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Marini E, De Bernardi A, Tagliabue F, Casucci C, Tiano L, Marcheggiani F, Vaccari F, Taskin E, Puglisi E, Brunetti G, Vischetti C. Copper toxicity on Eisenia fetida in a vineyard soil: a combined study with standard tests, genotoxicity assessment and gut metagenomic analysis. Environ Sci Pollut Res Int 2024; 31:13141-13154. [PMID: 38240981 PMCID: PMC10881645 DOI: 10.1007/s11356-024-31946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
Copper (Cu) toxicity is a pressing concern for several soils, especially in organic viticulture. The objective of this work was to assess Cu toxicity on the non-target organism Eisenia fetida, employing both traditional and novel tools for early identification of Cu-induced damages. In addition to traditional tests like avoidance and reproductive toxicity experiments, other tests such as the single cell gel electrophoresis (SCGE) and gut microbiome analysis were evaluated to identify early and more sensitive pollution biomarkers. Four sub-lethal Cu concentrations were studied, and the results showed strong dose-dependent responses by the earthworm avoidance test and the exceeding of habitat threshold limit at the higher Cu doses. An inverse proportionality was observed between reproductive output and soil Cu concentration. Bioaccumulation was not detected in earthworms; soil concentrations of potentially bioavailable Cu were not affected by E. fetida presence or by time. On the contrary, the SCGE test revealed dose-dependent genotoxicity for the 'tail length' parameter already at the second day of Cu exposition. Gut microbiome analysis a modulation of microbial composition, with the most aboundant families being Pectobateriaceae, Comamonadaceae and Microscillaceae. Bacillaceae increased over time and showed adaptability to copper up to 165 mg/kg, while at the highest dose even the sensitive Acetobacteriaceae family was affected. The research provided new insights into the ecotoxicity of Cu sub-lethal doses highlighting both alterations at earthworms' cellular level and changes in their gut microbiota.
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Affiliation(s)
- Enrica Marini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Arianna De Bernardi
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Francesca Tagliabue
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Cristiano Casucci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Luca Tiano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Fabio Marcheggiani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Filippo Vaccari
- Department for Sustainable Food Process, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Eren Taskin
- Department for Sustainable Food Process, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Gianluca Brunetti
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Future Industries Institute, University of South Australia, Mawson Lakes Boulevard, Mawson Lakes, South Australia, SA5095, Australia
| | - Costantino Vischetti
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
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Wang Y, Zeng X, Zhang Y, Zhang N, Xu L, Wu C. Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil. J Environ Sci (China) 2023; 127:15-29. [PMID: 36522049 DOI: 10.1016/j.jes.2022.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/17/2023]
Abstract
Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.
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Affiliation(s)
- Yanan Wang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Xibai Zeng
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China.
| | - Yang Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Nan Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Liyang Xu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Cuixia Wu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
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Bai J, Yu P, Wen X, Wang W, Jia J, Wang X. Effects of cadmium addition on net nitrogen mineralization processes in the urban constructed wetland soils of a Chinese delta. Environ Geochem Health 2021; 43:1155-1164. [PMID: 32419088 DOI: 10.1007/s10653-020-00597-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Heavy metal pollution is a serious problem in wetland ecosystems, and the toxicity of heavy metals affects microorganisms, thus influencing the biogeochemical process of nitrogen (N). To investigate the effects of heavy metal cadmium (Cd) pollution on N mineralization in urban constructed wetland soils of the Pearl River Delta, a 40-day aerobic incubation experiment was conducted under three Cd addition treatments [no Cd addition (control), low Cd addition (LCA) and high Cd addition (HCA)]. The results showed that compared with the control, the LCA treatment enhanced the soil N mineralization rate (RM), while the HCA treatment inhibited RM, with the average RM values in the control treatment of 0.40 mg kg-1 day-1, LCA treatments (0.66 mg kg-1 day-1), and HCA treatments (0.21 mg kg-1 day-1). The average ammonification rate values in the LCA treatments (- 3.15 to 2.25 mg kg-1 day-1) were higher than those in the HCA treatments (- 2.39 to 0.74 mg kg-1 day-1) and the control treatment (- 0.68 to 0.90 mg kg-1 day-1) (P < 0.05). However, the nitrification values in the HCA treatments (- 0.37 to 3.36 mg kg-1 day-1) were higher than those in the LCA treatments (0.42-1.93 mg kg-1 day-1) and the control treatment (0.20-1.45 mg kg-1 day-1) (P < 0.05). The net N mineralization accumulation generally increased over the entire incubation time in different Cd addition treatments. The percentage of NH4+-N to total inorganic N showed a decrease, while an increase was observed for NO3--N over the incubation time. The urease activities were significantly inhibited in the LCA and HCA treatments and showed a "decreasing before increasing" trend. The abundance of ammonia oxidizing archaea (AOA) was higher in the two Cd addition treatments than the control treatment, and higher in the LCA treatments than in the HCA treatment. AOA was the dominant microorganism in the ammonia oxidation process of N mineralization in constructed wetland soils. The findings of this work indicate that Cd addition has a profound effect on the balance of N mineralization and may further impact the plant productivity and water quality of constructed wetlands.
