNF and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in a glasshouse with N fertilizer (150 kg N ha-1) and without N fertilizer for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone, but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3- reduced by DNRA (0.42 to 0.52 μg g-1 soil day-1 and 45 to 55%, respectively) were similar to or higher than the amount and proportion reduced by denitrification. However, with N the amount of NO3- reduced by DNRA (0.32 to 0.40 μg g-1 soil day-1) was 40 to 50% lower than the amount of NO3- reduced by denitrification. Denitrification loss increased by >20% with N addition and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02 to 0.25 μg N g-1 soil day-1 We found that DNRA plays a significant positive role in paddy soil N retention, as it accounts for up to 55% of the total NO3- reduction, but this is reduced by N application.IMPORTANCE This study provides evidence that nitrogen addition reduces nitrogen retention through DNRA and increases nitrogen loss via denitrification in a paddy soil ecosystem. DNRA is one of the major NO3- reduction processes, and it can outcompete denitrification in NO3- consumption when rice paddies are low in nitrogen. A significant level of DNRA activity in paddy soils indicates that DNRA plays an important role in retaining nitrogen by reducing NO3- availability for denitrification and leaching. Our study shows that by reducing N addition to rice paddies, there is a positive effect from reduced nitrogen loss but, more importantly, from the conversion of NO3- to NH4+, which is the favored form of mineral nitrogen for plant uptake.
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Affiliation(s)
- Arjun Pandey
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Helen Suter
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Deli Chen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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