1
|
Rousset C, Bréfort H, Frederico Fonseca R, Guyerdet G, Bizouard F, Arkoun M, Hénault C. Surprising minimisation of CO 2 emissions from a sandy loam soil over a rye growing period achieved by liming (CaCO 3). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:175973. [PMID: 39245384 DOI: 10.1016/j.scitotenv.2024.175973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024]
Abstract
Agricultural liming improves acidic soils productivity and is considered a lever for mitigating nitrous oxide (N2O) emissions from soils. However, the benefit of liming in reducing soil greenhouse gas (GHG) emissions depends on the evolution of carbon from the calcium carbonate (CaCO3), and on the evolution of soil organic carbon (SOC) after CaCO3 application. The literature, based on limited field data, presents contrasting effects of liming on inorganic- and SOC-derived CO2 emissions, raising concerns that the reduction in N2O emissions could be offset by increased CO2 emissions. Therefore, this study aimed to monitor N2O and CO2 emissions following the application of lime materials to an acidic soil. In situ, we monitored the effect of two liming products (SC = synthetic CaCO3 and MC = marine CaCO3) on soil CO2 emissions and compared this with control plots, during the growing season of a winter rye, using the static chamber method. Soil pH, N2O emissions, mineral nitrogen concentrations, soil moisture and temperature were measured during the experiment, as were plant biomass and SOC (stock and composition) on the day of harvest. Lime addition increased soil pH from 5.7 to around 7.0, kernel yield from 320 to >400 g m-2 and resulted in a significant reduction in soil CO2 emissions by approximately 40 % for both liming materials while it slightly increased N2O emissions, that had nevertheless remained very low during the experiment. SOC at harvest was not significantly affected, while an increase in dissolved organic and inorganic carbon in the soil was observed. Further investigations is needed to clarify the mechanisms explaining these observations and to define conditions where liming application could act as a potential lever for carbon storage. Our results suggest that the IPCC principles, predicting increased CO2 emissions from lime-derived C, may need to be re-examined in the future.
Collapse
Affiliation(s)
- Camille Rousset
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France; Integrative Agroecology, Agroscope, Reckenholzstrasse 191, 8046 Zurich, Switzerland
| | - Henri Bréfort
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Rafael Frederico Fonseca
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Guillaume Guyerdet
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Florian Bizouard
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Agroinnovation International - TIMAC AGRO, Saint-Malo, France
| | - Catherine Hénault
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France.
| |
Collapse
|
2
|
Zhao S, Liu Y, Xu L, Ye J, Zhang X, Xu X, Meng H, Xie W, He H, Wang G, Zhang L. nosZ II/nosZ I ratio regulates the N 2O reduction rates in the eutrophic lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175852. [PMID: 39214369 DOI: 10.1016/j.scitotenv.2024.175852] [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: 07/16/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Nitrous oxide (N2O) is a more potent greenhouse gas with an atmospheric lifetime of 121 years, contributing significantly to climate change and stratospheric ozone depletion. Lakes are hotspots for N2O release due to the imbalance between N2O sources and sinks. N2O-reducing bacteria are the only biological means to mitigate N2O emission, yet their roles in lakes are not well studied. This study investigated the potential for N2O reduction, keystones of typical and atypical N2O-reducing bacterial communities, and their correlations with environmental factors in the sediments of Lake Taihu through microcosm experiments, high-throughput sequencing of the nosZ gene, and statistical modeling. The results showed that potential N2O reduction rates in sediments ranged from 13.71 to 76.95 μg N2O g-1 d-1, with lower rates in December compared to March and July. Correlation analysis indicated that the nosZ II/nosZ I ratio and the trophic lake index (TLI) were the primary factors influencing N2O reduction rates and N2O-reducing bacterial community structures. The genera Pseudogulbenkiania and Ardenticatena were identified as the most abundant typical and atypical N2O-reducing bacteria, respectively, and were also recognized as the keystone taxa. Quantitative real-time PCR (qPCR) results revealed that nosZ II was more abundant than nosZ I in the sediments. Partial least squares path modeling (PLS-PM) further demonstrated that atypical N2O-reducing bacteria had significant positive effects on N2O reduction process in the sediments (p < 0.05). Overall, this study highlights the crucial ecological roles of atypical N2O-reducing bacteria in the sediments of the eutrophic lake of Taihu, underscoring their potential in mitigating N2O emissions.
Collapse
Affiliation(s)
- Sichuan Zhao
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Yihong Liu
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Lu Xu
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Jinliu Ye
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Xiaofeng Zhang
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Xiaoguang Xu
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Han Meng
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China; School of Environment, Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China.
| | - Wenming Xie
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Huan He
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Guoxiang Wang
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China
| | - Limin Zhang
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China; Green Economy Development Institute, Nanjing University of Finance and Economics, Nanjing 210023, PR China
| |
Collapse
|
3
|
Schacksen PS, Nielsen JL. Unraveling the genetic potential of nitrous oxide reduction in wastewater treatment: insights from metagenome-assembled genomes. Appl Environ Microbiol 2024; 90:e0217723. [PMID: 39136491 PMCID: PMC11409646 DOI: 10.1128/aem.02177-23] [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: 12/06/2023] [Accepted: 07/22/2024] [Indexed: 09/19/2024] Open
Abstract
This study explores the genetic landscape of nitrous oxide (N2O) reduction in wastewater treatment plants (WWTPs) by profiling 1,083 high-quality metagenome-assembled genomes (HQ MAGs) from 23 Danish full-scale WWTPs. The focus is on the distribution and diversity of nitrous oxide reductase (nosZ) genes and their association with other nitrogen metabolism pathways. A custom pipeline for clade-specific nosZ gene identification with higher sensitivity revealed 503 nosZ sequences in 489 of these HQ MAGs, outperforming existing Kyoto Encyclopedia of Genes and Genomes (KEGG) module-based methods. Notably, 48.7% of the total 1,083 HQ MAGs harbored nosZ genes, with clade II being predominant, accounting for 93.7% of these genes. Taxonomic profiling highlighted the prevalence of nosZ-containing taxa within Bacteroidota and Pseudomonadota. Chloroflexota exhibited unexpected affiliations with both the sec and tat secretory pathways, and all were found to contain the accessory nosB gene, underscoring the importance of investigating the secretory pathway. The majority of non-denitrifying N2O reducers were found within Bacteroidota and Chloroflexota. Additionally, HQ MAGs with genes for dissimilatory nitrate reduction to ammonium and assimilatory nitrate reduction frequently co-occurred with the nosZ gene. Traditional primers targeting nosZ often focus on short-length amplicons. Therefore, we introduced custom-designed primer sets targeting near-full-length nosZ sequences. These new primers demonstrate efficacy in capturing diverse and well-characterized sequences, providing a valuable tool with higher resolution for future research. In conclusion, this comprehensive analysis enhances our understanding of N2O-reducing organisms in WWTPs, highlighting their potential as N2O sinks with the potential for optimizing wastewater treatment processes and mitigating greenhouse gas emissions. IMPORTANCE This study provides critical insights into the genetic diversity of nitrous oxide reductase (nosZ) genes and the microorganisms harboring them in wastewater treatment plants (WWTPs) by exploring 1,083 high-quality metagenome-assembled genomes (MAGs) from 23 Danish full-scale WWTPs. Despite the pivotal role of nosZ-containing organisms, their diversity remains largely unexplored in WWTPs. Our custom pipeline for detecting nosZ provides near-full-length genes with detailed information on secretory pathways and accessory nos genes. Using these genes as templates, we developed taxonomically diverse clade-specific primers that generate nosZ amplicons for phylogenetic annotation and gene-to-MAG linkage. This approach improves detection and expands the discovery of novel sequences, highlighting the prevalence of non-denitrifying N2O reducers and their potential as N2O sinks. These findings have the potential to optimize nitrogen removal processes and mitigate greenhouse gas emissions from WWTPs by fully harnessing the capabilities of the microbial communities.
Collapse
Affiliation(s)
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| |
Collapse
|
4
|
Mao TQ, Zhang Y, Ou YF, Li XF, Zheng YL, Liang X, Liu M, Hou LJ, Dong HP. Temperature differentially regulates estuarine microbial N 2O production along a salinity gradient. WATER RESEARCH 2024; 267:122454. [PMID: 39293343 DOI: 10.1016/j.watres.2024.122454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 09/04/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024]
Abstract
Nitrous oxide (N2O) is atmospheric trace gas that contributes to climate change and affects stratospheric and ground-level ozone concentrations. Ammonia oxidizers and denitrifiers contribute to N2O emissions in estuarine waters. However, as an important climate factor, how temperature regulates microbial N2O production in estuarine water remains unclear. Here, we have employed stable isotope labeling techniques to demonstrate that the N2O production in estuarine waters exhibited differential thermal response patterns between nearshore and offshore regions. The optimal temperatures (Topt) for N2O production rates (N2OR) were higher at nearshore than offshore sites. 15N-labeled nitrite (15NO2-) experiments revealed that at the nearshore sites dominated by ammonia-oxidizing bacteria (AOB), the thermal tolerance of 15N-N2OR increases with increasing salinity, suggesting that N2O production by AOB-driven nitrifier denitrification may be co-regulated by temperature and salinity. Metatranscriptomic and metagenomic analyses of enriched water samples revealed that the denitrification pathway of AOB is the primary source of N2O, while clade II N2O-reducers dominated N2O consumption. Temperature regulated the expression patterns of nitrite reductase (nirK) and nitrous oxide reductase (nosZ) genes from different sources, thereby influencing N2O emissions in the system. Our findings contribute to understanding the sources of N2O in estuarine waters and their response to global warming.
