101
|
Nechayeva A, Boyarshin K, Bespalova O, Klyueva V, Makanina O, Batlutskaya I. Analysis of 16S rRNA gene variability in soil nitrifying bacteria of the genus Nitrosomonas. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213005007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The main goal of the work was to assess variability of 16S rRNA gene sequence within the nitrifying bacterial genus Nitrosomonas to find specific sequences for its detection. To achieve it, we had to find and to assess sequences that are highly conservative on the level of the genus and to find and to assess sequences variable on the level of genus but conserved on the level of species. In the SILVA database of ribosomal RNA sequences, 231 sequences of 16S rRNAs of bacteria of the genus Nitrosomonas were collected, of which were sorted 132 sequences by length from 1400 to 1541 (full-sized gene) nucleotides. We conducted an analysis of the taxon-specificity of sequences conserved at the genus level. More than a hundred full matches were found by the BLAST program in the nr database with other genera of the same and other families. So, in Nitrosomonas 16S rRNA gene are present some highly conservative regions, but they are not genus-specific due to high coincidence with other genera. Wherein, a variable region 994-1041 is highly species-specific for the species N. eutropha. Generally, the sequence of 994-1041 region of Nitrosomonas 16S rRNA genes tends to be clustered, being very close between some species.
Collapse
|
102
|
Papadopoulou ES, Bachtsevani E, Lampronikou E, Adamou E, Katsaouni A, Vasileiadis S, Thion C, Menkissoglu-Spiroudi U, Nicol GW, Karpouzas DG. Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates. Front Microbiol 2020; 11:581283. [PMID: 33250872 PMCID: PMC7672009 DOI: 10.3389/fmicb.2020.581283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; "Candidatus Nitrosocosmicus franklandus," "Candidatus Nitrosotalea sinensis"), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3-0.7 μM) compared to EQ (EC50 = 1-1.4 μM) and EQNL (EC50 = 26.6-129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9-248.7 μM vs EC50 = 0.6-2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8-2.1 and 1.0-6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.
Collapse
Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Adamou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Afroditi Katsaouni
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Cécile Thion
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Graeme W. Nicol
- Laboratoire Ampère, École Centrale de Lyon, University of Lyon, Ecully, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| |
Collapse
|
103
|
Elrys AS, Raza S, Elnahal ASM, Na M, Ahmed M, Zhou J, Chen Z. Do soil property variations affect dicyandiamide efficiency in inhibiting nitrification and minimizing carbon dioxide emissions? ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110875. [PMID: 32580081 DOI: 10.1016/j.ecoenv.2020.110875] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Nitrification inhibitors (NIs) are used to retard the nitrification process and reduce nitrogen (N) losses. However, the effects of soil properties on NI efficacy are less clear. Moreover, the direct and indirect effects of soil property variations on NI efficiency in minimizing carbon dioxide (CO2) emissions have not been previously studied. An incubation experiment was conducted for 40 days with two treatments, N (200 mg N-urea kg-1) and N + dicyandiamide (DCD) (20 mg DCD kg-1), and a control group (without the N) to investigate the response of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to DCD application and the consequences for CO2, nitrous oxide (N2O) and ammonia (NH3) emissions from six soils from the Loess Plateau with different properties. The nitrification process completed within 6-18 days for the N treatment and within 30->40 days for the N + DCD treatment. AOB increased significantly with N fertilizer application, while this effect was inhibited in soils when DCD was applied. AOA was not sensitive to N fertilizer and DCD application. The nitrification rate was positively correlated with the clay (p < 0.05) and SOM contents (p < 0.01); DCD was more effective in loam soil with low SOM and high soil pH. Soil pH significantly was decreased with N fertilizer application, while it increased when DCD was applied. Moreover, DCD application decreased CO2 emissions from soils by 22%-172%; CO2 emissions were negatively correlated with the clay and SOM contents. DCD application decreased N2O emissions in each soil by 1.0- to 94-fold compared with those after N fertilizer application. In contrast, DCD application increased NH3 release from soils by 59-278%. NH3 volatilization was negatively correlated with clay (p < 0.05) and SOM (p < 0.01) contents and positively correlated with soil pH (p < 0.01). Therefore, soil texture, SOM and soil pH have significant effects on the DCD performance, nitrification process and gaseous emissions.
