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Zhang Z, Zhao L, Yang J, Pang J, Lambers H, He H. Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22663-22678. [PMID: 38409385 DOI: 10.1007/s11356-024-32578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/17/2024] [Indexed: 02/28/2024]
Abstract
Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.
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Affiliation(s)
- Zekun Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Le Zhao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiayin Pang
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Hans Lambers
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Honghua He
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Institute of Soil and Water Conservation, Yangling, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, Shaanxi, China.
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Neyret M, Le Provost G, Boesing AL, Schneider FD, Baulechner D, Bergmann J, de Vries FT, Fiore-Donno AM, Geisen S, Goldmann K, Merges A, Saifutdinov RA, Simons NK, Tobias JA, Zaitsev AS, Gossner MM, Jung K, Kandeler E, Krauss J, Penone C, Schloter M, Schulz S, Staab M, Wolters V, Apostolakis A, Birkhofer K, Boch S, Boeddinghaus RS, Bolliger R, Bonkowski M, Buscot F, Dumack K, Fischer M, Gan HY, Heinze J, Hölzel N, John K, Klaus VH, Kleinebecker T, Marhan S, Müller J, Renner SC, Rillig MC, Schenk NV, Schöning I, Schrumpf M, Seibold S, Socher SA, Solly EF, Teuscher M, van Kleunen M, Wubet T, Manning P. A slow-fast trait continuum at the whole community level in relation to land-use intensification. Nat Commun 2024; 15:1251. [PMID: 38341437 PMCID: PMC10858939 DOI: 10.1038/s41467-024-45113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.
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Affiliation(s)
- Margot Neyret
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Laboratoire d'Écologie Alpine, Université Grenoble Alpes - CNRS - Université Savoie Mont Blanc, Grenoble, France.
| | | | | | - Florian D Schneider
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- ISOE - Institute for social-ecological research, Frankfurt am Main, Germany
| | - Dennis Baulechner
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Joana Bergmann
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Stefan Geisen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, The Netherlands
| | - Kezia Goldmann
- Helmholtz Centre for Environmental Research (UFZ), Soil Ecology Department, Halle/Saale, Germany
| | - Anna Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Ruslan A Saifutdinov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Nadja K Simons
- Ecological Networks, Technical University Darmstadt, Darmstadt, Germany
- Applied Biodiversity Sciences, University of Würzburg, Würzburg, Germany
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Andrey S Zaitsev
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- Senckenberg Museum for Natural History Görlitz, Görlitz, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
| | - Kirsten Jung
- Institut of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Michael Schloter
- Helmholtz Zentrum Muenchen, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
- Chair of Environmental Microbiology, Technical University of Munich, Freising, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum Muenchen, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
| | - Michael Staab
- Ecological Networks, Technical University Darmstadt, Darmstadt, Germany
| | - Volkmar Wolters
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Antonios Apostolakis
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
- Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Steffen Boch
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Runa S Boeddinghaus
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
- Department Plant Production and Production Related Environmental Protection, Center for Agricultural Technology Augustenberg (LTZ), Karlsruhe, Germany
| | - Ralph Bolliger
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research (UFZ), Soil Ecology Department, Halle/Saale, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena-, Leipzig, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Huei Ying Gan
- Senckenberg Centre for Human Evolution and Palaeoenvironments Tübingen (SHEP), Tübingen, Germany
| | - Johannes Heinze
- Department of Biodiversity, Heinz Sielmann Foundation, Wustermark, Germany
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Katharina John