Collapse
Affiliation(s)
- Tie-Qiang Mao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yong Zhang
- College of Environmental and Resource Sciences, College of Carbon Neutral Modern Industry, Fujian Key Laboratory of Pollution Control and Resource Recycling, Fujian Normal University, Fuzhou 350117, China
| | - Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Xiao-Fei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| |
Collapse
|
5
|
Wang X, Zhang Y, Zhou H, Wu M, Shan J, Yan X. Investigating drivers of N 2 loss and N 2O reducers in paddy soils across China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176287. [PMID: 39288877 DOI: 10.1016/j.scitotenv.2024.176287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 09/02/2024] [Accepted: 09/12/2024] [Indexed: 09/19/2024]
Abstract
Denitrification plays a pivotal role in nitrogen (N) cycling in rice paddies, significantly impacting N loss and greenhouse gas emissions. Accurate quantification of net N2 emissions from paddy fields is therefore essential for improving fertilizer N use efficiency. However, challenges in directly measuring gaseous N2 hinder our understanding of microbially-mediated N loss in paddy soils at large scales. In this study, we investigated net N2 loss and its influencing factors in 45 paddy soils across China using membrane inlet mass spectrometry and N2/Ar technique, complemented by microbial community analysis via metagenomics. Potential N2 loss rates varied from 0.41 to 3.58 nmol N g-1 h-1, with no significant regional differences. However, soils from rice-upland rotation (1.72 ± 0.64 nmol N g-1 h-1) and mono-rice cropping systems (1.41 ± 0.53 nmol N g-1 h-1) exhibited higher N2 loss rates compared to double-rice cropping soils (1.13 ± 0.62 nmol N g-1 h-1). Our results revealed a unimodal relationship between soil N2 loss rates and soil pH, with N2O reducers and soil properties primarily regulating regional variations in N2 loss. Significant ecological differentiation was observed within both nosZ Clade I and Clade II, with soil pH emerging as the key factor shaping their community composition. Specifically, in rice-upland rotations, soil moisture and pH significantly influenced nosZ Clade I, while in double-rice cropping systems, soil texture and pH were the main factors affecting nosZ Clade II, thereby driving N2 loss. These findings enhance our understanding of N2 loss dynamics in paddy soil ecosystems, underscoring the critical role of N2O reducers on microbial-derived N2 loss and highlighting the importance of developing strategies to mitigate N2O emissions by balancing N2 loss through the manipulation of N2O-reducing and N2O-producing microbes.
Collapse
Affiliation(s)
- Xiaomin Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yumeng Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Han Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
6
|
Hernández-Magaña E, Kraft B. Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion. Front Microbiol 2024; 15:1410251. [PMID: 39296305 PMCID: PMC11408285 DOI: 10.3389/fmicb.2024.1410251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 08/15/2024] [Indexed: 09/21/2024] Open
Abstract
Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N2O coupled with oxygen accumulation, N2O has been proposed as an intermediate in this novel archaeal pathway. In this study, we spiked N2O to oxygen-depleted incubations with pure cultures of two marine AOA isolates that were performing NO dismutation. By using combinations of N compounds with different isotopic signatures (15NO2 - pool +44N2O spike and 14NO2 - pool +46N2O spike), we evaluated the N2O spike effects on the production of oxygen and the isotopic signature of N2 and N2O. The experiments confirmed that N2O is an intermediate in NO dismutation by AOA, distinguishing it from similar pathways in other microbial clades. Furthermore, we showed that AOA rapidly reduce high concentrations of spiked N2O to N2. These findings advance our understanding of microbial N2O production and consumption in oxygen-depleted settings and highlight AOA as potentially important key players in N2O turnover.
Collapse
Affiliation(s)
- Elisa Hernández-Magaña
- Nordcee, Department of Biology, Faculty of Sciences, Nordcee, University of Southern Denmark, Odense, Denmark
| | - Beate Kraft
- Nordcee, Department of Biology, Faculty of Sciences, Nordcee, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
7
|
Múgica L, Le Roux X, San Emeterio L, Cantarel A, Durán M, Gervaix J, Creuzé des Châtelliers C, Canals RM. Pyric herbivory decreases soil denitrification despite increased nitrate availability in a temperate grassland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121695. [PMID: 38968891 DOI: 10.1016/j.jenvman.2024.121695] [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: 05/23/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Pyric herbivory, the combination of controlled burning and targeted grazing, is an effective strategy for restoring abandoned, shrub-encroached rangelands to open ecosystems. This practice may impact soil nitrogen pools by altering soil nitrification and denitrification rates, and may lead to an increase of nitrogen losses through nitrate leaching and N-gas emissions. This research, located in the south-western Pyrenees, investigated the effects of pyric herbivory on soil nitrification and denitrification potentials and mineral nitrogen content in a gorse-encroached temperate rangeland six months after the burning was implemented. The study included three treatments: high-severity burning plus grazing, low-severity burning plus grazing, and unburned and ungrazed areas (control). We measured soil nitrification and denitrification potentials (net and gross), the limitation of denitrifiers by nitrogen or organic carbon, and the abundance of nitrite- and nitrous oxide-reducing bacteria. Additional soil and vegetation data complemented these measurements. Results showed that pyric herbivory did not significantly affect nitrification potential, which was low and highly variable. However, it decreased gross denitrification potential and nitrous oxide reduction to dinitrogen in high-severely burned areas compared to the control. Denitrification rates directly correlated with microbial biomass nitrogen, soil organic carbon, soil water content and abundance of nirS-harbouring bacteria. Contrary to the expected, soil nitrate availability did not directly influence denitrification despite being highest in burned areas. Overall, the study suggests that pyric herbivory does not significantly affect mid-term nitrification rates in temperate open ecosystems, but may decrease denitrification rates in intensely burned areas. These findings highlight the importance of assessing the potential impacts of land management practices, such as pyric herbivory, on soil nutrient cycling and ecosystem functioning.
Collapse
Affiliation(s)
- Leire Múgica
- Instituto de Innovación y Sostenibilidad en la Cadena Agroalimentaria (IS-FOOD), Departamento de Agronomía, Biotecnología y Alimentación, Universidad Pública de Navarra (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain; Laboratoire d'Ecologie Microbienne LEM, INRAE, CNRS, Université Lyon 1, Université de Lyon, VetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, 69622, Villeurbanne, France.
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne LEM, INRAE, CNRS, Université Lyon 1, Université de Lyon, VetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, 69622, Villeurbanne, France
| | - Leticia San Emeterio
- Instituto de Innovación y Sostenibilidad en la Cadena Agroalimentaria (IS-FOOD), Departamento de Agronomía, Biotecnología y Alimentación, Universidad Pública de Navarra (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - Amélie Cantarel
- Laboratoire d'Ecologie Microbienne LEM, INRAE, CNRS, Université Lyon 1, Université de Lyon, VetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, 69622, Villeurbanne, France
| | - María Durán
- Instituto de Innovación y Sostenibilidad en la Cadena Agroalimentaria (IS-FOOD), Departamento de Agronomía, Biotecnología y Alimentación, Universidad Pública de Navarra (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - Jonathan Gervaix
- Laboratoire d'Ecologie Microbienne LEM, INRAE, CNRS, Université Lyon 1, Université de Lyon, VetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, 69622, Villeurbanne, France
| | - Charline Creuzé des Châtelliers
- Laboratoire d'Ecologie Microbienne LEM, INRAE, CNRS, Université Lyon 1, Université de Lyon, VetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, 69622, Villeurbanne, France
| | - Rosa M Canals
- Instituto de Innovación y Sostenibilidad en la Cadena Agroalimentaria (IS-FOOD), Departamento de Agronomía, Biotecnología y Alimentación, Universidad Pública de Navarra (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| |
Collapse
|
8
|
Pathak A, Marquez M, Stothard P, Chukwujindu C, Su JQ, Zhou Y, Zhou XY, Jagoe CH, Chauhan A. A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential. iScience 2024; 27:110193. [PMID: 38984199 PMCID: PMC11231605 DOI: 10.1016/j.isci.2024.110193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/09/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.
