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Zhang Y, Cheng X, van Groenigen KJ, García-Palacios P, Cao J, Zheng X, Luo Y, Hungate BA, Terrer C, Butterbach-Bahl K, Olesen JE, Chen J. Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions. GLOBAL CHANGE BIOLOGY 2024; 30:e16989. [PMID: 37888833 DOI: 10.1111/gcb.16989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Xiaoli Cheng
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Kees Jan van Groenigen
- Department of Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Junji Cao
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Xunhua Zheng
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Yiqi Luo
- School of Integrative Plant Science, Cornell University, New York, Ithaca, USA
| | - Bruce A Hungate
- Department of Biological Sciences, Northern Arizona University, Arizona, Flagstaff, USA
| | - Cesar Terrer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Massachusetts, Cambridge, USA
| | - Klaus Butterbach-Bahl
- Institute for Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
- Center for Landscape Research in Sustainable Agricultural Futures, Land-CRAFT, Department of Agroecology, Aarhus University, Aarhus, Denmark
| | - Jørgen Eivind Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
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Habteselassie M, Woodruff L, Norton J, Ouyang Y, Sintim H. Changes in microbial communities in soil treated with organic or conventional N sources. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:1144-1154. [PMID: 36001948 DOI: 10.1002/jeq2.20406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Despite the extensive use of N fertilizers in agricultural soils, we are yet to fully understand their impact on soil microbial communities that mediate important soil processes. A 3-yr field study was undertaken in Georgia, where sweet corn (Zea mays L.) was grown under conventional or organic systems. Nitrogen (N) was supplied with ammonium sulfate at 112 kg N ha-1 (AS100) or 224 kg N ha-1 (AS200) or a combination of poultry litter, cover crop, and blood meal at 112 kg N ha-1 (PL100) or no N (control). Soil samples were collected from field plots to assess the impact of treatments on bacteria, fungi, and ammonia oxidizers using molecular methods that targeted 16S RNA, ITS2, and amoA genes, respectively. Treatment had significant impact on bacterial but not fungal composition. The AS200 significantly changed the relative abundances of Verrucomicrobia and Acidobacteria and decreased bacterial alpha diversity as compared with control. Beta-diversity analysis showed clear separation of microbial communities in AS200 vs. control and PL100. The abundance of ammonia-oxidizing bacteria (AOB) was more responsive to N input than ammonia oxidizing-archaea. It was also significantly and positively correlated with nitrification potential and soil nitrate with increasing N rates, indicating AOB's dominance in driving nitrification under high N input. Overall, the results indicated that AS200 changed bacterial composition and diversity, suggesting corresponding changes in soil processes related to N mineralization and nitrification. Understanding such changes in microbial communities can help us predict changes in soil processes to adopt sustainable management systems.
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Affiliation(s)
- Mussie Habteselassie
- Dep. of Crop and Soil Sciences, Univ. of Georgia-Griffin Campus, 1109 Experiment St., Griffin, GA, 30223, USA
| | - Lisa Woodruff
- Dep. of Crop and Soil Sciences, Univ. of Georgia-Griffin Campus, 1109 Experiment St., Griffin, GA, 30223, USA
| | - Jeanette Norton
- Dep. of Plant, Soils and Climate, Utah State Univ., 4820 Old Main Hill, Logan, UT, 84322, USA
| | - Yang Ouyang
- Institute for Environmental Genomics, Dep. of Microbiology and Plant Biology, Univ. of Oklahoma, Norman, OK, 73019, USA
| | - Henry Sintim
- Dep. of Crop and Soil Sciences, Univ. of Georgia-Tifton Campus, 2360 Rainwater Rd., Tifton, GA, 31793, USA
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3
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Bhaduri D, Sihi D, Bhowmik A, Verma BC, Munda S, Dari B. A review on effective soil health bio-indicators for ecosystem restoration and sustainability. Front Microbiol 2022; 13:938481. [PMID: 36060788 PMCID: PMC9428492 DOI: 10.3389/fmicb.2022.938481] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.