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Affiliation(s)
- Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China.
| | - Peidong Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiaojun Wen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Jia Jia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
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Corrochano-Monsalve M, González-Murua C, Bozal-Leorri A, Lezama L, Artetxe B. Mechanism of action of nitrification inhibitors based on dimethylpyrazole: A matter of chelation. Sci Total Environ 2021; 752:141885. [PMID: 32890835 DOI: 10.1016/j.scitotenv.2020.141885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 05/25/2023]
Abstract
In agriculture, the applied nitrogen (N) can be lost in the environment in different forms because of microbial transformations. It is of special concern the nitrate (NO3-) leaching and the nitrous oxide (N2O) emissions, due to their negative environmental impacts. Nitrification inhibitors (NIs) based on dimethylpyrazole (DMP) are applied worldwide in order to reduce N losses. These compounds delay ammonium (NH4+) oxidation by inhibiting ammonia-oxidizing bacteria (AOB) growth. However, their mechanism of action has not been demonstrated, which represent an important lack of knowledge to use them correctly. In this work, through chemical and biological analysis, we unveil the mechanism of action of the commonly applied 3,4-dimethyl-1H-pyrazole dihydrogen phosphate (DMPP) and the new DMP-based NI, 2-(3,4-dimethyl-1H-pyrazol-1-yl)-succinic acid (DMPSA). Our results show that DMP and DMPSA form complexes with copper (Cu2+) cations, an indispensable cofactor in the nitrification pathway. Three coordination compounds namely [Cu(DMP)4Cl2] (CuDMP1), [Cu(DMP)4SO4]n (CuDMP2) and [Cu(DMPSA)2]·H2O (CuDMPSA) have been synthesized and chemical and structurally characterized. The CuDMPSA complex is more stable than those containing DMP ligands; however, both NIs show the same nitrification inhibition efficiency in soils with different Cu contents, suggesting that the active specie in both cases is DMP. Our soil experiment reveals that the usual application dose is enough to inhibit nitrification within the range of Cu and Zn contents present in agricultural soils, although their effects vary depending on the content of these elements. As a result of AOB inhibition by these NIs, N2O-reducing bacteria seem to be beneficed in Cu-limited soils due to a reduction in the competence. This opens up the possibility to induce N2O reduction to N2 through Cu fertilization. On the other hand, when fertilizing with micronutrients such as Cu and Zn, the use of NIs could be beneficial to counteract the increase of nitrification derived from their application.