Collapse
Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Mario Marquez
- Texas Sea Grant College Program, 4115 TAMU Eller O&M 306, Texas A&M University, College Station, TX 77843, USA
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, General Services Bldg, Edmonton, AB 2-31 T6G 2H1, Canada
| | - Christian Chukwujindu
- Material & Energy Technology Department, Projects Development Institute, Emene Industrial Layout, Enugu-Nigeria 400104
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Yuan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Charles H. Jagoe
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| |
Collapse
|
9
|
Liu B, Ahnemann H, Arlotti D, Huyghebaert B, Cuperus F, Tebbe CC. Impact of diversified cropping systems and fertilization strategies on soil microbial abundance and functional potentials for nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172954. [PMID: 38723956 DOI: 10.1016/j.scitotenv.2024.172954] [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: 02/16/2024] [Revised: 04/09/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024]
Abstract
Diversified cropping systems and fertilization strategies were proposed to enhance the abundance and diversity of the soil microbiome, thereby stabilizing their beneficial services for maintaining soil fertility and supporting plant growth. Here, we assessed across three different long-term field experiments in Europe (Netherlands, Belgium, Northern Germany) whether diversified cropping systems and fertilization strategies also affect their functional gene abundance. Soil DNA was analyzed by quantitative PCR for quantifying bacteria, archaea and fungi as well as functional genes related to nitrogen (N) transformations; including bacterial and archaeal nitrification (amoA-bac,arch), three steps of the denitrification process (nirK, nirS and nosZ-cladeI,II) and N2 assimilation (nifH), respectively. Crop diversification and fertilization strategies generally enhanced soil total carbon (C), N and microbial abundance, but with variation between sites. Overall effects of diversified cropping systems and fertilization strategies on functional genes were much stronger than on the abundance of bacteria, archaea and fungi. The legume-based cropping systems showed great potential not only in stimulating the growth of N-fixing microorganisms but also in boosting downstream functional potentials for N cycling. The sorghum-based intercropping system suppressed soil ammonia oxidizing prokaryotes. N fertilization reduced the abundance of nitrifiers and denitrifiers except for ammonia-oxidizing bacteria, while the application of the synthetic nitrification inhibitor DMPP combined with mineral N reduced growth of both ammonia-oxidizing bacteria and archaea. In conclusion, this study demonstrates a strong impact of diversified agricultural practices on the soil microbiome and their functional potentials mediating N transformations.
Collapse
Affiliation(s)
- Bei Liu
- Thünen Institute of Biodiversity, Bundesallee 65, D-38116 Braunschweig, Germany
| | - Hauke Ahnemann
- Chamber of Agriculture, Lower Saxony, Vor dem Zoll 2, D-31582 Nienburg, Germany
| | - Donatienne Arlotti
- Walloon agricultural Research Centre; Soil, water and integrated production Unit, 4, rue du Bordia, B-5030 Gembloux, Belgium
| | - Bruno Huyghebaert
- Walloon agricultural Research Centre; Soil, water and integrated production Unit, 4, rue du Bordia, B-5030 Gembloux, Belgium
| | - Fogelina Cuperus
- Wageningen University & Research, Edelhertweg 1, NL-8219 PH Lelystad, Netherlands
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, D-38116 Braunschweig, Germany.
| |
Collapse
|
10
|
Song K, Wang S, Xu X, Ma J, Yang Y, Zeng Y, Li J, Zhou X, Zhou Y. Benthic clade II-type nitrous oxide reducers suppress nitrous oxide emissions in shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172908. [PMID: 38697552 DOI: 10.1016/j.scitotenv.2024.172908] [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: 02/22/2024] [Revised: 04/07/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Shallow lakes, recognized as hotspots for nitrogen cycling, contribute to the emission of the potent greenhouse gas nitrous oxide (N2O), but the current emission estimates for this gas have a high degree of uncertainty. However, the role of N2O-reducing bacteria (N2ORB) as N2O sinks and their contribution to N2O reduction in aquatic ecosystems in response to N2O dynamics have not been determined. Here, we investigated the N2O dynamics and microbial processes in the nitrogen cycle, which included both N2O production and consumption, in five shallow lakes spanning approximately 500 km. The investigated sites exhibited N2O oversaturation, with excess dissolved N2O concentrations (ΔN2O) ranging from 0.55 ± 0.61 to 53.17 ± 15.75 nM. Sediment-bound N2O (sN2O) was significantly positively correlated with the nitrate concentration in the overlying water (p < 0.05), suggesting that nitrate accumulation contributes to benthic N2O generation. High N2O consumption activity (RN2O) corresponded to low ΔN2O. In addition, a significant negative correlation was found between RN2O and nir/nosZ, showing that bacteria encoding nosZ contributed to N2O consumption in the benthic sediments. Redundancy analysis indicated that benthic functional genes effectively reflected the variations in RN2O and ∆N2O. qPCR analysis revealed that the clade II nosZ gene was more sensitive to ΔN2O than the clade I nosZ gene. Furthermore, four novel genera of potential nondenitrifying N2ORB were identified based on metagenome-assembled genome analysis. These genera, which are affiliated with clade II, lack genes responsible for N2O production. Collectively, benthic N2ORB, especially for clade II-type N2ORB, harnesses N2O consumption activity leading to low N2O emissions from shallow lakes. This study advances our knowledge of the role of benthic clade II-type N2ORB in regulating N2O emissions in shallow lakes.
Collapse
Affiliation(s)
- Kang Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaoguang Xu
- School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Jie Ma
- Ministry of Ecology and Environment, Nanjing Institute of Environment Sciences, Nanjing 210042, China
| | - Yuxuan Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Yuli Zeng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jining Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaohong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yiwen Zhou
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
11
|
Govednik A, Eler K, Mihelič R, Suhadolc M. Mineral and organic fertilisation influence ammonia oxidisers and denitrifiers and nitrous oxide emissions in a long-term tillage experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172054. [PMID: 38569950 DOI: 10.1016/j.scitotenv.2024.172054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Nitrous oxide (N2O) emissions from different agricultural systems have been studied extensively to understand the mechanisms underlying their formation. While a number of long-term field experiments have focused on individual agricultural practices in relation to N2O emissions, studies on the combined effects of multiple practices are lacking. This study evaluated the effect of different tillage [no-till (NT) vs. conventional plough tillage (CT)] in combination with fertilisation [mineral (MIN), compost (ORG), and unfertilised control (CON)] on seasonal N2O emissions and the underlying N-cycling microbial community in one maize growing season. Rainfall events after fertilisation, which resulted in increased soil water content, were the main triggers of the observed N2O emission peaks. The highest cumulative emissions were measured in MIN fertilisation, followed by ORG and CON fertilisation. In the period after the first fertilisation CT resulted in higher cumulative emissions than NT, while no significant effect of tillage was observed cumulatively across the entire season. A higher genetic potential for N2O emissions was observed under NT than CT, as indicated by an increased (nirK + nirS)/(nosZI + nosZII) ratio. The mentioned ratio under NT decreased in the order CON > MIN > ORG, indicating a higher N2O consumption potential in the NT-ORG treatment, which was confirmed in terms of cumulative emissions. The AOB/16S ratio was strongly affected by fertilisation and was higher in the MIN than in the ORG and CON treatments, regardless of the tillage system. Multiple regression has revealed that this ratio is one of the most important variables explaining cumulative N2O emissions, possibly reflecting the role of bacterial ammonia oxidisers in minerally fertilised soil. Although the AOB/16S ratio aligned well with the measured N2O emissions in our experimental field, the higher genetic potential for denitrification expressed by the (nirK + nirS)/(nosZI + nosZII) ratio in NT than CT was not realized in the form of increased emissions. Our results suggest that organic fertilisation in combination with NT shows a promising combination for mitigating N2O emissions; however, addressing the yield gap is necessary before incorporating it in recommendations for farmers.
Collapse
Affiliation(s)
- Anton Govednik
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Klemen Eler
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Rok Mihelič
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Marjetka Suhadolc
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
| |
Collapse
|
12
|
Pessi IS, Delmont TO, Zehr JP, Hultman J. Discovery of Eremiobacterota with nifH homologues in tundra soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13277. [PMID: 38881156 PMCID: PMC11180709 DOI: 10.1111/1758-2229.13277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 06/18/2024]
Abstract
We describe the genome of an Eremiobacterota population from tundra soil that contains the minimal set of nif genes needed to fix atmospheric N2. This putative diazotroph population, which we name Candidatus Lamibacter sapmiensis, links for the first time Eremiobacterota and N2 fixation. The integrity of the genome and its nif genes are well supported by both environmental and taxonomic signals. Ca. Lamibacter sapmiensis contains three nifH homologues and the complementary set of nifDKENB genes that are needed to assemble a functional nitrogenase. The putative diazotrophic role of Ca. Lamibacter sapmiensis is supported by the presence of genes that regulate N2 fixation and other genes involved in downstream processes such as ammonia assimilation. Similar to other Eremiobacterota, Ca. Lamibacter sapmiensis encodes the potential for atmospheric chemosynthesis via CO2 fixation coupled with H2 and CO oxidation. Interestingly, the presence of a N2O reductase indicates that this population could play a role as a N2O sink in tundra soils. Due to the lack of activity data, it remains uncertain if Ca. Lamibacter sapmiensis is able to assemble a functional nitrogenase and participate in N2 fixation. Confirmation of this ability would be a testament to the great metabolic versatility of Eremiobacterota, which appears to underlie their ecological success in cold and oligotrophic environments.