Collapse
Affiliation(s)
- Ahmed S Elrys
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China; Soil Science Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Sajjad Raza
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Ahmed S M Elnahal
- College of Plant Protection, Northwest A&F University, Yangling, 712100, China
| | - Miao Na
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Muneer Ahmed
- Lasbela University of Agriculture, Water and Marine Sciences, Uthal, Pakistan
| | - Jianbin Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
| | - Zhujun Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
104
|
Ervinia A, Huang J, Zhang Z. Nitrogen sources, processes, and associated impacts of climate and land-use changes in a coastal China watershed: Insights from the INCA-N model. MARINE POLLUTION BULLETIN 2020; 159:111502. [PMID: 32739631 DOI: 10.1016/j.marpolbul.2020.111502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The Integrated Nitrogen CAtchments (INCA-N) model was applied to identify the sources and processes controlling riverine nitrogen (N) export in the Jiulong River watershed, coastal China. Future riverine N exports were simulated under various scenarios of climate and land-use changes. The modeling results showed good agreement between the observed and simulated values of streamflow, N concentrations, and loads. It was revealed that fertilizer application, atmospheric N deposition, and sewage discharges were the main N sources, while the primary N cycling processes included soil nitrification, soil denitrification, and N leaching. Nitrate-N exports were predominantly impacted by climate change, whereas ammonium-N exports were more affected by land-use change. The coupled effects of climate and land-use changes were projected to amplify nitrogen export by 30%, 36%, and 36% for nitrate-N and 32%, 48%, and 71% for ammonium-N during the years for 2030s, 2050s, and 2080s, respectively.
Collapse
Affiliation(s)
- Ayu Ervinia
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361102, China; Coastal and Ocean Management Institute, Xiamen University, Xiamen 361102, China
| | - Jinliang Huang
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361102, China; Coastal and Ocean Management Institute, Xiamen University, Xiamen 361102, China.
| | - Zhenyu Zhang
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361102, China; Coastal and Ocean Management Institute, Xiamen University, Xiamen 361102, China
| |
Collapse
|
105
|
Blaser SRGA, Koebernick N, Spott O, Thiel E, Vetterlein D. Dynamics of localised nitrogen supply and relevance for root growth of Vicia faba ('Fuego') and Hordeum vulgare ('Marthe') in soil. Sci Rep 2020; 10:15776. [PMID: 32978408 PMCID: PMC7519116 DOI: 10.1038/s41598-020-72140-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/17/2020] [Indexed: 11/29/2022] Open
Abstract
Root growth responds to local differences in N-form and concentration. This is known for artificial systems and assumed to be valid in soil. The purpose of this study is to challenge this assumption for soil mesocosms locally supplied with urea with and without nitrification inhibitor. Soil column experiments with Vicia faba ('Fuego') and Hordeum vulgare ('Marthe') were performed to investigate soil solution chemistry and root growth response of these two species with contrasting root architectures to the different N-supply simultaneously. Root growth was analysed over time and separately for the fertiliser layer and the areas above and below with X-ray CT (via region growing) and WinRHIZO. Additionally, NO3- and NH4+ in soil and soil solution were analysed. In Vicia faba, no pronounced differences were observed, although CT analysis indicated different root soil exploration for high NH4+. In Hordeum vulgare, high NO3- inhibited lateral root growth while high NH4+ stimulated the formation of first order laterals. The growth response to locally distributed N-forms in soil is species specific and less pronounced than in artificial systems. The combination of soil solution studies and non-invasive imaging of root growth can substantially improve the mechanistic understanding of root responses to different N-forms in soil.
Collapse
Affiliation(s)
- Sebastian R G A Blaser
- Department of Soil System Science, Helmholtz-Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany.
| | - Nicolai Koebernick
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120, Halle (Saale), Germany
| | - Oliver Spott
- Agricultural Application Research, SKW Piesteritz GmbH, Am Wieseneck 7, 04451, Cunnersdorf, Germany
| | - Enrico Thiel
- Agricultural Application Research, SKW Piesteritz GmbH, Am Wieseneck 7, 04451, Cunnersdorf, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz-Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120, Halle (Saale), Germany
| |
Collapse
|
106
|
Musiani F, Broll V, Evangelisti E, Ciurli S. The model structure of the copper-dependent ammonia monooxygenase. J Biol Inorg Chem 2020; 25:995-1007. [PMID: 32926231 PMCID: PMC7584546 DOI: 10.1007/s00775-020-01820-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022]
Abstract
Abstract Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01820-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| | - Valquiria Broll
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Elisa Evangelisti
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| |
Collapse
|
107
|
Frąc M, Lipiec J, Usowicz B, Oszust K, Brzezińska M. Structural and functional microbial diversity of sandy soil under cropland and grassland. PeerJ 2020; 8:e9501. [PMID: 32953254 PMCID: PMC7474522 DOI: 10.7717/peerj.9501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background Land use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties. Methods We investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests. Results It was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.