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Affiliation(s)
- Mario Corrochano-Monsalve
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adrián Bozal-Leorri
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Luis Lezama
- Department of Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Beñat Artetxe
- Department of Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Taskin E, Boselli R, Fiorini A, Misci C, Ardenti F, Bandini F, Guzzetti L, Panzeri D, Tommasi N, Galimberti A, Labra M, Tabaglio V, Puglisi E. Combined Impact of No-Till and Cover Crops with or without Short-Term Water Stress as Revealed by Physicochemical and Microbiological Indicators. Biology (Basel) 2021; 10:biology10010023. [PMID: 33401423 PMCID: PMC7824270 DOI: 10.3390/biology10010023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 01/05/2023]
Abstract
Simple Summary Farming systems in which no-till (NT) and cover crops (CC) are preferred as alternatives to conventional practices have the promise of being more resilient and climate smart. Our field study aimed to assess the long-term impact of NT plus CC, with vs. without short-term water stress, on soil microbial biodiversity, enzymatic activities, and the distribution of C and N pools within soil aggregates. We found that the diversity of bacteria and fungi in the soil was positively affected by NT + CC, especially under water stress conditions. Under NT + CC, the presence of important plant growth-promoting rhizobacteria was revealed. Soil enzymatic activity confirmed the depleting impact of conventional tillage. Soil C and N were increased under NT + CC due to their inclusion into large soil aggregates that are beneficial for long-term C and N stabilization in soils. Water stress was found to have detrimental effects on aggregates formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a valuable strategy for sustainable agroecosystems, due to its contribution to soil C and N stabilization while enhancing the biodiversity and enzymes. Abstract Combining no-till and cover crops (NT + CC) as an alternative to conventional tillage (CT) is generating interest to build-up farming systems’ resilience while promoting climate change adaptation in agriculture. Our field study aimed to assess the impact of long-term NT + CC management and short-term water stress on soil microbial communities, enzymatic activities, and the distribution of C and N within soil aggregates. High-throughput sequencing (HTS) revealed the positive impact of NT + CC on microbial biodiversity, especially under water stress conditions, with the presence of important rhizobacteria (e.g., Bradyrhizobium spp.). An alteration index based on soil enzymes confirmed soil depletion under CT. C and N pools within aggregates showed an enrichment under NT + CC mostly due to C and N-rich large macroaggregates (LM), accounting for 44% and 33% of the total soil C and N. Within LM, C and N pools were associated to microaggregates within macroaggregates (mM), which are beneficial for long-term C and N stabilization in soils. Water stress had detrimental effects on aggregate formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a promising alternative to CT, due to the contribution to soil C and N stabilization while enhancing the biodiversity and enzymes.
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Affiliation(s)
- Eren Taskin
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Roberta Boselli
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Andrea Fiorini
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Chiara Misci
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Federico Ardenti
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Francesca Bandini
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Lorenzo Guzzetti
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Davide Panzeri
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Nicola Tommasi
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Andrea Galimberti
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Massimo Labra
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Vincenzo Tabaglio
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
- Correspondence: ; Tel.: +39-05-2359-9222
| | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
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Sillen WMA, Thijs S, Abbamondi GR, De La Torre Roche R, Weyens N, White JC, Vangronsveld J. Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis. Microbiome 2020; 8:127. [PMID: 32907632 PMCID: PMC7488162 DOI: 10.1186/s40168-020-00904-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/03/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver's effects on this environment is lacking because the impact on the natural soil microbiome is not known. In a study assessing the use of nanosilver for phytopathogen control with maize, we analyzed the metatranscriptome of the maize rhizosphere and observed multiple unintended effects of exposure to 100 mg kg-1 nanosilver in soil during a growth period of 117 days. RESULTS We found several unintended effects of nanosilver which could interfere with agricultural systems in the long term. Firstly, the archaea community was negatively impacted with a more than 30% decrease in relative abundance, and as such, their involvement in nitrogen cycling and specifically, nitrification, was compromised. Secondly, certain potentially phytopathogenic fungal groups showed significantly increased abundances, possibly due to the negative effects of nanosilver on bacteria exerting natural biocontrol against these fungi as indicated by negative interactions in a network analysis. Up to 5-fold increases in relative abundance have been observed for certain possibly phytopathogenic fungal genera. Lastly, nanosilver exposure also caused a direct physiological impact on maize as illustrated by increased transcript abundance of aquaporin and phytohormone genes, overall resulting in a stress level with the potential to yield hormetically stimulated plant root growth. CONCLUSIONS This study indicates the occurrence of significant unintended effects of nanosilver use on corn, which could turn out to be negative to crop productivity and ecosystem health in the long term. We therefore highlight the need to include the microbiome when assessing the risk associated with nano-enabled agriculture. Video Abstract.