Collapse
Affiliation(s)
- Igor S. Pessi
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiHelsinkiFinland
- Marine and Freshwater SolutionsFinnish Environment Institute (Syke)HelsinkiFinland
| | | | - Jonathan P. Zehr
- Ocean Sciences DepartmentUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | - Jenni Hultman
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiHelsinkiFinland
- Natural Resources UnitNatural Resources Institute Finland (Luke)HelsinkiFinland
| |
Collapse
|
13
|
He Q, Qin H, Yang L, Tan W, Ji D, Zhang J, Zhang X. N 2O emission in temperate seagrass meadows: Fluxes, pathway and molecular mechanism. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106542. [PMID: 38788475 DOI: 10.1016/j.marenvres.2024.106542] [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: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Seagrass meadows act as filters for nitrogen in coastal areas, but whether they are a source or sink for N2O has been still controversy. Additionally, the production pathways of N2O as well as the microbial driving mechanism in seagrass meadows are seldom reported. In this study, the air-sea fluxes, sediment release potential, and production pathway of N2O in a temperate Zostera marina and Z. japonica mixed meadow were investigated by using gas chromatography and 15N isotopic tracing methods. The qPCR and metagenome sequencing were used to compare the difference in functional gene abundance and expression between seagrass vegetated and non-grass sediments. The results showed that the N2O air-sea fluxes in the meadow ranged from -1.97 to -1.77 nmol m⁻2 h⁻1, which was slightly lower in the seagrass region than in the adjacent bare region. Seagrass sediment N2O release potential dramatically increased after warming and nitrogen enrichment treatments. Heterotrophic nitrification was firstly investigated in seagrass meadows, and the process (26.80%-62.41%) and denitrification (37.55%-72.83%) contributed significantly to N2O production in the meadow, affected deeply by sediment organic content, while the contribution of autotrophic nitrification can be neglected. Compared with the bare sediments, the ammonia monooxygenase genes amoA, amoB and amoC, and nitrite oxidoreductase genes nxrA and nxrB, as well as nitrite reductase gene nirS and nitric oxide reductase gene norB were down-regulated, while the nitrous oxide reductase gene nosZ was up-regulated in the seagrass sediments, explaining less N2O emission in seagrass regions from the perspective of molecular. The nosZII-bearing bacteria like Bacteroidia, Polyangia, Anaerolineae, and Verrucomicrobiae could play important roles in N2O reduction in the seagrass meadow. The result is of great significance for highlighting the ability of seagrass meadows to mitigate climate changes.
Collapse
Affiliation(s)
- Qianling He
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Huawei Qin
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, China
| | - Lin Yang
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Wenwen Tan
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Daode Ji
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Jianbai Zhang
- Yantai Marine Economic Research Institute, Yantai, 264000, China.
| | - Xiaoli Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
| |
Collapse
|
14
|
Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [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: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
Collapse
Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| |
Collapse
|
15
|
Intrator N, Jayakumar A, Ward BB. Aquatic nitrous oxide reductase gene ( nosZ) phylogeny and environmental distribution. Front Microbiol 2024; 15:1407573. [PMID: 38835481 PMCID: PMC11148229 DOI: 10.3389/fmicb.2024.1407573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the gene nosZ. Organisms that contain nosZ are the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades of nosZ (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of nosZ containing organisms in the environment. A database of over 11,000 nosZ sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I nosZ genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I nosZ genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the nosZ gene displays regional and environmental separation. This study expands the known diversity of nosZ genes and provides a clearer picture of how the clades and phylogeny of nosZ organisms are distributed across diverse environments.
Collapse
Affiliation(s)
- Naomi Intrator
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| |
Collapse
|
16
|
Deng M, Yeerken S, Wang Y, Li L, Li Z, Oon YS, Oon YL, Xue Y, He X, Zhao X, Song K. Greenhouse gases emissions from aquaculture ponds: Different emission patterns and key microbial processes affected by increased nitrogen loading. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172108. [PMID: 38556013 DOI: 10.1016/j.scitotenv.2024.172108] [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: 01/09/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Global aquaculture production is expected to rise to meet the growing demand for food worldwide, potentially leading to increased anthropogenic greenhouse gases (GHG) emissions. As the demand for fish protein increases, so will stocking density, feeding amounts, and nitrogen loading in aquaculture ponds. However, the impact of GHG emissions and the underlying microbial processes remain poorly understood. This study investigated the GHG emission characteristics, key microbial processes, and environmental drivers underlying GHG emissions in low and high nitrogen loading aquaculture ponds (LNP and HNP). The N2O flux in HNP (43.1 ± 11.3 μmol m-2 d-1) was significantly higher than in LNP (-11.3 ± 25.1 μmol m-2 d-1), while the dissolved N2O concentration in HNP (52.8 ± 7.1 nmol L-1) was 150 % higher than in LNP (p < 0.01). However, the methane (CH4) and carbon dioxide (CO2) fluxes and concentrations showed no significant differences (p > 0.05). N2O replaced CH4 as the main source of Global Warming Potential in HNP. Pond sediments acted as a sink for N2O but a source for CH4 and CO2. The △N2O/(△N2O + △N2) in HNP (0.015 ± 0.007 %) was 7.7-fold higher than in LNP (0.002 ± 0.001 %) (p < 0.05). The chemical oxygen demand to NO2-N ratio was the most important environmental factor explaining the variability of N2O fluxes. Ammonia-oxidizing bacteria driven nitrification in water was the predominant N2O source, while comammox-driven nitrification and nosZII-driven N2O reduction in water were key processes for reducing N2O emission in LNP but decreased in HNP. The strong CH4 oxidization by Methylocystis and CO2 assimilation by algae resulted in low CH4 emissions and CO2 sink in the aquaculture pond. The Mantel test indicated that HNP increased N2O fluxes mainly through altering functional genes composition in water and sediment. Our findings suggest that there is a significant underestimation of N2O emissions without considering the significantly increased △N2O/(△N2O + △N2) caused by increased nitrogen loading.
Collapse
Affiliation(s)
- Min Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Senbati Yeerken
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuren Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhouyang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yoong-Sin Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yoong-Ling Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yunpeng Xue
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xugang He
- College of Fisheries, Huazhong Agricultural University, Wuhan 430072, China
| | - Xiaoli Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Kang Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
17
|
Zhang S, Xia X, Yu L, Liu S, Li X, Wang J, Zheng Y, Han L, Tan Q, Yang Z. Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates. Environ Microbiol 2024; 26:e16622. [PMID: 38757466 DOI: 10.1111/1462-2920.16622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024]
Abstract
Microbial communities that reduce nitrous oxide (N2O) are divided into two clades, nosZI and nosZII. These clades significantly differ in their ecological niches and their implications for N2O emissions in terrestrial environments. However, our understanding of N2O reducers in aquatic systems is currently limited. This study investigated the relative abundance and diversity of nosZI- and nosZII-type N2O reducers in rivers and their impact on N2O emissions. Our findings revealed that stream sediments possess a high capacity for N2O reduction, surpassing N2O production under high N2O/NO3- ratio conditions. This study, along with others in freshwater systems, demonstrated that nosZI marginally dominates more often in rivers. While microbes containing either nosZI and nosZII were crucial in reducing N2O emissions, the net contribution of nosZII-containing microbes was more significant. This can be attributed to the nir gene co-occurring more frequently with the nosZI gene than with the nosZII gene. The diversity within each clade also played a role, with nosZII species being more likely to function as N2O sinks in streams with higher N2O concentrations. Overall, our findings provide a foundation for a better understanding of the biogeography of stream N2O reducers and their effects on N2O emissions.
Collapse
Affiliation(s)
- Sibo Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Leilei Yu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Shaoda Liu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xiaokang Li
- School of Environmental and Material Engineering, Yantai University, Yantai, China
| | - Junfeng Wang
- Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lanfang Han
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Qian Tan
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| |
Collapse
|
18
|
Xu Z, Gao X, Li G, Nghiem LD, Luo W, Zhang F. Microbial Sources and Sinks of Nitrous Oxide during Organic Waste Composting. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7367-7379. [PMID: 38644786 DOI: 10.1021/acs.est.3c10341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Composting is widely used for organic waste management and is also a major source of nitrous oxide (N2O) emission. New insight into microbial sources and sinks is essential for process regulation to reduce N2O emission from composting. This study used genome-resolved metagenomics to decipher the genomic structures and physiological behaviors of individual bacteria for N2O sources and sinks during composting. Results showed that several nosZ-lacking denitrifiers in feedstocks drove N2O emission at the beginning of the composting. Such emission became negligible at the thermophilic stage, as high temperatures inhibited all denitrifiers for N2O production except for those containing nirK. The nosZ-lacking denitrifiers were notably enriched to increase N2O production at the cooling stage. Nevertheless, organic biodegradation limited energy availability for chemotaxis and flagellar assembly to restrain nirKS-containing denitrifiers for nitrate reduction toward N2O sources but insignificantly interrupt norBC- and nosZ-containing bacteria (particularly nosZ-containing nondenitrifiers) for N2O sinks by capturing N2O and nitric oxide (NO) for energy production, thereby reducing N2O emission at the mature stage. Furthermore, nosZII-type bacteria included all nosZ-containing nondenitrifiers and dominated N2O sinks. Thus, targeted strategies can be developed to restrict the physiological behaviors of nirKS-containing denitrifiers and expand the taxonomic distribution of nosZ for effective N2O mitigation in composting.