Collapse
Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Jerzy Lipiec
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Bogusław Usowicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Karolina Oszust
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | | |
Collapse
|
108
|
Duan P, Zhang Q, Xiong Z. Temperature decouples ammonia and nitrite oxidation in greenhouse vegetable soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139391. [PMID: 32446093 DOI: 10.1016/j.scitotenv.2020.139391] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
The influence of temperature on soil ammonia (NH3) and nitrite (NO2-) oxidation and related NO2- accumulation in soils remain unclear. The soil potential NH3 oxidation (PAO) and NO2- oxidation (PNO) rates were evaluated over a temperature gradient of 5-45 °C in six greenhouse vegetable soils using inhibitors. The values of temperature sensitivity traits such as temperature minimum (Tmin), temperature optimum (Topt), and maximum absolute temperature sensitivity (Tm_sens) were also fitted to the square root growth (SQRT) and macromolecular rate theory (MMRT) models. The ammonia-oxidizing archaea (AOA) and bacteria (AOB) were determined by quantifying amoA, and nitrite-oxidizing bacteria (NOB) were determined by quantifying the nxrA and nxrB. Both models identified that Topt for PAO (34.0 °C) was significantly greater than that for PNO (26.0 °C). The Tm_sens (23.4 ± 2.1 °C) and Tmin (1.0 ± 2.0 °C) for PAO were higher than those for PNO (16.8 ± 3.2 °C and - 11.7 ± 6.7 °C). PAO was positively correlated with AOB-amoA at 20-30 °C and with AOA-amoA at 30-35 °C, while PNO was positively correlated with nxrB at 5-30 °C. Additionally, NO2- and N2O were positively correlated with the (AOA + AOB amoA) to (nxrA + nxrB) ratio, and the concentration of N2O was positively correlated with NO2- accumulation. These results highlight that elevated temperatures resulted in the uncoupling of NH3 oxidation and NO2- oxidation, leading to NO2- accumulation, which could stimulate N2O emissions.
Collapse
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; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, 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
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
109
|
Berger K, Verrelst J, Féret JB, Wang Z, Wocher M, Strathmann M, Danner M, Mauser W, Hank T. Crop nitrogen monitoring: Recent progress and principal developments in the context of imaging spectroscopy missions. REMOTE SENSING OF ENVIRONMENT 2020; 242:111758. [PMID: 36082364 PMCID: PMC7613361 DOI: 10.1016/j.rse.2020.111758] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is considered as one of the most important plant macronutrients and proper management of N therefore is a pre-requisite for modern agriculture. Continuous satellite-based monitoring of this key plant trait would help to understand individual crop N use efficiency and thus would enable site-specific N management. Since hyperspectral imaging sensors could provide detailed measurements of spectral signatures corresponding to the optical activity of chemical constituents, they have a theoretical advantage over multi-spectral sensing for the detection of crop N. The current study aims to provide a state-of-the-art overview of crop N retrieval methods from hyperspectral data in the agricultural sector and in the context of future satellite imaging spectroscopy missions. Over 400 studies were reviewed for this purpose, identifying those estimating mass-based N (N concentration, N%) and area-based N (N content, Narea) using hyperspectral remote sensing data. Retrieval methods of the 125 studies selected in this review can be grouped into: (1) parametric regression methods, (2) linear nonparametric regression methods or chemometrics, (3) nonlinear nonparametric regression methods or machine learning regression algorithms, (4) physically-based or radiative transfer models (RTM), (5) use of alternative data sources (sun-induced fluorescence, SIF) and (6) hybrid or combined techniques. Whereas in the last decades methods for estimation of Narea and N% from hyperspectral data have been mainly based on simple parametric regression algorithms, such as narrowband vegetation indices, there is an increasing trend of using machine learning, RTM and hybrid techniques. Within plants, N is invested in proteins and chlorophylls stored in the leaf cells, with the proteins being the major nitrogen-containing biochemical constituent. However, in most studies, the relationship between N and chlorophyll content was used to estimate crop N, focusing on the visible-near infrared (VNIR) spectral domains, and thus neglecting protein-related N and reallocation of nitrogen to non-photosynthetic compartments. Therefore, we recommend exploiting the estimation of nitrogen via the proxy of proteins using hyperspectral data and in particular the short-wave infrared (SWIR) spectral domain. We further strongly encourage a standardization of nitrogen terminology, distinguishing between N% and Narea. Moreover, the exploitation of physically-based approaches is highly recommended combined with machine learning regression algorithms, which represents an interesting perspective for future research in view of new spaceborne imaging spectroscopy sensors.