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Affiliation(s)
- Debarati Bhaduri
- ICAR-National Rice Research Institute, Cuttack, India
- *Correspondence: Debarati Bhaduri
| | - Debjani Sihi
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States
| | - Arnab Bhowmik
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
- Arnab Bhowmik
| | - Bibhash C. Verma
- Central Rainfed Upland Rice Research Station (ICAR-NRRI), Hazaribagh, India
| | | | - Biswanath Dari
- Agriculture and Natural Resources, Cooperative Extension at North Carolina Agricultural and Technical State University, Greensboro, NC, United States
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Fisk LM, Barton L, Maccarone LD, Jenkins SN, Murphy DV. Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil. Sci Rep 2022; 12:7299. [PMID: 35508560 PMCID: PMC9068766 DOI: 10.1038/s41598-022-10711-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.
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Affiliation(s)
- L M Fisk
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - L Barton
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - L D Maccarone
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - S N Jenkins
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - D V Murphy
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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5
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Liang D, Robertson GP. Nitrification is a minor source of nitrous oxide (N 2 O) in an agricultural landscape and declines with increasing management intensity. GLOBAL CHANGE BIOLOGY 2021; 27:5599-5613. [PMID: 34383336 PMCID: PMC9291997 DOI: 10.1111/gcb.15833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 05/15/2023]
Abstract
The long-term contribution of nitrification to nitrous oxide (N2 O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N2 O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N2 O, we test the relative importance of nitrification-derived N2 O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N2 O fluxes was 13%-17% in a conventionally fertilized annual cropping system, 27%-42% in a low-input cover-cropped annual cropping system, and 52%-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be <10% of these values because of low N2 O yields in cultured nitrifiers (typically 0.04%-8% of NH3 oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N2 O was produced by ammonia-oxidizing bacteria rather than archaea, who appeared responsible for no more than 30% of nitrification-derived N2 O production in all but one ecosystem. Although the proportion of nitrification-derived N2 O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N2 O (higher Vmax ) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N2 O in all ecosystems examined.
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Affiliation(s)
- Di Liang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichiganUSA
| | - G. Philip Robertson
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichiganUSA
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Tagele SB, Kim RH, Shin JH. Interactions between Brassica Biofumigants and Soil Microbiota: Causes and Impacts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11538-11553. [PMID: 34551253 DOI: 10.1021/acs.jafc.1c03776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biofumigation is used to control soil-borne plant diseases, and it has paramount importance to reduce the cost of chemical fumigants. Information about the field control efficacies and impacts of Brassica-based biofumigation (BBF) on soil bacterial and fungal microbiota is scattered in the literature. Therefore, this review summarizes and discusses the nature and the underlying causes of soil bacterial and fungal community dynamics in response to BBF. In addition, the major factors influencing the interaction between a biofumigant and soil microbiota are discussed. The pros and cons of BBF to soil microbiota and the subsequent impacts on sustainable farming practices are also highlighted.
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Affiliation(s)
- Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ryeong-Hui Kim
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
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7
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Different nutrient levels, rather than seasonal changes, significantly affected the spatiotemporal dynamic changes of ammonia-oxidizing microorganisms in Lake Taihu. World J Microbiol Biotechnol 2021; 37:91. [PMID: 33939019 DOI: 10.1007/s11274-021-03053-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 04/09/2021] [Indexed: 01/23/2023]
Abstract
Ammonia-oxidizing microorganisms (AOM) play crucial roles in the degradation of ammonia nitrogen in freshwater lakes. Hence, it is necessary to reveal the spatiotemporal dynamic changes of AOM in freshwater lakes. Here, we conducted a study on the spatial and temporal dynamic changes of AOM in different lake regions under gradient nutrient levels in Lake Taihu, and found that the abundance of AOM had significant spatial changes, while the seasonal changes had relatively little effect on the abundance of AOM. We also found that ammonia-oxidizing archaea (AOA) were adapted to freshwater habitats with low nutrient levels, while ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing bacteria (AAOB) had higher abundance in high nutrient level lake regions. Moreover, the amoA gene abundance of AOB was much higher than that of AOA, indicating that AOB was the dominant aerobic ammonia oxidizer in the water of Lake Taihu. In addition, temperature, pH and dissolved oxygen all had a positive effect on AOM, especially AOB; while C- and N-related physicochemical factors had a significant positive effect on AAOB, but exhibited a significant negative correlation with AOA. The community structure of AOM also had obvious spatial changes and Group I.1a, Nitrosomonas and Candidatus Brocadia fulgida were the dominant cluster of AOA, AOB and AAOB, respectively.