Collapse
Affiliation(s)
- Zhicheng Xu
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xingzu Gao
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo 2007, NSW, Australia
| | - Wenhai Luo
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Fusuo Zhang
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| |
Collapse
|
19
|
Hellman M, Juhanson J, Wallnäs F, Herbert RB, Hallin S. Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120607. [PMID: 38537471 DOI: 10.1016/j.jenvman.2024.120607] [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: 11/09/2023] [Revised: 02/08/2024] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.
Collapse
Affiliation(s)
- Maria Hellman
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Jaanis Juhanson
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Felicia Wallnäs
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Roger B Herbert
- Uppsala University, Department of Earth Sciences, Villavägen 16, 75226, Uppsala, Sweden.
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| |
Collapse
|
20
|
Yang N, Lv Y, Ji M, Wu S, Zhang Y. High hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions. Nat Commun 2024; 15:2473. [PMID: 38503798 PMCID: PMC10951307 DOI: 10.1038/s41467-024-46897-2] [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: 07/12/2023] [Accepted: 03/13/2024] [Indexed: 03/21/2024] Open
Abstract
Hadal trenches are extreme environments situated over 6000 m below sea surface, where enormous hydrostatic pressure affects the biochemical cycling of elements. Recent studies have indicated that hadal trenches may represent a previously overlooked source of fixed nitrogen loss; however, the mechanisms and role of hydrostatic pressure in this process are still being debated. To this end, we investigate the effects of hydrostatic pressure (0.1 to 115 MPa) on the chemical profile, microbial community structure and functions of surface sediments from the Mariana Trench using a Deep Ocean Experimental Simulator supplied with nitrate and oxygen. We observe enhanced denitrification activity at high hydrostatic pressure under oxic conditions, while the anaerobic ammonium oxidation - a previously recognized dominant nitrogen loss pathway - is not detected. Additionally, we further confirm the simultaneous occurrence of nitrate reduction and aerobic respiration using a metatranscriptomic dataset from in situ RNA-fixed sediments in the Mariana Trench. Taken together, our findings demonstrate that hydrostatic pressure can influence microbial contributions to nitrogen cycling and that the hadal trenches are a potential nitrogen loss hotspot. Knowledge of the influence of hydrostatic pressure on anaerobic processes in oxygenated surface sediments can greatly broaden our understanding of element cycling in hadal trenches.
Collapse
Affiliation(s)
- Na Yang
- School of Oceanography; Shanghai Key Laboratory of Polar Life and Environment Sciences; MOE Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Shanghai, China
| | - Yongxin Lv
- School of Oceanography; Shanghai Key Laboratory of Polar Life and Environment Sciences; MOE Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Shanghai, China
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Shiguo Wu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Science, Sanya, China
| | - Yu Zhang
- School of Oceanography; Shanghai Key Laboratory of Polar Life and Environment Sciences; MOE Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Shanghai, China.
- Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
| |
Collapse
|
21
|
Jiang L, Liu S, Wang S, Sun L, Zhu G. Effect of tillage state of paddy soils with heavy metal pollution on the nosZ gene of N 2O reductase. J Environ Sci (China) 2024; 137:469-477. [PMID: 37980031 DOI: 10.1016/j.jes.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 11/20/2023]
Abstract
Paddy soils are an important source of atmospheric nitrous oxide (N2O). However, numerous studies have focused on N2O production during the soil tillage period, neglecting the N2O production during the dry fallow period. In this study, we conducted an incubation experiment using the acetylene inhibition technique to investigate N2O emission and reduction rates of paddy soil profiles (0-1 m) from Guangdong Province and Jinlin Province in China, with different heavy-metal pollution levels. The abundance and community structures of denitrifying bacteria were determined via quantitative-PCR and Illumina MiSeq sequencing of nosZ, nirK, and nirS genes. Our results showed that the potential N2O emission rate, N2O production rate, and denitrification rate have decreased with increasing soil vertical depth and heavy-metal pollution. More importantly, we found that the functional gene type of N2O reductase switched with the tillage state of paddy soils, which clade Ⅱ nosZ genes were the dominant gene during the tillage period, while clade Ⅰ nosZ genes were the dominant gene during the dry fallow period. The heavy-metal pollution has less effect on the niche differentiation of the nosZ gene. The N2O emission rate was significantly regulated by the genus Bradyhizobium, which contains both N2O reductase and nitrite reductase genes. Our findings suggests that the nosZ gene of N2O reductase can significantly impact the N2O emission from paddy soils.
Collapse
Affiliation(s)
- Liping Jiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiguang Liu
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libo Sun
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
22
|
Zhong L, Li X, Sun Y, Xiao H, Tang Y, Wang R, Su X. Effects of microplastics on N 2O production and reduction potential in crop soils of northern China. CHEMOSPHERE 2024; 351:141256. [PMID: 38246503 DOI: 10.1016/j.chemosphere.2024.141256] [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: 08/22/2023] [Revised: 12/27/2023] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Microplastics (MPs) pollution are found to be increasing in vegetable soils and potentially affecting N2O production and their associated pathways; however, its specific effects remain unclear. Here, we selected two common MPs, PE and PP at four different concentration levels of 0, 0.5, 1.5 and 3%, and conducted several incubation experiments aiming to explore soil bacterial and fungal N2O production. Results showed that the bacteria were the main contributors for the production of N2O, regardless of the absence or presence of MPs; and its contribution was decreased with increasing concentrations of PE and PP. The nosZ clade I and II genes were positively correlated with N2O reduction rates, indicating a combined regulation on soil N2O reduction. PE significantly inhibited the bacterial nitrification and denitrification, but did not affect the total N2O production rates; while PP significantly reduced both the bacterial and fungal N2O production rates. The resistance of fungal N2O production to MPs pollution was stronger than that of the bacterial N2O production. It highlights that the MPs pollution could reduce the potential of N2O production and reduction, and thus disturb soil nitrogen cycling system; while the inhibition on N2O production via bacteria and fungi varies with different types of MPs. This study is conducive to an improved and more comprehensive understanding of the ecological impacts of MPs within the agroecosystem.
Collapse
Affiliation(s)
- Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China.
| | - Xinhao Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Yuru Sun
- Beijing Construction Engineering Group Environmental Remediation Co., Ltd, National Engineering Laboratory for Site Remediation Technologies, Beijing, 100015, China
| | - Hui Xiao
- Institute of Agricultural Resources and Environment, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Yafang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Ruying Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xiaoxuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
23
|
Lewin S, Wende S, Wehrhan M, Verch G, Ganugi P, Sommer M, Kolb S. Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168794. [PMID: 38000749 DOI: 10.1016/j.scitotenv.2023.168794] [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: 05/30/2023] [Revised: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.
Collapse
Affiliation(s)
- Simon Lewin
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Sonja Wende
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Marc Wehrhan
- Working Group Landscape Pedology, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Gernot Verch
- Experimental Station Dedelow, Experimental Infrastructure Platform, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Paola Ganugi
- Department of Agricultural, Forest and Food sciences, University of Turin, Grugliasco, Italy
| | - Michael Sommer
- Working Group Landscape Pedology, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany; Institute of Environmental Science & Geography, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Steffen Kolb
- Working Group Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany; Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany.
| |
Collapse
|
24
|
Zhang F, Gu Z, Wang H, Wang R, Qing J, Xu X, Baoyin T, Zhong L, Rui Y, Li FY. Short term grazing increased growing-season N 2O production and decreased its reduction potential by reducing the abundance and expression of nosZ clade II gene in a semi-arid steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168361. [PMID: 37944603 DOI: 10.1016/j.scitotenv.2023.168361] [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: 05/20/2023] [Revised: 10/23/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
Understanding nitrous oxide (N2O) production as well as reduction in response to grazing and mowing is essential for designing better management strategies to improve sustainability of grassland ecosystems. We evaluated how four years of grazing or mowing altered N2O production and reduction potential, gene abundance, and expression of microbial functional groups pertinent to N2O production in situ on a typical grassland in Inner Mongolia. In our study, we found that grazing dramatically raised soil ammonium (NH4+-N) and nitrate (NO3--N) concentrations, AOB gene abundance and potential of N2O production through nitrification (NN2O) and denitrification (DN2O) in summer, but lessened the expression of nosZ clade II gene in all seasons. Mowing had minor effect on soil inorganic nitrogen (N) concentrations. Mowing diminished the quantity of denitrification genes (narG and nosZ), expression of nosZ and nosZ clade II genes, and DN2O concentration. The expression and abundance of nosZ clade II gene were related to DN2. These results suggested that short-term grazing could enhance N2O production potential in peak growing season, while the reduction in abundance and expression of nosZ calde II gene might be an important contributor to the enhanced N2O production of semi-arid typical steppe grasslands.