Collapse
Affiliation(s)
- Katja Berger
- Department of Geography, Ludwig-Maximilians-Universitaet München, Luisenstr 37, 80333 Munich, Germany
| | - Jochem Verrelst
- Image Processing Laboratory (IPL), Parc Científic, Universitat de València, Paterna, València 46980, Spain
| | - Jean-Baptiste Féret
- TETIS, INRAE, AgroParisTech, CIRAD, CNRS, Université Montpellier, Montpellier, France
| | - Zhihui Wang
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA
| | - Matthias Wocher
- Department of Geography, Ludwig-Maximilians-Universitaet München, Luisenstr 37, 80333 Munich, Germany
| | - Markus Strathmann
- Department of Geography, Ludwig-Maximilians-Universitaet München, Luisenstr 37, 80333 Munich, Germany
| | - Martin Danner
- Department of Geography, Ludwig-Maximilians-Universitaet München, Luisenstr 37, 80333 Munich, Germany
| | - Wolfram Mauser
- Department of Geography, Ludwig-Maximilians-Universitaet München, Luisenstr 37, 80333 Munich, Germany
| | - Tobias Hank
- Department of Geography, Ludwig-Maximilians-Universitaet München, Luisenstr 37, 80333 Munich, Germany
| |
Collapse
|
110
|
Cover Crop Impact on Soil Organic Carbon, Nitrogen Dynamics and Microbial Diversity in a Mediterranean Semiarid Vineyard. SUSTAINABILITY 2020. [DOI: 10.3390/su12083256] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cover crop (CC) management in vineyards increases sustainability by improving soil chemical and biological fertility, but knowledge on its effects in semiarid soils is lacking. This study evaluated the effect of leguminous CC management on soil organic carbon (SOC) sequestration, soil nitrate content and microbial diversity in a semiarid vineyard, in comparison to conventional tillage (CT). SOC and nitrate were monitored during vine-growing season; soil respiration, determined by incubation experiments, microbial biomass and diversity was analyzed after CC burial. The microbial diversity was evaluated by bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA) and high-throughput sequencing of 16SrDNA. CC increased nitrate content and, although it had no relevant effect on SOC, almost doubled its active microbial component, which contributes to SOC stabilization. An unexpected stability of the microbial communities under different soil managements was assessed, fungal diversity being slightly enhanced under CT while bacterial diversity increased under CC. The complete nitrifying genus Nitrospira and plant growth-promoting genera were increased under CC, while desiccation-tolerant genera were abundant in CT. Findings showed that temporary CC applied in semiarid vineyards does not optimize the provided ecosystem services, hence a proper management protocol for dry environments should be set up.
Collapse
|
111
|
Xu S, Wang B, Li Y, Jiang D, Zhou Y, Ding A, Zong Y, Ling X, Zhang S, Lu H. Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135684. [PMID: 31862588 DOI: 10.1016/j.scitotenv.2019.135684] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
The recent discovery of complete ammonia oxidation (comammox) process in a single organism challenged the division of labor between two functional groups in the classical two-step nitrification model. However, the distribution and activity of comammox bacteria in various environments remain largely unknown. This study presented a large-scale investigation of the geographical distribution, phylogenetic diversity, and activity of comammox Nitrospira in typical agricultural soils. Among the 23 samples harvested across China, comammox Nitrospira clade A was ubiquitously detected at 4.14 × 104-1.65 × 107amoA gene copies/g dry soil, with 90% belonging to the subclade A2. The abundance of comammox Nitrospira clade B was two orders of magnitude lower than clade A. In all samples, comammox Nitrospira were 1-2 orders of magnitude less abundant than canonical nitrifiers, and soils with slightly high pH and C/N tended to enrich more comammox Nitrospira. Unlike canonical nitrifiers, comammox Nitrospira had sustained amoA gene transcription regardless of external ammonia supply, indicating their competitive advantage over other nitrifiers under low-ammonia conditions. When fed with 1 mM ammonium for 15 days, comammox Nitrospira in tested soils were enriched 2.36 times higher than those enriched by the same amount of nitrite, indicating their preference to utilizing ammonia as the substrate. DNA-SIP further confirmed the in situ nitrification activity of comammox Nitrospira. This study provided new insights into the broad distribution and diversity of comammox Nitrospira in agricultural soils, which could potentially play an important role in the microbial nitrogen cycle in soils.