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Affiliation(s)
- Wouter M. A. Sillen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Gennaro Roberto Abbamondi
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, Pozzuoli, 80078 Napoli, Italy
| | - Roberto De La Torre Roche
- Department Analytical Chemistry, Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT USA
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Jason C. White
- Department Analytical Chemistry, Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT USA
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
- Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Lublin, Poland
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Abd El-Azeem SAEMM. Impacts of Climate Change on Microbial Activity in Agricultural Egyptian Soils. Climate Change Impacts on Agriculture and Food Security in Egypt 2020:97-114. [DOI: 10.1007/978-3-030-41629-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Gustave W, Yuan ZF, Sekar R, Toppin V, Liu JY, Ren YX, Zhang J, Chen Z. Relic DNA does not obscure the microbial community of paddy soil microbial fuel cells. Res Microbiol 2019; 170:97-104. [DOI: 10.1016/j.resmic.2018.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/11/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
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Liu J, Cao W, Jiang H, Cui J, Shi C, Qiao X, Zhao J, Si W. Impact of Heavy Metal Pollution on Ammonia Oxidizers in Soils in the Vicinity of a Tailings Dam, Baotou, China. Bull Environ Contam Toxicol 2018; 101:110-116. [PMID: 29744521 DOI: 10.1007/s00128-018-2345-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
Soil heavy metal pollution has received increasing attention due to their toxicity to soil microorganisms. We have analyzed the effects of heavy metal pollution on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soils in the vicinity of a tailings dam of Baotou region, China. Results showed that AOB were dominated with Nitrosomonas-like clusters, while AOA was dominated by group1.1b (Nitrososphaera cluster). Single Cd and Cr contents, as well as compound heavy metal pollution levels, had a significant negative impact on soil potential nitrification rate and both diversities of AOA and AOB. No clear relationship was found between any single heavy metal and abundance of AOA or AOB. But compound pollution could significantly decrease AOA abundance. The results indicated that heavy metal pollution had an obviously deleterious effect on the abundance, diversity, activity and composition of ammonia oxidizers in natural soils.
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Affiliation(s)
- Jumei Liu
- School of Life Sciences, Inner Mongolia University, Huhhot, 010021, China
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Weiwei Cao
- School of Ecology and Environment, Inner Mongolia University, Huhhot, 010021, China
| | - Haiming Jiang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jing Cui
- School of Life Sciences, Inner Mongolia University, Huhhot, 010021, China
| | - Chunfang Shi
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xiaohui Qiao
- School of Ecology and Environment, Inner Mongolia University, Huhhot, 010021, China
| | - Ji Zhao
- School of Ecology and Environment, Inner Mongolia University, Huhhot, 010021, China.
| | - Wantong Si
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
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Li J, Liu YR, Cui LJ, Hu HW, Wang JT, He JZ. Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime. Microb Ecol 2017; 74:877-887. [PMID: 28492987 DOI: 10.1007/s00248-017-0992-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Increasing efforts have been devoted to exploring the impact of environmental stresses on soil bacterial communities, but the work on the archaeal community is seldom. Here, we constructed microcosm experiments to investigate the responses of archaeal communities to the subsequent dry-rewetting (DW) disturbance in two contrasting soils (fluvo-aquic and red soil) after 6 years of copper pollution. Ten DW cycles were exerted on the two soils with different copper levels, followed by a 6-week recovery period. In both soils, archaeal diversity (Shannon index) in the high copper-level treatments increased over the incubation period, and archaeal community structure changed remarkably as revealed by the non-metric multidimensional scaling ordinations. In both soils, copper pollution altered the response of dominant operational taxonomic units (OTUs) to the DW disturbance. Throughout the incubation and recovery period, the resistance of archaeal abundance to the DW disturbance was higher in the copper-polluted soils than soils without pollution. Taken together, copper pollution altered the response of soil archaeal diversity and community composition to the DW disturbance and increased the resistance of the archaeal abundance. These findings have important implications for understanding soil microbial responses to ongoing environmental change.