Collapse
Affiliation(s)
- Feifan Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Zhibin Gu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Hongyue Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Ruying Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jinwu Qing
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing 100101, China
| | - Taogetao Baoyin
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
| | - Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Yichao Rui
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
| |
Collapse
|
25
|
Bell E, Chen J, Richardson WDL, Fustic M, Hubert CRJ. Denitrification genotypes of endospore-forming Bacillota. ISME COMMUNICATIONS 2024; 4:ycae107. [PMID: 39263550 PMCID: PMC11388526 DOI: 10.1093/ismeco/ycae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024]
Abstract
Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR, and sNOR) that may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.
Collapse
Affiliation(s)
- Emma Bell
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Jianwei Chen
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - William D L Richardson
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Milovan Fustic
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
- Department of Geology, Nazarbayev University, 53 Kabanbay Batyr Ave, Astana 010000, Kazakhstan
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| |
Collapse
|
26
|
Pold G, Bonilla-Rosso G, Saghaï A, Strous M, Jones CM, Hallin S. Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles. ISME COMMUNICATIONS 2024; 4:ycae020. [PMID: 38584645 PMCID: PMC10999283 DOI: 10.1093/ismeco/ycae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 04/09/2024]
Abstract
The two evolutionarily unrelated nitric oxide-producing nitrite reductases, NirK and NirS, are best known for their redundant role in denitrification. They are also often found in organisms that do not perform denitrification. To assess the functional roles of the two enzymes and to address the sequence and structural variation within each, we reconstructed robust phylogenies of both proteins with sequences recovered from 6973 isolate and metagenome-assembled genomes and identified 32 well-supported clades of structurally distinct protein lineages. We then inferred the potential niche of each clade by considering other functional genes of the organisms carrying them as well as the relative abundances of each nir gene in 4082 environmental metagenomes across diverse aquatic, terrestrial, host-associated, and engineered biomes. We demonstrate that Nir phylogenies recapitulate ecology distinctly from the corresponding organismal phylogeny. While some clades of the nitrite reductase were equally prevalent across biomes, others had more restricted ranges. Nitrifiers make up a sizeable proportion of the nitrite-reducing community, especially for NirK in marine waters and dry soils. Furthermore, the two reductases showed distinct associations with genes involved in oxidizing and reducing other compounds, indicating that the NirS and NirK activities may be linked to different elemental cycles. Accordingly, the relative abundance and diversity of NirS versus NirK vary between biomes. Our results show the divergent ecological roles NirK and NirS-encoding organisms may play in the environment and provide a phylogenetic framework to distinguish the traits associated with organisms encoding the different lineages of nitrite reductases.
Collapse
Affiliation(s)
- Grace Pold
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| |
Collapse
|
27
|
Sun Y, Yin Y, He G, Cha G, Ayala-del-Río HL, González G, Konstantinidis KT, Löffler FE. pH selects for distinct N 2O-reducing microbiomes in tropical soil microcosms. ISME COMMUNICATIONS 2024; 4:ycae070. [PMID: 38808123 PMCID: PMC11131594 DOI: 10.1093/ismeco/ycae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.
Collapse
Affiliation(s)
- Yanchen Sun
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Yongchao Yin
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, MA 02148, United States
| | - Guang He
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | | | - Grizelle González
- USDA Forest Service, International Institute of Tropical Forestry, San Juan 00926, Puerto Rico
| | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
| |
Collapse
|
28
|
An Z, Zhang Q, Gao X, Ding J, Shao B, Peng Y. Nitrous oxide emissions in novel wastewater treatment processes: A comprehensive review. BIORESOURCE TECHNOLOGY 2024; 391:129950. [PMID: 37926354 DOI: 10.1016/j.biortech.2023.129950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/22/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
The proliferation of novel wastewater treatment processes has marked recent years, becoming particularly pertinent in light of the strive for carbon neutrality. One area of growing attention within this context is nitrous oxide (N2O) production and emission. This review provides a comprehensive overview of recent research progress on N2O emissions associated with novel wastewater treatment processes, including Anammox, Partial Nitrification, Partial Denitrification, Comammox, Denitrifying Phosphorus Removal, Sulfur-driven Autotrophic Denitrification and n-DAMO. The advantages and challenges of these processes are thoroughly examined, and various mitigation strategies are proposed. An interesting angle that delve into is the potential of endogenous denitrification to act as an N2O sink. Furthermore, the review discusses the potential applications and rationale for novel Anammox-based processes to reduce N2O emissions. The aim is to inform future technology research in this area. Overall, this review aims to shed light on these emerging technologies while encouraging further research and development.
Collapse
Affiliation(s)
- Zeming An
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Qiong Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China.
| | - Xinjie Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Jing Ding
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Baishuo Shao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| |
Collapse
|
29
|
Wei C, Su F, Yue H, Song F, Li H. Spatial distribution characteristics of denitrification functional genes and the environmental drivers in Liaohe estuary wetland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1064-1078. [PMID: 38030842 DOI: 10.1007/s11356-023-30938-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
Genes nirS, nirK, and nosZ are specific for the denitrification process, which is associated with greenhouse gas N2O emission. The abundances and diversities of community containing these three genes are usually used as a common index to reflect the denitrification process, and they would be affected by differences in environmental factors caused by changes from warm to cold conditions. The quantification of denitrification in natural wetlands is complex, and straightforward identification of spatial distribution and drivers affecting the process is still developing. In this study, the bacterial communities, gene diversities, and relative abundances involved in denitrification were investigated in Liaohe Estuary Wetland. We analyzed the relative abundances, diversities, and communities of bacteria containing the three genes at warm and cold conditions using Illumina MiSeq sequencing and detected the potential environmental factors influencing their distribution by using a random forest algorithm. There are great differences in the community composition of the bacteria containing genes nirS, nirK, and nosZ. All the abundant taxa of nirS and nirK communities belonged to phylum Proteobacteria. Compared with the community composition of bacteria containing nirS and nirK, the community of bacteria containing nosZ is more diverse, and the subdivision taxa of phylum Euryarchaeota was also abundant in the community containing nosZ. The distribution characteristics of the relative abundance of nirS and nirK showed obvious differences both at warm and cold climate conditions. The oxidation-reduction potential, nitrite nitrogen, and salinity were detected as potential variables that might explain the diversity of nirS. The total nitrogen and nitrite nitrogen were the important variables for predicting the relative abundance of nirS at warm climate condition, while oxidation-reduction potential and pH contributed to the diversity of nirS at cold condition. The bulk density of sediment was detected as a potential variable affecting the relative abundance of nirK at warm and cold conditions, and diversity of nirK at warm condition, while nitrite nitrogen was detected as an important environmental factor for predicting the diversity of nirK at cold condition. Overall, our results show that the key environmental factors, which affect the relative abundance, diversity, and community of bacteria containing the functional denitrification genes, are not exactly the same, and the diversities of nirS, nirK, and nosZ have a higher environmental sensitivity than their relative abundances.
Collapse
Affiliation(s)
- Chao Wei
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| | - Fangli Su
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China.
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China.
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China.
| | - Hangyu Yue
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Fei Song
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| | - Haifu Li
- College of Water Conservancy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Liaoning Panjin Wetland Ecosystem National Observation and Research Station, Shenyang, 110866, Liaoning, China
- Liaoning Shuangtai Estuary Wetland Ecosystem Research Station, Panjin, 124112, Liaoning, China
- Liaoning Provincial Key Laboratory of Soil Erosion and Ecological Restoration, Shenyang, 110866, Liaoning, China
| |
Collapse
|
30
|
Wan Z, Wang L, Huang G, Rasul F, Awan MI, Cui H, Liu K, Yu X, Tang H, Wang S, Xu H. nirS and nosZII bacterial denitrifiers as well as fungal denitrifiers are coupled with N 2O emissions in long-term fertilized soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165426. [PMID: 37429471 DOI: 10.1016/j.scitotenv.2023.165426] [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: 03/18/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
Fertilizer application plays a critical role in soil fertility and crop yield and has been reported to significantly affect soil denitrification. However, the mechanisms by which denitrifying bacteria (nirK, nirS, nosZI, and nosZII) and fungi (nirK and p450nor) affect soil denitrification are poorly understood. Therefore, in this study, we investigated the effect of different fertilization treatments on the abundance, community structure, and function of soil denitrifying microorganisms in an agricultural ecosystem with long-term fertilization using mineral fertilizer or manure and their combination. The results showed that the application of organic fertilizer significantly increased the abundance of nirK-, nirS-, nosZI-, and nosZII-type denitrifying bacteria as the soil pH and phosphorus content increased. However, only the community structure of nirS- and nosZII-type denitrifying bacteria was influenced by the application of organic fertilizer, which led to a higher contribution of bacteria to nitrous oxide (N2O) emissions than that observed after inorganic fertilizer application. The increase in soil pH reduced the abundance of nirK-type denitrifying fungi, which may have presented a competitive disadvantage relative to bacteria, resulting in a lower contribution of fungi to N2O emissions than that observed after inorganic fertilizer application. The results demonstrated that organic fertilization had a significant impact on the community structure and activity of soil denitrifying bacteria and fungi. Our results also highlighted that after organic fertilizer application, nirS- and nosZII-denitrifying bacteria communities represent likely hot spots of bacterial soil N2O emissions while nirK-type denitrifying fungi represent hot spots for fungal soil N2O emissions.