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Valentin H Klaus
- Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forage Production and Grassland Systems, Agroscope, Zürich, Switzerland
| | - Till Kleinebecker
- Institute for Landscape Ecology and Resources Management (ILR), Research Centre for BioSystems, Land Use and Nutrition (iFZ), Justus Liebig University Giessen, Giessen, Germany
- Centre for International Development and Environmental Research (ZEU), Justus Liebig University Giessen, Giessen, Germany
| | - Sven Marhan
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Jörg Müller
- Department of Nature Conservation, Heinz Sielmann Foundation, Wustermark, Germany
| | - Swen C Renner
- Ornithology, Natural History Museum Vienna, Vienna, Autria, Germany
| | | | - Noëlle V Schenk
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Marion Schrumpf
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Sebastian Seibold
- Technical University of Munich, TUM School of Life Sciences, Freising, Germany
- TUD Dresden University of Technology, Forest Zoology, Tharandt, Germany
| | - Stephanie A Socher
- Paris Lodron University Salzburg, Department Environment and Biodiversity, Salzburg, Austria
| | - Emily F Solly
- Helmholtz Centre for Environmental Research (UFZ), Computation Hydrosystems Department, Leipzig, Germany
| | - Miriam Teuscher
- University of Göttingen, Centre of Biodiversity and Sustainable Land Use, Göttingen, Germany
| | - Mark van Kleunen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena-, Leipzig, Germany
- Helmholtz Centre for Environmental Research (UFZ), Community Ecology Department, Halle/Saale, Germany
| | - Peter Manning
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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Zhou C, Gao Y, Ma Q, Xia Z, Zhu M, Zhang X, An S, Li S, Yu W. The single and combined effects of sulfamethazine and cadmium on soil nitrification and ammonia-oxidizing microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:56108-56120. [PMID: 36913014 DOI: 10.1007/s11356-023-26141-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The coexistence of antibiotics and heavy metals in soil has attracted increasing attention due to their negative effects on microorganisms. However, how antibiotics and heavy metals affect functional microorganisms related to nitrogen cycle remains unclear. The goals of this work were to explore the individual and combined effects of sulfamethazine (SMT) and cadmium (Cd), selected as target pollutants in soil, on potential nitrification rates (PNR) and ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) structure and diversity by 56-day cultivation experiment. Results showed that PNR in Cd- or SMT-treated soil decreased at the beginning of the experiment and then increased over time. PNR was significantly correlated with AOA and AOB-amoA relative abundance (P < 0.01). SMT addition (10 and 100 mg kg-1) significantly improved AOA activity by 13.93% and 17.93%, respectively, and had no effect on AOB at day 1. Conversely, Cd at 10 mg kg-1 significantly inhibited AOA and AOB by 34.34% and 37.39%, respectively. Moreover, the relative abundance of AOA and AOB in combined SMT and Cd addition clearly higher relative to single Cd at 1 day. The single and combined Cd and SMT increased and reduced the community richness of AOA and AOB, respectively, but reduced the diversity of both after 56 days. Cd and SMT treatments significantly changed the relative abundance of AOA phylum levels and AOB genus levels in the soil. It was mainly manifested in reducing the relative abundance of AOA Thaumarchaeota, and increasing the relative abundance of AOB Nitrosospira. Besides, AOB Nitrosospira was more tolerant to the compound addition of both than single application.
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Affiliation(s)
- Changrui Zhou
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yun Gao
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Ma
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China
| | - Zhuqing Xia
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengmeng Zhu
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinhui Zhang
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyu An
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuailin Li
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China.
| | - Wantai Yu
- Institute of Applied Ecology Chinese Academy of Sciences, Shenhe District, 72 Wenhua Road, Shenyang, 110016, People's Republic of China.