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8
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Lourenço KS, Cassman NA, Pijl AS, van Veen JA, Cantarella H, Kuramae EE. Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop. Front Microbiol 2018; 9:674. [PMID: 29692763 PMCID: PMC5902487 DOI: 10.3389/fmicb.2018.00674] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.
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Affiliation(s)
- Késia S Lourenço
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Noriko A Cassman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Agata S Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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9
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Wastewater Reuse in Agriculture: A Review about Its Limitations and Benefits. SUSTAINABILITY 2017. [DOI: 10.3390/su9101734] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
For centuries, wastewater has been improperly used in agriculture, presenting potential risks to public health and the environment. In the context of scientific development, and confronted by an increasing water crisis, wastewater reuse merits consideration because the practice helps decrease water use pressure and moderates water pollution. Thus, this article presents a literature review that addresses the effects, both positive and negative, of wastewater use in agriculture, emphasizing the effects on the soil environment. The literature review reveals that, until the 1990s, research studies promoted the use of wastewater for irrigation purposes from a treatment approach, while proposing “end of pipe” conventional solutions. However, more recent research studies (2012–2016) reveal that agricultural reuse significantly affects soil texture properties, while also causing possible alterations of the biomass and microbiota. In addition, research in this period has been oriented to the quantitative evaluation of microbiological risk.
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Mundepi A, Norton J, Cabrera M, Franklin D, Habteselassie MY. Ammonia Oxidizers in a Grazing Land with a History of Poultry Litter Application. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:994-1002. [PMID: 28991982 DOI: 10.2134/jeq2017.04.0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Poultry litter (PL) is widely applied on grazing lands in Georgia. However, it is not clear how its long-term use affects soil microorganisms and their function. We examined changes in activity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a grazing land with a history of PL application and compared it to treatment with urea ammonium nitrate (UAN). Soil samples (0-15 cm) were collected in 2009 (after 15 yr of PL application) and in 2013 (after 2 yr of no application). The abundance and community composition of ammonia oxidizers (AO) were determined with molecular techniques that targeted Nitrification potential (NP) was used for measuring their activity. Abundance of AO was significantly higher in PL (7.41 and 7.10 log copies g soil for AOB and AOA, respectively) than in UAN plots (6.82 and 6.50 log copies g soil for AOB and AOA, respectively) in 2009. This is consistent with NP, which was higher in PL (0.78 mg NO -N kg h) than in UAN (0.50 mg NO-N kg h) plots in 2009. The abundance of AO and NP decreased in 2013. There was no treatment effect on the composition of AO. Correlation analysis suggested that AOB were functionally more important than AOA, indicating the need to target AOB for efficient management of N in PL-receiving soils. Overall, the difference in nitrification between PL and UAN was mainly caused by the change in AO abundance rather than composition, and AO were not negatively affected by an increase in PL-derived trace metal concentrations.
