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Aigle A, Gubry-Rangin C, Thion C, Estera-Molina KY, Richmond H, Pett-Ridge J, Firestone MK, Nicol GW, Prosser JI. Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria. Environ Microbiol 2021; 22:4032-4045. [PMID: 32783333 DOI: 10.1111/1462-2920.15192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/10/2020] [Indexed: 11/28/2022]
Abstract
Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.
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Affiliation(s)
- A Aigle
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Thion
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - K Y Estera-Molina
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - H Richmond
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - J Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, 94551, USA
| | - M K Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - G W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - J I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
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Vasileiadis S, Puglisi E, Papadopoulou ES, Pertile G, Suciu N, Pappolla RA, Tourna M, Karas PA, Papadimitriou F, Kasiotakis A, Ipsilanti N, Ferrarini A, Sułowicz S, Fornasier F, Menkissoglu-Spiroudi U, Nicol GW, Trevisan M, Karpouzas DG. Blame It on the Metabolite: 3,5-Dichloroaniline Rather than the Parent Compound Is Responsible for the Decreasing Diversity and Function of Soil Microorganisms. Appl Environ Microbiol 2018; 84:e01536-18. [PMID: 30194100 PMCID: PMC6210116 DOI: 10.1128/aem.01536-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022] Open
Abstract
Pesticides are key stressors of soil microorganisms with reciprocal effects on ecosystem functioning. These effects have been mainly attributed to the parent compounds, while the impact of their transformation products (TPs) has been largely overlooked. We assessed in a meadow soil (soil A) the transformation of iprodione and its toxicity in relation to (i) the abundance of functional microbial groups, (ii) the activity of key microbial enzymes, and (iii) the diversity of bacteria, fungi, and ammonia-oxidizing microorganisms (AOM) using amplicon sequencing. 3,5-Dichloroaniline (3,5-DCA), the main iprodione TP, was identified as a key explanatory factor for the persistent reduction in enzymatic activities and potential nitrification (PN) and for the observed structural changes in the bacterial and fungal communities. The abundances of certain bacterial (Actinobacteria, Hyphomicrobiaceae, Ilumatobacter, and Solirubrobacter) and fungal (Pichiaceae) groups were negatively correlated with 3,5-DCA. A subsequent study in a fallow agricultural soil (soil B) showed limited formation of 3,5-DCA, which concurred with the lack of effects on nitrification. Direct 3,5-DCA application in soil B induced a dose-dependent reduction of PN and NO3--N, which recovered with time. In vitro assays with terrestrial AOM verified the greater toxicity of 3,5-DCA over iprodione. "Candidatus Nitrosotalea sinensis" Nd2 was the most sensitive AOM to both compounds. Our findings build on previous evidence on the sensitivity of AOM to pesticides, reinforcing their potential utilization as indicators of the soil microbial toxicity of pesticides in pesticide environmental risk analysis and stressing the need to consider the contribution of TPs in the toxicity of pesticides on the soil microbial community.IMPORTANCE Pesticide toxicity on soil microorganisms is an emerging issue in pesticide risk assessment, dictated by the pivotal role of soil microorganisms in ecosystem services. However, the focus has traditionally been on parent compounds, while transformation products (TPs) are largely overlooked. We tested the hypothesis that TPs can be major contributors to the soil microbial toxicity of pesticides using iprodione and its main TP, 3,5-dichloroaniline, as model compounds. We demonstrated, by measuring functional and structural endpoints, that 3,5-dichloroaniline and not iprodione was associated with adverse effects on soil microorganisms, with nitrification being mostly affected. Pioneering in vitro assays with relevant ammonia-oxidizing bacteria and archaea verified the greater toxicity of 3,5-dichloroaniline. Our findings are expected to advance environmental risk assessment, highlighting the potential of ammonia-oxidizing microorganisms as indicators of the soil microbial toxicity of pesticides and stressing the need to consider the contribution of TPs to pesticide soil microbial toxicity.
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Affiliation(s)
- S Vasileiadis
- Universita Cattolica del Sacro Cuore, Department for Sustainable Food Process, Piacenza, Italy
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
| | - E Puglisi
- Universita Cattolica del Sacro Cuore, Department for Sustainable Food Process, Piacenza, Italy
| | - E S Papadopoulou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
- Aristotle University of Thessaloniki, Faculty of Agriculture Forestry and Natural Environment, School of Agriculture, Pesticide Science Laboratory, Thessaloniki, Greece
| | - G Pertile
- Universita Cattolica del Sacro Cuore, Department for Sustainable Food Process, Piacenza, Italy
| | - N Suciu
- Universita Cattolica del Sacro Cuore, Department for Sustainable Food Process, Piacenza, Italy
| | - R A Pappolla
- Universita Cattolica del Sacro Cuore, Department for Sustainable Food Process, Piacenza, Italy
| | - M Tourna
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
| | - P A Karas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
| | - F Papadimitriou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
| | - A Kasiotakis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
| | - N Ipsilanti
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
| | - A Ferrarini
- Universita Cattolica del Sacro Cuore, Department of Sustainable Crop Production, Piacenza, Italy
| | - S Sułowicz
- University of Silesia, Department of Microbiology, Katowice, Poland
| | - F Fornasier
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per lo Studio delle Relazioni tra Pianti e Suolo, Gorizia, Italy
| | - U Menkissoglu-Spiroudi
- Aristotle University of Thessaloniki, Faculty of Agriculture Forestry and Natural Environment, School of Agriculture, Pesticide Science Laboratory, Thessaloniki, Greece
| | - G W Nicol
- Ecole Centrale de Lyon, Group of Environmental Microbial Genomics, Lyon, France
| | - M Trevisan
- Universita Cattolica del Sacro Cuore, Department for Sustainable Food Process, Piacenza, Italy
| | - D G Karpouzas
- Universita Cattolica del Sacro Cuore, Department for Sustainable Food Process, Piacenza, Italy
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, Greece
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Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006; 442:806-9. [PMID: 16915287 DOI: 10.1038/nature04983] [Citation(s) in RCA: 1128] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 06/19/2006] [Indexed: 01/03/2023]
Abstract
Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.
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Affiliation(s)
- S Leininger
- Department of Biology, University of Bergen, Jahnebakken 5, N-5020 Bergen, Norway
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