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Wu J, Zhang Y, Huang M, Zou Z, Guo S, Wang J, Zou J. Sulfonamide antibiotics alter gaseous nitrogen emissions in the soil-plant system: A mesocosm experiment and meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154230. [PMID: 35271923 DOI: 10.1016/j.scitotenv.2022.154230] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 05/28/2023]
Abstract
Veterinary antibiotics are widely used in many countries worldwide to treat diseases and protect the health of animals. However, the effects of sulfonamide antibiotics introduced via manure and wastewater irrigation on nitrogen (N) loss in the soil-plant system remain poorly understood. Here, we conducted a pot experiment to assess the effects of sulfamethazine (SMZ) and its degradation product (2-amino-4,6-dimethylpyrimidine, ADPD) at four concentration gradients (i.e., 0, 1, 10, 100 mg kg-1) on nitrous oxide (N2O) and ammonia (NH3) emissions, and the abundances of N-cycling functional genes and sulfonamide resistance genes. We also collated 350 observations from 62 published papers and performed a meta-analysis of antibiotic addition effects on N2O emission and soil net nitrification and denitrification. Antibiotics additions showed an inhibitory effect on N2O emissions, which accords with the trend of our meta-analysis showing a significant decrease of 32%. The decreased N2O emissions were attributed to the significant reduction in the abundances of total bacterial communities, ammonia oxidizers, and nir-type denitrifiers and to the resultant changes in soil inorganic N. N2O emissions did not differ between non-environmentally relevant concentrations for SMZ but lowered with increasing ADPD concentrations. This discrepancy can be explained by differential responses of the gene abundances of ammonia oxidizers and nirK-type denitrifiers and the development of antibiotic resistance genes in the highest concentration following antibiotic additions. Antibiotic additions increased soil NH3 volatilization but did not affect vegetable yield. Therefore, these findings provide insight into how the prevalence of antibiotics in soils could alter the N-cycling process and associated gas emissions, with implications for understanding the ecological risks of antibiotics in agriculture.
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Affiliation(s)
- Jie Wu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihe Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengyuan Huang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziheng Zou
- School of Earth System Science, Tianjin University, 300072 Tianjin, China
| | - Shumin Guo
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinyang Wang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jianwen Zou
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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Li S, Peng L, Yang C, Song S, Xu Y. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms during wastewater treatment processes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114336. [PMID: 34953231 DOI: 10.1016/j.jenvman.2021.114336] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/27/2021] [Accepted: 12/16/2021] [Indexed: 05/04/2023]
Abstract
Studies on antibiotic removal during wastewater treatment processes are crucial since their release into the environment could bring potential threats to human health and ecosystem. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms (AOMs) has received special attentions due to the enhanced removal of antibiotics during nitrification processes. However, the interactions between antibiotics and AOMs are less well-elucidated. In this review, the recent research proceedings on cometabolic biodegradation of antibiotics by AOMs were summarized. Ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) played significant roles in both nitrification and cometabolic biodegradation of antibiotics. Antibiotics at varying concentrations might pose inhibiting or stimulating effect on AOMs, influencing the microbial activity, community abundance and ammonia monooxygenase subunit A gene expression level. AOMs-induced cometabolic biodegradation products were analyzed as well as the corresponding pathways for each type of antibiotics. The effects of ammonium availability, initial antibiotic concentration, sludge retention time and temperature were assessed on the cometabolic biodegradation efficiencies of antibiotics. This work might provide further insights into the fate and removal of antibiotics during nitrification processes.
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Affiliation(s)
- Shengjun Li
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China
| | - Lai Peng
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China.
| | - Chenguang Yang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya Hainan, 572000, China
| | - Shaoxian Song
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China
| | - Yifeng Xu
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China.