Collapse
Affiliation(s)
- Shaoyi Xu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yong Li
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Daqian Jiang
- Environmental Engineering Department, Montana Tech, Butte, United States
| | - Yuting Zhou
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Aqiang Ding
- College of Resource and Environmental Science, Chongqing University, Chongqing, China
| | - Yuxiao Zong
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoting Ling
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Senyin Zhang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
| |
Collapse
|
112
|
Wendeborn S. Chemie, Biologie und Regulierung der Nitrifikation von Ammonium im Boden. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201903014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sebastian Wendeborn
- Fachhochschule Nordwestschweiz FHNWHochschule für Life SciencesInstitut für Chemie und Bioanalytik Hofackerstrasse 30 CH-4132 Muttenz Schweiz
| |
Collapse
|
113
|
Heaney N, Ukpong E, Lin C. Low-molecular-weight organic acids enable biochar to immobilize nitrate. CHEMOSPHERE 2020; 240:124872. [PMID: 31550589 DOI: 10.1016/j.chemosphere.2019.124872] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/09/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Batch experiments were conducted using two biochar materials produced from different feedstocks to examine the behavior of solution-borne nitrate in the presence and absence of three model low-molecular weight organic acids (LMWOAs). The results showed that the biochar materials alone were not able to remove the solution-borne nitrate. LMWOAs caused protonation of the biochar surfaces and consequently enabled the biochar materials to adsorb nitrate from the solution. Different types of LMWOA had different capacities to immobilize solution-borne nitrate. Over 80% of the solution-borne nitrate could be removed within 72 h in the presence of citric acid or malic acid. By comparison, removal rate of nitrate was lower in the presence of oxalic acid, possibly due to competition of oxalate ion with nitrate for the available adsorption sites on the biochar surfaces. Nitrate adsorption onto the MSP700 biochar in the presence of all three-LMWOAs followed first order and second order kinetics, suggesting that the immobilization of nitrate involved complex interplay of physisorption and chemisorption. Nitrate adsorption onto RH700 biochar in citric and malic acid treatment systems followed second order kinetics. In the presence of oxalic acid for both biochar materials, nitrate adsorption showed perfect correlation R2 = 1 for both models.
Collapse
Affiliation(s)
- Natalie Heaney
- School of Environment and Life Science, University of Salford, Greater Manchester M5 4WT United Kingdom
| | - Emem Ukpong
- School of Environment and Life Science, University of Salford, Greater Manchester M5 4WT United Kingdom
| | - Chuxia Lin
- School of Environment and Life Science, University of Salford, Greater Manchester M5 4WT United Kingdom.
| |
Collapse
|
114
|
Ding J, Ma M, Jiang X, Liu Y, Zhang J, Suo L, Wang L, Wei D, Li J. Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field. Microbiologyopen 2020; 9:e00942. [PMID: 31568679 PMCID: PMC6957403 DOI: 10.1002/mbo3.942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 11/21/2022] Open
Abstract
In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the long-term fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples. Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.