Collapse
Affiliation(s)
- Ziwei Wan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ling Wang
- Faculty of Resources and Environmental Science, Hubei University, Wuhan 430000, China
| | - Guoqin Huang
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fahd Rasul
- Irrigated Agriculture Research and Extension Center, Washington State University, Washington 99350, United States
| | - Masood Iqbal Awan
- Department of Agronomy, Sub-Campus Depalpur, Okara, University of Agriculture, Faisalabad 38000, Pakistan
| | - Huanming Cui
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kailou Liu
- Jiangxi Institute of Red Soil and Germplasm Resources, Nanchang 331717, China
| | - Xichu Yu
- Jiangxi Institute of Red Soil and Germplasm Resources, Nanchang 331717, China
| | - Haiying Tang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Shubin Wang
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Huifang Xu
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China.
| |
Collapse
|
31
|
Li S, Liao Y, Jiang Z, Ji G. Life strategies and metabolic interactions of core microbes during thiosulphate-based denitrification. Environ Microbiol 2023; 25:1925-1939. [PMID: 37231629 DOI: 10.1111/1462-2920.16430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 05/13/2023] [Indexed: 05/27/2023]
Abstract
Sulphur-driven denitrification is a low-cost process for the treatment of nitrate-contaminated water. However, a comprehensive understanding of core populations and microbial interactions of a sulphur-based denitrifying system is lacking. This study presents results from three replicated denitrifying systems amended with thiosulphate and operated under a low C/N ratio. Amplicon sequencing revealed gradual enrichments of a few abundant denitrifiers. Based on genome-centred metagenomics and metatranscriptomics, a core set of microbes was identified in the systems, with Pseudomonas 1 and Thauera 2 being the most abundant ones. Although the replicates showed different enrichments, generalized observations were summarized. Most core populations conserved energy from denitrification coupled with sulphur. Pseudomonas 1 and Thauera 2 were able to finish complete denitrification. Surprisingly, they were also able to synthesize almost all amino acids and vitamins. In contrast, less abundant members, including Pseudomonas 2, were relatively auxotrophic and required an exogenous supply of amino acids and vitamins. The high expression of enzymes involved in biosynthesis and transport systems indicated their syntrophic relationships. The genomic findings suggested life strategies and interactions of the core thiosulphate-based denitrifying microbiome, with implications for nitrate-polluted water remediation.
Collapse
Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| | - Zhuo Jiang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| |
Collapse
|
32
|
Mujakić I, Cabello-Yeves PJ, Villena-Alemany C, Piwosz K, Rodriguez-Valera F, Picazo A, Camacho A, Koblížek M. Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota. Microbiol Spectr 2023; 11:e0111223. [PMID: 37732776 PMCID: PMC10581226 DOI: 10.1128/spectrum.01112-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023] Open
Abstract
Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.
Collapse
Affiliation(s)
- Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Pedro J. Cabello-Yeves
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| |
Collapse
|
33
|
Robertson GP. Denitrification and the challenge of scaling microsite knowledge to the globe. MLIFE 2023; 2:229-238. [PMID: 38817807 PMCID: PMC10989938 DOI: 10.1002/mlf2.12080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/21/2023] [Accepted: 07/16/2023] [Indexed: 06/01/2024]
Abstract
Our knowledge of microbial processes-who is responsible for what, the rates at which they occur, and the substrates consumed and products produced-is imperfect for many if not most taxa, but even less is known about how microsite processes scale to the ecosystem and thence the globe. In both natural and managed environments, scaling links fundamental knowledge to application and also allows for global assessments of the importance of microbial processes. But rarely is scaling straightforward: More often than not, process rates in situ are distributed in a highly skewed fashion, under the influence of multiple interacting controls, and thus often difficult to sample, quantify, and predict. To date, quantitative models of many important processes fail to capture daily, seasonal, and annual fluxes with the precision needed to effect meaningful management outcomes. Nitrogen cycle processes are a case in point, and denitrification is a prime example. Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are-by themselves-insufficient for revealing process-level knowledge gaps or predicting outcomes under novel environmental conditions. Hybrid models that incorporate well-calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced. Incorporating trait-based models into such efforts promises to improve predictions and understanding still further, but much more development is needed.
Collapse
Affiliation(s)
- G. Philip Robertson
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichiganUSA
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
| |
Collapse
|
34
|
McGuire PM, Butkevich N, Saksena AV, Walter MT, Shapleigh JP, Reid MC. Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors. Environ Microbiol 2023; 25:1696-1712. [PMID: 37105180 DOI: 10.1111/1462-2920.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 - removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.
Collapse
Affiliation(s)
- Philip M McGuire
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Natalie Butkevich
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Aryaman V Saksena
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Matthew C Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| |
Collapse
|
35
|
Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2023; 8:1574-1586. [PMID: 37429908 PMCID: PMC10390337 DOI: 10.1038/s41564-023-01425-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/14/2023] [Indexed: 07/12/2023]
Abstract
Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.
Collapse
Affiliation(s)
| | | | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- School of Science, Constructor University, Bremen, Germany.
| |
Collapse
|
36
|
Lian T, Cheng L, Liu Q, Yu T, Cai Z, Nian H, Hartmann M. Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress. ISME COMMUNICATIONS 2023; 3:71. [PMID: 37433864 PMCID: PMC10336055 DOI: 10.1038/s43705-023-00282-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
Waterlogging in soil can limit the availability of nitrogen to plants by promoting denitrification and reducing nitrogen fixation and nitrification. The root-associated microorganisms that determine nitrogen availability at the root-soil interface can be influenced by plant genotype and soil type, which potentially alters the nitrogen uptake capacity of plants in waterlogged soils. In a greenhouse experiment, two soybean genotypes with contrasting capacities to resist waterlogging stress were grown in Udic Argosol and Haplic Alisol soils with and without waterlogging, respectively. Using isotope labeling, high-throughput amplicon sequencing and qPCR, we show that waterlogging negatively affects soybean yield and nitrogen absorption from fertilizer, atmosphere, and soil. These effects were soil-dependent and more pronounced in the waterlogging-sensitive than tolerant genotype. The tolerant genotype harbored more ammonia oxidizers and less nitrous oxide reducers. Anaerobic, nitrogen-fixing, denitrifying and iron-reducing bacteria such as Geobacter/Geomonas, Sphingomonas, Candidatus Koribacter, and Desulfosporosinus were proportionally enriched in association with the tolerant genotype under waterlogging. These changes in the rhizosphere microbiome might ultimately help the plant to improve nitrogen uptake under waterlogged, anoxic conditions. This research contributes to a better understanding of the adaptability of soybean genotypes under waterlogging stress and might help to formulate fertilization strategies that improve nitrogen use efficiency of soybean. Schematic representation of the effects of waterlogging on nitrogen uptake and rhizosphere microbiota in dependence of soil type and soybean genotype.
Collapse
Affiliation(s)
- Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Taobing Yu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Martin Hartmann
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
37
|
Xiang H, Hong Y, Wu J, Wang Y, Ye F, Ye J, Lu J, Long A. Denitrification contributes to N 2O emission in paddy soils. Front Microbiol 2023; 14:1218207. [PMID: 37396352 PMCID: PMC10313071 DOI: 10.3389/fmicb.2023.1218207] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
Denitrification is vital to nitrogen removal and N2O release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of N2O emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential N2O emission rate, enzymatic activity for N2O production and reduction, gene abundance, and community composition during denitrification were investigated using the 15N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential N2O emission rates were 0.51 ± 0.20 μmol⋅N⋅kg-1⋅h-1, which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for N2O production was 2.77-8.94 times than that for N2O reduction, indicating an imbalance between N2O production and reduction. The gene abundance ratio of nir to nosZ from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the norB gene without nosZ genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to N2O emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g N2O⋅m-2⋅yr-1 in surface paddy soils.