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Ouyang Y, Norton JM. Nitrite Oxidizer Activity and Community Are More Responsive Than Their Abundance to Ammonium-Based Fertilizer in an Agricultural Soil. Front Microbiol 2020; 11:1736. [PMID: 32849372 PMCID: PMC7417772 DOI: 10.3389/fmicb.2020.01736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
Autotrophic nitrification is mediated by ammonia oxidizing bacteria (AOB) or ammonia oxidizing archaea (AOA) and nitrite oxidizing bacteria (NOB). Mounting studies have examined the impact of nitrogen (N) fertilization on the dynamic and diversity of AOA and AOB, while we have limited information on the response of the activity, abundance, and diversity of NOB to N fertilization. We investigated the influence of organic and inorganic N fertilizers on soil NOB in silage corn field plots that received contrasting nitrogen (N) treatments: control (no additional N), ammonium sulfate (AS 100 and 200 kg N ha-1), and compost (200 kg N ha-1). Nitrifying community was examined using a universal marker (16S rRNA gene), functional gene markers (AOB amoA and Nitrospira nxrB), and metagenomics. The overall nitrifying community was not altered after the first fertilization but was significantly shifted by 4-year repeated application of ammonium fertilizers. Nitrospira were the dominant NOB (>99.7%) in our agricultural soil. Both community compositions of AOB and Nitrospira were significantly changed by ammonium fertilizers but not by compost after 4 years of repeated applications. All nitrifiers, including comammox, were recovered in soil metagenomes based on a gene-targeted assembly, but their sequence counts were very low. Although N treatment did not affect the abundance of Nitrospira nxrB determined by real-time quantitative PCR, ammonium fertilizers significantly promoted rates of potential nitrite oxidation determined at 0.15 mM nitrite in soil slurries. Understanding the response of both ammonia oxidizers and nitrite oxidizers to N fertilization may initiate or improve strategies for mitigating potential environmental impacts of nitrate production in agricultural ecosystems.
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Affiliation(s)
- Yang Ouyang
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Jeanette M. Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
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7
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Wang B, Ni BJ, Yuan Z, Guo J. Insight into the nitrification kinetics and microbial response of an enriched nitrifying sludge in the biodegradation of sulfadiazine. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113160. [PMID: 31521996 DOI: 10.1016/j.envpol.2019.113160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/27/2019] [Accepted: 09/01/2019] [Indexed: 06/10/2023]
Abstract
The intensive use of antibiotics results in the continuous release of antibiotics into wastewater treatment systems, leading to the spread of antibiotic resistance. Nitrifying system is reported to be capable of degrading antibiotics, yet few studies have systematically investigated the inherent correlation among ammonium oxidation rate, antibiotic degradation and genetic expression of nitrifying bacteria along the process. This study selected a widely used sulfonamide antibiotic, sulfadiazine (SDZ), to investigate its biodegradation potential by an enriched nitrifying culture and the response of nitrifying bacteria against antibiotic exposure. Our results demonstrated that SDZ degradation was mainly contributed by cometabolism of ammonia-oxidizing bacteria (AOB), rather than biomass adsorption. The quantitative reverse transcription PCR (RT-qPCR) analysis revealed that the expression level of amoA gene was down-regulated due to the SDZ exposure. In addition, the degradation products of SDZ did not exhibit inhibitory effect on Escherichia coli K12, indicating the biotoxicity of SDZ could be mitigated after biodegradation. The findings offer insights regarding the biodegradation process of sulfonamide antibiotics via cometabolism by AOB.
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Affiliation(s)
- Bingzheng Wang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Bing-Jie Ni
- School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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Han S, Li X, Luo X, Wen S, Chen W, Huang Q. Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil. Front Microbiol 2018; 9:885. [PMID: 29867799 PMCID: PMC5951965 DOI: 10.3389/fmicb.2018.00885] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/17/2018] [Indexed: 11/25/2022] Open
Abstract
Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.