Collapse
Affiliation(s)
- Jianli Ding
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Xin Jiang
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Yao Liu
- National Center for Science and Technology EvaluationMOSTBeijingChina
| | - Junzheng Zhang
- School of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbinChina
| | - Linna Suo
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Lei Wang
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Dan Wei
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jun Li
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
115
|
Elrys AS, Desoky ESM, Abo El-Maati MF, Elnahal AS, Abdo AI, Raza S, Zhou J. Can secondary metabolites extracted from Moringa seeds suppress ammonia oxidizers to increase nitrogen use efficiency and reduce nitrate contamination in potato tubers? ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 185:109689. [PMID: 31550566 DOI: 10.1016/j.ecoenv.2019.109689] [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: 07/29/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 05/10/2023]
Abstract
Nitrification inhibition as an alleviation tool to decrease nitrogen (N) losses and increase N use efficiency (NUE) as well as reducing NO3- accumulation in plants is a promising technology. No study thus far has directly or indirectly to use the secondary metabolites extracted from Moringa (Moringa oleifera Lam) seeds as nitrification inhibitors. Moringa seed extract (MSE) was studied based on its content of phenolic compounds (PC) and for its antioxidant characteristic. A 2-year field experiment and 30-day incubation experiment were conducted with three treatments of control (CK), N fertilizer (300 kg N ha-1 and 200 mg N kg-1 soil for the field and incubation experiment, respectively), and N fertilizer with MSE (500 ppm as a TPC) to investigate the responses of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to MSE and the consequences for NUE and NO3- accumulation in potato tubers. Total phenolics amount was 144 mg gallic acid equivalent g-1 MSE, while flavonoid contents were 76.6 quercetin equivalent g-1 MSE. MSE showed antioxidant activity that was comparable to the standard antioxidants TBHQ and gallic acid. MSE application with N fertilizer retarded the nitrification process, as indicated by a higher NH4+-N and lower NO3--N content, compared with N fertilizer application alone. NH4+-N content reduced to initial CK level on Day 20 under N fertilizer application alone. However, NH4+-N content decreased to initial control level on Day 30 when MSE was applied. The mechanisms resulted from curbing AOB growth by phenolic compounds (TPC, TF, TAC), leading to a delay in nitrification process. AOB increased significantly when N fertilizer was applied alone; on the contrary, AOA was not sensitive to N fertilizer (with and without MSE). Increase in NUE from 37.5% to 66.3% in potato plants under MSE application with N fertilizer was also observed compared with N fertilizer application alone. The highest NO3- accumulation (569 mg NO3- kg-1) in tubers was recorded under N fertilizer application without MSE. MSE application significantly decreased NO3- accumulation (92 mg NO3- kg-1) in tubers which is lower than the maximum value of accepting tubers (200 mg NO3- kg-1). The highest average of N uptake, fresh and dry weight, carotenoids, chlorophyll a, chlorophyll b and nitrate reductase activity was recorded when MSE was applied with N fertilizer. Accordingly, using of Moringa extracted secondary metabolites to suppress AOB growth in the soil is a significant strategy to reduce nitrification rate and N loss from soils, and therefore increase NUE as well as reducing NO3- accumulation in potato tubers.
Collapse
Affiliation(s)
- Ahmed S Elrys
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China; Soil Science Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China.
| | - El-Sayed M Desoky
- Agriculture Botany Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt
| | - Mohamed F Abo El-Maati
- Agriculture Biochemistry Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt
| | - Ahmed S Elnahal
- College of Plant Protection, Northwest A&F University, Yangling, 712100, People's Republic of China; Department of Plant Pathology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ahmed I Abdo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China; Soil Science Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt
| | - Sajjad Raza
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianbin Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China; Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, People's Republic of China.
| |
Collapse
|
116
|
Wendeborn S. The Chemistry, Biology, and Modulation of Ammonium Nitrification in Soil. Angew Chem Int Ed Engl 2019; 59:2182-2202. [PMID: 31116902 DOI: 10.1002/anie.201903014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/15/2019] [Indexed: 11/11/2022]
Abstract
Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.
Collapse
Affiliation(s)
- Sebastian Wendeborn
- University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
| |
Collapse
|
117
|
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.
Collapse
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
| |
Collapse
|
118
|
Metzner R, Nomura T, Kitaoka N, Ando A, Ogawa J, Kato Y. Cobalt-dependent inhibition of nitrite oxidation in Nitrobacter winogradskyi. J Biosci Bioeng 2019; 128:463-467. [PMID: 31029538 DOI: 10.1016/j.jbiosc.2019.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/07/2019] [Accepted: 04/01/2019] [Indexed: 10/26/2022]
Abstract
Nitrobacter winogradskyi is an abundant, intensively studied autotrophic nitrite-oxidizing bacterium, which is frequently used as a model strain in the two-step nitrification of ammonia (NH3) to nitrate (NO3-) via nitrite (NO2-), either in activated sludge, agricultural field studies or more recently in artificial microbial consortia for organic hydroponics. We observed a hitherto unknown cobalt ion-dependent inhibition of cell growth and NO2- oxidation activity of N. winogradskyi in a mineral medium, which strongly depended on accompanying Ca2+ and Mg2+ concentrations. This inhibition was bacteriostatic, but susceptible to natural chelators. l-Histidine effectively restored cell growth and NO2- oxidation activity of N. winogradskyi in mineral media containing Co2+ with >90% recovery. Our results suggest that Co2+ competed with alkaline earth metals during uptake and that its toxicity was significantly reduced by complexation.