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Affiliation(s)
- Jing Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
- Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing, 101399, China
| | - Yu-Rong Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Li-Juan Cui
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
- Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing, 101399, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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11
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Li Y, Adams J, Shi Y, Wang H, He JS, Chu H. Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau. Sci Rep 2017; 7:46407. [PMID: 28401921 PMCID: PMC5388882 DOI: 10.1038/srep46407] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/17/2017] [Indexed: 11/29/2022] Open
Abstract
Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem.
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Affiliation(s)
- Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jonathan Adams
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Hao Wang
- Department of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
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12
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Reis MP, Ávila MP, Keijzer RM, Barbosa FAR, Chartone-Souza E, Nascimento AMA, Laanbroek HJ. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Front Microbiol 2015; 6:898. [PMID: 26379659 PMCID: PMC4553384 DOI: 10.3389/fmicb.2015.00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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Zhang J, Dai Y, Wang Y, Wu Z, Xie S, Liu Y. Distribution of ammonia-oxidizing archaea and bacteria in plateau soils across different land use types. Appl Microbiol Biotechnol 2015; 99:6899-909. [DOI: 10.1007/s00253-015-6625-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/13/2015] [Accepted: 04/16/2015] [Indexed: 10/23/2022]
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14
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Subrahmanyam G, Shen JP, Liu YR, Archana G, He JZ. Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India. Environ Monit Assess 2014; 186:4037-4050. [PMID: 24554021 DOI: 10.1007/s10661-014-3678-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 01/29/2014] [Indexed: 06/03/2023]
Abstract
Soil nitrifiers have been showing an important role in assessing environmental pollution as sensitive biomarkers. In this study, the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in long-term industrial waste effluent (IWE) polluted soils. Three different IWE polluted soils characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) were collected in triplicate along Mahi River basin, Gujarat, Western India. Quantitative numbers of ammonia monooxygenase α-subunit (amoA) genes as well as 16S rRNA genes indicated apparent deleterious effect of IWE on abundance of soil AOA, AOB, bacteria, and archaeal populations. Relatively, AOB was more abundant than AOA in the highly contaminated soil R3, while predominance of AOA was noticed in uncontaminated (R1) and moderately contaminated (R2) soils. Soil potential nitrification rate (PNR) significantly (P < 0.05) decreased in polluted soils R2 and R3. Reduced diversity accompanied by apparent community shifts of both AOB and AOA populations was detected in R2 and R3 soils. AOB were dominated with Nitrosospira-like sequences, whereas AOA were dominated by Thaumarchaeal "group 1.1b (Nitrososphaera clusters)." We suggest that the significant reduction in abundance and diversity AOA and AOB could serve as relevant bioindicators for soil quality monitoring of polluted sites. These results could be further useful for better understanding of AOB and AOA communities in polluted soils.
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Affiliation(s)
- Gangavarapu Subrahmanyam
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
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Angel R, Pasternak Z, Soares MIM, Conrad R, Gillor O. Active and total prokaryotic communities in dryland soils. FEMS Microbiol Ecol 2013; 86:130-8. [PMID: 23730745 DOI: 10.1111/1574-6941.12155] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 05/24/2013] [Accepted: 05/24/2013] [Indexed: 11/30/2022] Open
Abstract
The relationship between total and metabolically active soil microbial communities can change drastically with environment. In dry lands, water availability is a key factor limiting cells' activity. We surveyed the diversity of total and active Archaea and Bacteria in soils ranging from arid desert to Mediterranean forests. Thirty composited soil samples were retrieved from five sites along a precipitation gradient, collected from patches located between and under the dominant perennial plant at each site. Molecular fingerprinting was used to site-sort the communities according of their 16S rRNA genes (total community) and their rRNA (active community) amplified by PCR or RT-PCR from directly extracted soil nucleic acids. The differences between soil samples were much higher in total rather than active microbial communities: differences in DNA fingerprints between sites were 1.2 and 2.5 times higher than RNA differences (for Archaea and Bacteria, respectively). Patch-type discrepancies between DNA fingerprints were on average 2.7-19.7 times greater than RNA differences. Moreover, RNA-based community patterns were highly correlated with soil moisture but did not necessarily follow spatial distribution pattern. Our results suggest that in water-limited environments, the spatial patterns obtained by the analysis of active communities are not as robust as those drawn from total communities.
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Affiliation(s)
- Roey Angel
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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