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Affiliation(s)
- Shun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Shilin Wen
- Hengyang Red Soil Experimental Station, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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9
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Wang L, Wang J, Zhu L, Wang J. Toxic effects of oxytetracycline and copper, separately or combined, on soil microbial biomasses. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2018; 40:763-776. [PMID: 29027092 DOI: 10.1007/s10653-017-0022-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
The production of commercial livestock and poultry often involves using with antibiotics and feed additives, such as oxytetracycline (OTC) and copper (Cu). These are often excreted into the soil by animal feces; hence, combined pollutants may contaminate the soil. To evaluate single and combined toxic effects of OTC and Cu on the soil ecology, changes in quantities of bacteria, fungi, and actinomycetes in the soil were studied over a 28-d incubation period by a plate count method, microbes numbers counted on days 7, 14, 21, and 28. Abundances of ammonia monooxygenase (amoA) gene expression by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in soil samples also were tested by real-time polymerase chain reactions (RT-PCRs) on day 21. The results revealed that the numbers of bacteria, fungi and actinomycetes and amoA genes copies of AOA and AOB were reduced seriously by exposure to Cu (1.60 mmol/kg). Similarly, the combined pollution treatments (mole ratios of OTC: Cu was 1:2, 1:8, and 1:32) also had inhibitory effect on bacteria, fungi, and actinomycetes numbers and amoA gene copies of AOA and AOB; the inhibitory rate was on obvious growth trend with the increasing mole ratios. Effects from single OTC pollution were found on bacteria (days 7 and 14), fungi (days 7, 14, 21, and 28), and AOA-amoA gene copies (day 21), with promotion at a low concentration (0.05 mmol/kg) and suppression at higher concentrations (0.2 and 0.8 mmol/kg). Also, numbers of bacteria, fungi, and actinomycetes decreased with longer culture times. Combining OTC and Cu led to a higher inhibition of soil microbes than when either chemical was used alone. However, there was no significant relationship between single and combined toxic chemicals because of their complicated interactions, either antagonistic or synergistic. The results also indicated the sensitivity of bacteria, fungi, actinomycetes on toxic chemicals existed difference and that the AOA were more tolerant than the AOB to these chemicals.
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Affiliation(s)
- Lanjun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Jinhua Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China.
| | - Lusheng Zhu
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
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10
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11
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Simonin M, Martins JM, Le Roux X, Uzu G, Calas A, Richaume A. Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose–response relationships. Nanotoxicology 2017; 11:247-255. [DOI: 10.1080/17435390.2017.1290845] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marie Simonin
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | | | - Xavier Le Roux
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
| | - Gaëlle Uzu
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | - Aude Calas
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | - Agnès Richaume
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
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12
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Luo X, Han S, Lai S, Huang Q, Chen W. Long-term straw returning affectsNitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil. J Basic Microbiol 2016; 57:309-315. [DOI: 10.1002/jobm.201600400] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Xuesong Luo
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University; Wuhan China
| | - Shun Han
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
| | - Songsong Lai
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University; Wuhan China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
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Schaeffer A, Amelung W, Hollert H, Kaestner M, Kandeler E, Kruse J, Miltner A, Ottermanns R, Pagel H, Peth S, Poll C, Rambold G, Schloter M, Schulz S, Streck T, Roß-Nickoll M. The impact of chemical pollution on the resilience of soils under multiple stresses: A conceptual framework for future research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 568:1076-1085. [PMID: 27372890 DOI: 10.1016/j.scitotenv.2016.06.161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/20/2016] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
Soils are faced with man-made chemical stress factors, such as the input of organic or metal-containing pesticides, in combination with non-chemical stressors like soil compaction and natural disturbance like drought. Although multiple stress factors are typically co-occurring in soil ecosystems, research in soil sciences on this aspect is limited and focuses mostly on single structural or functional endpoints. A mechanistic understanding of the reaction of soils to multiple stressors is currently lacking. Based on a review of resilience theory, we introduce a new concept for research on the ability of polluted soil (xenobiotics or other chemical pollutants as one stressor) to resist further natural or anthropogenic stress and to retain its functions and structure. There is strong indication that pollution as a primary stressor will change the system reaction of soil, i.e., its resilience, stability and resistance. It can be expected that pollution affects the physiological adaption of organisms and the functional redundancy of the soil to further stress. We hypothesize that the recovery of organisms and chemical-physical properties after impact of a follow-up stressor is faster in polluted soil than in non-polluted soil, i.e., polluted soil has a higher dynamical stability (dynamical stability=1/recovery time), whereas resilience of the contaminated soil is lower compared to that of not or less contaminated soil. Thus, a polluted soil might be more prone to change into another system regime after occurrence of further stress. We highlight this issue by compiling the literature exemplarily for the effects of Cu contamination and compaction on soil functions and structure. We propose to intensify research on effects of combined stresses involving a multidisciplinary team of experts and provide suggestions for corresponding experiments. Our concept offers thus a framework for system level analysis of soils paving the way to enhance ecological theory.