Collapse
Affiliation(s)
- Richard Metzner
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoki Kitaoka
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Akinori Ando
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan; Research Unit for Physiological Chemistry, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan; Research Unit for Physiological Chemistry, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
| |
Collapse
|
119
|
Liu L, Li S, Han J, Lin W, Luo J. A Two-Step Strategy for the Rapid Enrichment of Nitrosocosmicus-Like Ammonia-Oxidizing Thaumarchaea. Front Microbiol 2019; 10:875. [PMID: 31105671 PMCID: PMC6491936 DOI: 10.3389/fmicb.2019.00875] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/04/2019] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are widely distributed on the earth and play a significant role in the global nitrogen cycle. Although dozens of AOA strains were obtained in the last 13 years, it is still necessary to obtain more AOA strains for the entire exploration of their ecology, physiology, and underlying biochemistry in different environments. In this study, we designed a two-step strategy for the rapid enrichment of Nitrosocosmicus–like AOA from soils. Firstly, combination of kanamycin and ampicillin was chosen as the selective stress for bacteria and quartz sands were used as the attachment of AOA cells during the first step cultivation; only after 40–75 days cultivation, AOA enrichments with abundance >20% were obtained. Secondly, combination of ciprofloxacin and azithromycin was chosen as the selective stress for the following cultivation; it is able to penetrate the biofilms and kill the bacterial cells inside the aggregate, contributing to the AOA enrichments reached high abundances (90%) only after one-time cultivation. Basing on this strategy, three AOA strains were obtained from agricultural soils only after 90–150 days cultivation. Phylogenetic analysis suggested these AOA belong to the soil group I.1b Thaumarchaeota and are closely related to the genus Nitrosocosmicus. In general, AOA enrichment or isolation is very difficult and time-consuming (an average of 2–3 years). Here, we provide a new strategy for the rapid enrichment of high abundance of Nitrosocosmicus-like AOA from soil, which gives a new solution to the AOA enrichment and cultivation in a short period.
Collapse
Affiliation(s)
- Liangting Liu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Surong Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiamin Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Weitie Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianfei Luo
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|
120
|
Duan P, Fan C, Zhang Q, Xiong Z. Overdose fertilization induced ammonia-oxidizing archaea producing nitrous oxide in intensive vegetable fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:1787-1794. [PMID: 30278423 DOI: 10.1016/j.scitotenv.2018.09.341] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N2O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha-1 yr-1, respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N2O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N2O production with negligible N2O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N2O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N2O production than AOB, whereas urea supply led to higher AOB-dependent N2O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N2O production and NO2- accumulation during the incubation. Further mechanisms for NO2--dependent N2O production in intensive vegetable soils therefore deserve urgent attention.
Collapse
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
| | - Changhua Fan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan 571737, 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
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
121
|
Zerfaß C, Christie-Oleza JA, Soyer OS. Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner. Appl Environ Microbiol 2019; 85:e02129-18. [PMID: 30413475 PMCID: PMC6328764 DOI: 10.1128/aem.02129-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
Manganese biomineralization is a widespread process among bacteria and fungi. To date, there is no conclusive experimental evidence for how and if this process impacts microbial fitness in the environment. Here, we show how a model organism for manganese oxidation is growth inhibited by nitrite, and that this inhibition is mitigated in the presence of manganese. We show that such manganese-mediated mitigation of nitrite inhibition is dependent on the culture inoculum size, and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (nontoxic) nitrate under physiological conditions and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e., mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS.IMPORTANCE We present here a direct fitness benefit (i.e., growth advantage) for manganese oxide biomineralization activity in Roseobacter sp. strain AzwK-3b, a model organism used to study this process. We find that strain AzwK-3b in a laboratory culture experiment is growth inhibited by nitrite in manganese-free cultures, while the inhibition is considerably relieved by manganese supplementation and manganese oxide (MnOX) formation. We show that biogenic MnOX interacts directly with nitrite and possibly with reactive oxygen species and find that its beneficial effects are established through formation of dispersed MnOX granules in a manner dependent on the population size. These experiments raise the possibility that manganese biomineralization could confer protection against nitrite toxicity to a population of cells. They open up new avenues of interrogating this process in other species and provide possible routes to their biotechnological applications, including in metal recovery, biomaterials production, and synthetic community engineering.