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11
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Wang Q, Zhang LM, Shen JP, Du S, Han LL, He JZ. Effects of dicyandiamide and acetylene on N 2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:23023-23033. [PMID: 27581050 DOI: 10.1007/s11356-016-7519-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are crucial for N2O emission as they carry out the key step of nitrification. Dicyandiamide (DCD) and acetylene (C2H2) are typical nitrification inhibitors (NIs), while the comparative effects of these NIs on N2O production and ammonia oxidizers' (AOB and AOA) growth are unclear. Four treatments including a control, urea, urea + DCD, and urea + C2H2 were set up to investigate their effect of inhibiting soil nitrification, nitrification-related N2O emission as well as the growth of ammonia oxidizers with a fluvo-aquic soil using microcosms for 28 days. N2O emission and net nitrification rate increased after the application of urea, but were significantly restrained in urea + NI treatments, while C2H2 was more effective in reducing N2O emission and nitrification rate than DCD. The abundance of AOB, which was significantly correlated with N2O emission and net nitrification rate, was more inhibited by C2H2 than DCD. Furthermore, the application of urea in all the soils had little impact on the AOA community, while obvious shifts of AOB community structure were found compared with the control. All AOB sequences fell within Nitrosospira cluster 3, and the AOA community was clustered to group 1.1b. Collectively, it indicated that application of urea combined with NIs (DCD or C2H2) could potentially alter N2O emission, mainly through regulating the growth of AOB but not AOA in this fluvo-aquic soil.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Melbourne School of Land and Environment, The University of Melbourne, Parkville, Victoria, Australia.
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12
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Lu S, Liu X, Ma Z, Liu Q, Wu Z, Zeng X, Shi X, Gu Z. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond. Front Microbiol 2016; 6:1539. [PMID: 26834709 PMCID: PMC4718984 DOI: 10.3389/fmicb.2015.01539] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster.
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Affiliation(s)
- Shimin Lu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xingguo Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhuojun Ma
- Chinese Academy of Fishery Sciences Beijing, China
| | - Qigen Liu
- College of Fisheries and Life, Shanghai Ocean University Shanghai, China
| | - Zongfan Wu
- Tongren Municipal Agricultural Commission (Government, Public) Tongren, China
| | - Xianlei Zeng
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xu Shi
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhaojun Gu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
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Sterngren AE, Hallin S, Bengtson P. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil. Front Microbiol 2015; 6:1350. [PMID: 26648926 PMCID: PMC4663241 DOI: 10.3389/fmicb.2015.01350] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/16/2015] [Indexed: 12/02/2022] Open
Abstract
Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.
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Affiliation(s)
- Anna E Sterngren
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
| | - Sara Hallin
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Per Bengtson
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
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14
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Becerra-Castro C, Lopes AR, Vaz-Moreira I, Silva EF, Manaia CM, Nunes OC. Wastewater reuse in irrigation: a microbiological perspective on implications in soil fertility and human and environmental health. ENVIRONMENT INTERNATIONAL 2015; 75:117-35. [PMID: 25461421 DOI: 10.1016/j.envint.2014.11.001] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/04/2014] [Accepted: 11/04/2014] [Indexed: 05/25/2023]
Abstract
The reuse of treated wastewater, in particular for irrigation, is an increasingly common practice, encouraged by governments and official entities worldwide. Irrigation with wastewater may have implications at two different levels: alter the physicochemical and microbiological properties of the soil and/or introduce and contribute to the accumulation of chemical and biological contaminants in soil. The first may affect soil productivity and fertility; the second may pose serious risks to the human and environmental health. The sustainable wastewater reuse in agriculture should prevent both types of effects, requiring a holistic and integrated risk assessment. In this article we critically review possible effects of irrigation with treated wastewater, with special emphasis on soil microbiota. The maintenance of a rich and diversified autochthonous soil microbiota and the use of treated wastewater with minimal levels of potential soil contaminants are proposed as sine qua non conditions to achieve a sustainable wastewater reuse for irrigation.
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Affiliation(s)
- Cristina Becerra-Castro
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana Rita Lopes
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Elisabete F Silva
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viseu, Campus Politécnico de Repeses, 3504-510 Viseu, Portugal
| | - Célia M Manaia
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 4202-401 Porto, Portugal.
| | - Olga C Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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