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Affiliation(s)
- Andreas Schaeffer
- RWTH Aachen University, Institute for Environmental Research (Biology 5), 52074 Aachen, Germany.
| | - Wulf Amelung
- Soil Science and Soil Ecology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Nussallee 13, 53115 Bonn, Germany
| | - Henner Hollert
- RWTH Aachen University, Institute for Environmental Research (Biology 5), 52074 Aachen, Germany
| | - Matthias Kaestner
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, 04318 Leipzig, Germany
| | - Ellen Kandeler
- Soil Science and Land Evaluation, University of Hohenheim, Emil Wolff Str. 27, 70599 Stuttgart, Germany
| | - Jens Kruse
- Soil Science and Soil Ecology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Nussallee 13, 53115 Bonn, Germany
| | - Anja Miltner
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, 04318 Leipzig, Germany
| | - Richard Ottermanns
- RWTH Aachen University, Institute for Environmental Research (Biology 5), 52074 Aachen, Germany
| | - Holger Pagel
- Soil Science and Land Evaluation, University of Hohenheim, Emil Wolff Str. 27, 70599 Stuttgart, Germany
| | - Stephan Peth
- Department of Soil Science, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Christian Poll
- Soil Science and Land Evaluation, University of Hohenheim, Emil Wolff Str. 27, 70599 Stuttgart, Germany
| | - Gerhard Rambold
- Systematic Botany and Mycology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, Research Unit for Environmental Genomics, Ingolstädter Landstr. 1, 85758 Oberschleissheim, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum München, Research Unit for Environmental Genomics, Ingolstädter Landstr. 1, 85758 Oberschleissheim, Germany
| | - Thilo Streck
- Soil Science and Land Evaluation, University of Hohenheim, Emil Wolff Str. 27, 70599 Stuttgart, Germany
| | - Martina Roß-Nickoll
- RWTH Aachen University, Institute for Environmental Research (Biology 5), 52074 Aachen, Germany
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14
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Simonin M, Richaume A, Guyonnet JP, Dubost A, Martins JMF, Pommier T. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers. Sci Rep 2016; 6:33643. [PMID: 27659196 PMCID: PMC5034236 DOI: 10.1038/srep33643] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/31/2016] [Indexed: 11/08/2022] Open
Abstract
Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg-1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function.
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Affiliation(s)
- Marie Simonin
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
- LTHE, UMR 5564 CNRS – Univ. Grenoble Alpes 38041 Grenoble Cedex 9, France
| | - Agnès Richaume
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Julien P. Guyonnet
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Jean M. F. Martins
- LTHE, UMR 5564 CNRS – Univ. Grenoble Alpes 38041 Grenoble Cedex 9, France
| | - Thomas Pommier
- Univ Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, Laboratoire d’Ecologie Microbienne, UMR INRA 1418, bât G. Mendel, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
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15
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Zhao Z, Zhang Y, Xuan Y, Song W, Si W, Zhao Z, Rao Q. Ion-exchange solid-phase extraction combined with liquid chromatography-tandem mass spectrometry for the determination of veterinary drugs in organic fertilizers. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1022:281-289. [DOI: 10.1016/j.jchromb.2016.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/27/2016] [Accepted: 04/03/2016] [Indexed: 11/28/2022]
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16
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Stempfhuber B, Richter-Heitmann T, Regan KM, Kölbl A, Wüst PK, Marhan S, Sikorski J, Overmann J, Friedrich MW, Kandeler E, Schloter M. Spatial Interaction of Archaeal Ammonia-Oxidizers and Nitrite-Oxidizing Bacteria in an Unfertilized Grassland Soil. Front Microbiol 2016; 6:1567. [PMID: 26834718 PMCID: PMC4722141 DOI: 10.3389/fmicb.2015.01567] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/27/2015] [Indexed: 12/18/2022] Open
Abstract
Interrelated successive transformation steps of nitrification are performed by distinct microbial groups - the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m(2). Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation.