Collapse
Affiliation(s)
- Christian Zerfaß
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| |
Collapse
|
122
|
Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol 2019; 103:177-189. [PMID: 30415428 PMCID: PMC6311188 DOI: 10.1007/s00253-018-9486-3] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 11/30/2022]
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.
Collapse
Affiliation(s)
- Hanna Koch
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Sebastian Lücker
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.
| |
Collapse
|
123
|
Jones CM, Hallin S. Geospatial variation in co-occurrence networks of nitrifying microbial guilds. Mol Ecol 2018; 28:293-306. [PMID: 30307658 PMCID: PMC6905385 DOI: 10.1111/mec.14893] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/20/2018] [Accepted: 10/01/2018] [Indexed: 01/07/2023]
Abstract
Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.
Collapse
Affiliation(s)
- Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| |
Collapse
|
124
|
Ning J, Ai S, Cui L. Dicyandiamide has more inhibitory activities on nitrification than thiosulfate. PLoS One 2018; 13:e0200598. [PMID: 30106965 PMCID: PMC6091914 DOI: 10.1371/journal.pone.0200598] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 07/01/2018] [Indexed: 11/18/2022] Open
Abstract
Dicyandiamide (DCD) and thiosulfates are two type of nitrification inhibitors (NIs) that have been widely used in agriculture to improve nitrogen (N) fertilizer use efficiency and mitigate negative effect of N on environment. Little information is available concerning the comparison of the efficacy of DCD and thiosulfate on N transformations in soil. The aim of this study was to compare the effects of DCD and thiosulfate (K2S2O3) on changes of NH4+-N, nitrification inhibition and N recovery in a latosolic red soil. An incubation experiment was conducted with four treatments of control (CK), N, N+DCD, and N+K2S2O3. Soil samples were collected periodically over 50 d to determine concentrations of mineral N, and the amoA gene abundance of ammonia monooxygenase (AMO) for ammonia-oxidizing bacteria (AOB) was estimated by qPCR after 10 d incubation. In the N treatment, 67.8% of the applied N as NH4+-N disappeared from the mineral N pool and only 2.7% and 30.8% of the applied N was accumulated as NO2--N and NO3--N, respectively. Addition of DCD and thiosulfate to the soil prevented NH4+-N disappearance by 63.0% and 13.6%, respectively. DCD suppressed the production of NO2--N by 97.41%, whereas thiosulfate increased accumulation of NO2--N by 14.6%. Application of N along with DCD and thiosulfate inhibited nitrification, respectively, by 72.6% and 33.1%, resulting in the delay of the nitrification process for 30 days and 10 days, respectively. Apparent N recovery in N treatment was 66.2%, which increased by 55.2% and 4.8% by DCD and thiosulfate, respectively. Numbers of AOB amoA gene copy was significantly inhibited by both DCD and thiosulfate, and the stronger inhibition induced by DCD than thiosulfate was recorded. Results indicated that both DCD and thiosulfate were effective inhibitors for NH4+-N oxidation, NO3--N production, mineral N losses and AOB growth. DCD showed a more pronounced effect on nitrification inhibition than thiosulfate.
Collapse
Affiliation(s)
- Jianfeng Ning
- College of Natural Resource & Environment, South China Agricultural University, Guangzhou, China
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou, China
| | - Shaoying Ai
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou, China
| | - Lihua Cui
- College of Natural Resource & Environment, South China Agricultural University, Guangzhou, China
| |
Collapse
|
125
|
in ‘t Zandt MH, de Jong AEE, Slomp CP, Jetten MSM. The hunt for the most-wanted chemolithoautotrophic spookmicrobes. FEMS Microbiol Ecol 2018; 94:4966976. [PMID: 29873717 PMCID: PMC5989612 DOI: 10.1093/femsec/fiy064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.
Collapse
Affiliation(s)
- Michiel H in ‘t Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Anniek EE de Jong
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Caroline P Slomp
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Department of Earth Sciences, Geochemistry, Utrecht University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
| | - Mike SM Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|