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Affiliation(s)
- Barbara Stempfhuber
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health Neuherberg, Germany
| | | | - Kathleen M Regan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Angelika Kölbl
- Lehrstuhl für Bodenkunde, Technische Universität München Freising, Germany
| | - Pia K Wüst
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | | | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Michael Schloter
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health Neuherberg, Germany
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Venterea RT, Clough TJ, Coulter JA, Breuillin-Sessoms F, Wang P, Sadowsky MJ. Ammonium sorption and ammonia inhibition of nitrite-oxidizing bacteria explain contrasting soil N2O production. Sci Rep 2015; 5:12153. [PMID: 26179972 PMCID: PMC4503984 DOI: 10.1038/srep12153] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/22/2015] [Indexed: 11/10/2022] Open
Abstract
Better understanding of process controls over nitrous oxide (N2O) production in urine-impacted ‘hot spots’ and fertilizer bands is needed to improve mitigation strategies and emission models. Following amendment with bovine (Bos taurus) urine (Bu) or urea (Ur), we measured inorganic N, pH, N2O, and genes associated with nitrification in two soils (‘L’ and ‘W’) having similar texture, pH, C, and C/N ratio. Solution-phase ammonia (slNH3) was also calculated accounting for non-linear ammonium (NH4+) sorption capacities (ASC). Soil W displayed greater nitrification rates and nitrate (NO3−) levels than soil L, but was more resistant to nitrite (NO2−) accumulation and produced two to ten times less N2O than soil L. Genes associated with NO2− oxidation (nxrA) increased substantially in soil W but remained static in soil L. Soil NO2− was strongly correlated with N2O production, and cumulative (c-) slNH3 explained 87% of the variance in c-NO2−. Differences between soils were explained by greater slNH3 in soil L which inhibited NO2− oxidization leading to greater NO2− levels and N2O production. This is the first study to correlate the dynamics of soil slNH3, NO2−, N2O and nitrifier genes, and the first to show how ASC can regulate NO2− levels and N2O production.
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Affiliation(s)
- Rodney T Venterea
- 1] USDA-ARS, Soil and Water Management Research Unit, St. Paul, MN 55108 [2] Dep. of Soil, Water, and Climate, Univ. of Minnesota, St. Paul, MN 55108
| | - Timothy J Clough
- Faculty of Agriculture and Life Science, Lincoln Univ., PO Box 85084, Lincoln 7647, Canterbury, New Zealand
| | - Jeffrey A Coulter
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN 55108
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Hirsch PR, Mauchline TH. The Importance of the Microbial N Cycle in Soil for Crop Plant Nutrition. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:45-71. [PMID: 26505688 DOI: 10.1016/bs.aambs.2015.09.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nitrogen is crucial for living cells, and prior to the introduction of mineral N fertilizer, fixation of atmospheric N2 by diverse prokaryotes was the primary source of N in all ecosystems. Microorganisms drive the N cycle starting with N2 fixation to ammonia, through nitrification in which ammonia is oxidized to nitrate and denitrification where nitrate is reduced to N2 to complete the cycle, or partially reduced to generate the greenhouse gas nitrous oxide. Traditionally, agriculture has relied on rotations that exploited N fixed by symbiotic rhizobia in leguminous plants, and recycled wastes and manures that microbial activity mineralized to release ammonia or nitrate. Mineral N fertilizer provided by the Haber-Bosch process has become essential for modern agriculture to increase crop yields and replace N removed from the system at harvest. However, with the increasing global population and problems caused by unintended N wastage and pollution, more sustainable ways of managing the N cycle in soil and utilizing biological N2 fixation have become imperative. This review describes the biological N cycle and details the steps and organisms involved. The effects of various agricultural practices that exploit fixation, retard nitrification, and reduce denitrification are presented, together with strategies that minimize inorganic fertilizer applications and curtail losses. The development and implementation of new technologies together with rediscovering traditional practices are discussed to speculate how the grand challenge of feeding the world sustainably can be met.
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Affiliation(s)
- Penny R Hirsch
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Tim H Mauchline
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
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19
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Fate and effects of veterinary antibiotics in soil. Trends Microbiol 2014; 22:536-45. [DOI: 10.1016/j.tim.2014.05.005] [Citation(s) in RCA: 337] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/15/2014] [Accepted: 05/21/2014] [Indexed: 12/15/2022]
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20
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Ma J, Lin H, Sun W, Wang Q, Yu Q, Zhao Y, Fu J. Soil microbial systems respond differentially to tetracycline, sulfamonomethoxine, and ciprofloxacin entering soil under pot experimental conditions alone and in combination. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:7436-7448. [PMID: 24590603 DOI: 10.1007/s11356-014-2685-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
This study investigated soil microbial responses to the application of tetracycline (TC), sulfamonomethoxine (SMM), and ciprofloxacin (CIP) alone and in combination in a soil culture pot experiment conducted at Hangzhou, China. Multiple approaches were applied for a better and complete depiction. Among the three antibiotics, SMM has a lowest dissipation and shows a most dramatic inhibition on microbial community and metabolism diversity. The combined application (AM) of SMM, CIP, and TC improved the dissipation of each antibiotic; similarly, SMM- and CIP-resistant bacteria showed larger populations in the AM than all single applications. Soils accumulated a large content of NO3-N at day 20 after multi-antibiotics perturbation. All antibiotics stimulated soil basal respirations and inhibited soil metabolism diversity, whereas the interruption exerted by SMM and AM lasted for a longer time. Six nitrogen-cycling genes including chiA, amoA, nifH, nirK, nirS, and narG were quantified and found to decrease owing to both single- and multi-antibiotics perturbation. Overall, AM was most interruptive for soils, followed by SMM perturbation, while other antibiotics could be less interruptive. These results provide systematic insights into how soil microbial systems would shift under each single- or multi-antibiotics perturbation.
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Affiliation(s)
- Junwei Ma
- Institute of Environment Resource and Soil Fertilizer, Zhejiang Academy of Agriculture Science, Hangzhou, 310021, China
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21
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Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine. PLoS One 2014; 9:e92958. [PMID: 24671113 PMCID: PMC3966856 DOI: 10.1371/journal.pone.0092958] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/27/2014] [Indexed: 11/30/2022] Open
Abstract
Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ.
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Effects of roxithromycin on ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in the rhizosphere of wheat. Appl Microbiol Biotechnol 2013; 98:263-72. [PMID: 24150789 DOI: 10.1007/s00253-013-5311-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
Abstract
In a pot-cultural experiment, the impact of the antibiotic roxithromycin (ROX) addition was assessed on the diversities of microbial structure and function communities, especially involved in ammonia and nitrite oxidation in wheat rhizosphere soil with and without the addition of earthworms. The abundances of ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and total bacteria were surveyed by the quantitative PCR. The quantities of total bacteria, AOB, and NOB with earthworms were higher than those without earthworms because of the synergistic effect. ROX inhibited the growth of AOB in all treatments, although the quantities of AOB were in a light increase in medium and heavy polluted treatments compared with that in the light polluted treatments. Different from AOB, the quantities of NOB were lowest in light polluted treatments, but the quantities of NOB were rapidly increased in medium and heavy polluted treatments compared with that in the control. These results indicated that the application of ROX principally had a negative effect on nitrification performance by affecting the abundances and relative ratios of both AOB and NOB in soil communities, which affected the N cycle in an agricultural ecosystem. According to the metabolic diversities evaluated by the biologic assay, the tendency of metabolic diversities was quite contrary to the quantities of NOB in all treatments and showed the contrast growing relation of autotrophic and heterotrophic bacteria under ROX pollution pressure in agricultural ecosystems.
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