Collapse
Affiliation(s)
- Hua Xiang
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay Area, Ministry of Education, Guangzhou University, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiguo Hong
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay Area, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jiapeng Wu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay Area, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Yu Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay Area, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Fei Ye
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay Area, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jiaqi Ye
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay Area, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jing Lu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Institute of Environmental Research at Greater Bay Area, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Aimin Long
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
38
|
Wang Y, Deng M, Li B, Li L, Oon YS, Zhao X, Song K. High nitrous oxide (N 2O) greenhouse gas reduction potential of Pseudomonas sp. YR02 under aerobic condition. BIORESOURCE TECHNOLOGY 2023; 378:128994. [PMID: 37004889 DOI: 10.1016/j.biortech.2023.128994] [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: 02/25/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Aerobic environments exist widely in wastewater treatment plants (WWTP) and are unfavorable for greenhouse gas nitrous oxide (N2O) reduction. Here, a novel strain Pseudomonas sp. YR02, which can perform N2O reduction under aerobic conditions, was isolated. The successful amplification of four denitrifying genes proved its complete denitrifying ability. The inorganic nitrogen (IN) removal efficiencies (NRE) were >98.0% and intracellular nitrogen and gaseous nitrogen account for 52.6-58.4% and 41.6-47.4% of input nitrogen, respectively. The priority of IN utilization was TAN > NO3--N > NO2--N. The optimal conditions for IN and N2O removal were consistent, except for the C/N ratio, which is 15 and 5 for IN and N2O removal, respectively. The biokinetic constants analysis indicated strain YR02 had high potential to treat high ammonia and dissolved N2O wastewater. Strain YR02 bioaugmentation mitigated 98.7% of N2O emission and improved 32% NRE in WWTP, proving its application potential for N2O mitigation.
Collapse
Affiliation(s)
- Yuren Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Min Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Biqing Li
- Guangzhou Sewage Purification Co. Ltd, Guangzhou 510655, China
| | - Lu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yoong-Sin Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaoli Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Kang Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
39
|
Fan X, Chen H, Yan G, Ye M, Yin C, Li T, Wakelin SA, Liang Y. Niche Differentiation Among Canonical Nitrifiers and N 2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils. MICROBIAL ECOLOGY 2023; 85:1434-1447. [PMID: 35420314 DOI: 10.1007/s00248-022-02006-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/29/2022] [Indexed: 05/10/2023]
Abstract
The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils.
Collapse
Affiliation(s)
- Xiaoping Fan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guochao Yan
- Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Mujun Ye
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chang Yin
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | | | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
40
|
Xiang H, Hong Y, Wu J, Wang Y, Ye F, Hu Z, Qu Z, Long A. NosZ-II-type N 2O-reducing bacteria play dominant roles in determining the release potential of N 2O from sediments in the Pearl River Estuary, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121732. [PMID: 37116571 DOI: 10.1016/j.envpol.2023.121732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/09/2023] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
The microbial reduction of N2O serves as a "gatekeeper" for N2O emissions, determining the flux of N2O release into the atmosphere. Estuaries are active regions for N2O emissions, but the microbial functions of N2O-reducing bacteria in estuarine ecosystems are not well understood. In this study, the 15N isotope tracer method, qPCR, and high-throughput sequencing were used to analyze N2O production, reduction, and emission processes in surface sediments of the Pearl River Estuary. The 15N isotope tracer experiment showed that the N2O production rates declined and the N2O reduction potential (Rr, the ratio of N2O reduction rates to N2O production rates) increased from upstream to downstream of the Pearl River Estuary, leading to a corresponding decrease of the N2O emission rates from upstream to downstream. The gene abundance ratio of nosZ/nir gradually increased from upstream to downstream and was negatively correlated with the water N2O saturation. The gene abundance of nosZ II was significantly higher than that of nosZ I in the estuary, and the nosZ II/nosZ I abundance ratio was positively correlated with N2O reduction potential. Furthermore, the community composition of NosZ-I- and NosZ-II-type N2O-reducing bacteria shifted from upstream to downstream. NosZ-II-type N2O-reducing bacteria, especially Myxococcales, Thiotrichales, and Gemmatimonadetes species, contributed to the high N2O reduction potential in the downstream. Our results suggest that NosZ-II-type N2O-reducing bacteria play a dominant role in determining the release potential of N2O from sediments in the Pearl River Estuary. This study provides a new insight into the function of microbial N2O reduction in estuarine ecosystems.
Collapse
Affiliation(s)
- Hua Xiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China; State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China.
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Zheng Hu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Zhiming Qu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 10006, PR China
| | - Aimin Long
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| |
Collapse
|
41
|
Lin Y, Hu HW, Deng M, Yang P, Ye G. Microorganisms carrying nosZ I and nosZ II share similar ecological niches in a subtropical coastal wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:162008. [PMID: 36739025 DOI: 10.1016/j.scitotenv.2023.162008] [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: 09/30/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Nitrous oxide (N2O) reducers are the only known sink for N2O and pivotal contributors to N2O mitigation in terrestrial and water ecosystems. However, the niche preference of nosZ I and nosZ II carrying microorganisms, two divergent clades of N2O reducers in coastal wetlands, is not yet well documented. In this study, we investigated the abundance, community structure and co-occurrence network of nosZ I and nosZ II carrying microorganisms and their driving factors at three depths in a subtropical coastal wetland with five plant species and a bare tidal flat. The taxonomic identities differed between nosZ I and nosZ II carrying microorganisms, with nosZ I sequences affiliated with Alphaproteobacteria and Betaproteobacteria while nosZ II sequences with Gemmatimonadetes, Verrucomicrobia, Gammaproteobacteria, and Chloroflexi. The abundances of nosZ I and nosZ II decreased with increasing soil depths, and were positively associated with salinity, total carbon (TC) and total nitrogen (TN). Random forest analysis showed that salinity was the strongest predictor for the abundances of nosZ I and nosZ II. Salinity, TC and TN were the major driving forces for the community structure of nosZ I and nosZ II carrying microorganisms. Moreover, co-occurrence analysis showed that 92.2 % of the links between nosZ I and nosZ II were positive, indicating that nosZ I and nosZ II carrying microorganisms likely shared similar ecological niches. Taken together, we provided new evidence that nosZ I and nosZ II carrying microorganisms shared similar ecological niches in a subtropical estuarine wetland, and identified salinity, TC and TN serving as the most important environmental driving forces. This study advances our understanding of the environmental adaptation and niche preference of nosZ I and nosZ II carrying microorganisms in coastal wetlands.
Collapse
Affiliation(s)
- Yongxin Lin
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China.
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Milin Deng
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ping Yang
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Guiping Ye
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China.
| |
Collapse
|
42
|
Khairunisa BH, Loganathan U, Ogejo JA, Mukhopadhyay B. Nitrogen transformation processes catalyzed by manure microbiomes in earthen pit and concrete storages on commercial dairy farms. ENVIRONMENTAL MICROBIOME 2023; 18:32. [PMID: 37041573 PMCID: PMC10091836 DOI: 10.1186/s40793-023-00483-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Storing manure is an essential aspect of nutrient management on dairy farms. It presents the opportunity to use manure efficiently as a fertilizer in crop and pasture production. Typically, the manure storages are constructed as earthen, concrete, or steel-based structures. However, storing manure can potentially emit aerial pollutants to the atmosphere, including nitrogen and greenhouse gases, through microbial and physicochemical processes. We have characterized the composition of the microbiome in two manure storage structures, a clay-lined earthen pit and an aboveground concrete storage tank, on commercial dairy farms, to discern the nitrogen transformation processes, and thereby, inform the development of mitigation practices to preserve the value of manure. First, we analyzed the 16S rRNA-V4 amplicons generated from manure samples collected from several locations and depths (0.3, 1.2, and 2.1-2.75 m below the surface) of the storages, identifying a set of Amplicon Sequence Variant (ASVs) and quantifying their abundances. Then, we inferred the respective metabolic capabilities. These results showed that the manure microbiome composition was more complex and exhibited more location-to-location variation in the earthen pit than in the concrete tank. Further, the inlet and a location with hard surface crust in the earthen pit had unique consortia. The microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to gaseous compounds. However, the microbial conversion of nitrate to gaseous N2, NO, and N2O via denitrification and to stable ammonia via dissimilatory nitrite reduction seemed possible; minor quantities of nitrate was present in manure, potentially originating from oxidative processes occurring on the barn floor. The nitrate-transformation linked ASVs were more prevalent at the near-surface locations and all depths of the inlet. Anammox bacteria and archaeal or bacterial autotrophic nitrifiers were not detected in either storage. Hydrogenotrophic Methanocorpusculum species were the primary methanogens or methane producers, exhibiting higher abundance in the earthen pit. These findings suggested that microbial activities were not the main drivers for nitrogen loss from manure storage, and commonly reported losses are associated with the physicochemical processes. Finally, the microbiomes of stored manure had the potential to emit greenhouse gases such as NO, N2O, and methane.
Collapse
Affiliation(s)
- Bela Haifa Khairunisa
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Usha Loganathan
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jactone A Ogejo
- Department of Biological System Engineering, Blacksburg, VA, 24061, USA.
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, 24061, USA.
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA.
| |
Collapse
|
43
|
Wang Z, Vishwanathan N, Kowaliczko S, Ishii S. Clarifying Microbial Nitrous Oxide Reduction under Aerobic Conditions: Tolerant, Intolerant, and Sensitive. Microbiol Spectr 2023; 11:e0470922. [PMID: 36926990 PMCID: PMC10100939 DOI: 10.1128/spectrum.04709-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/18/2023] [Indexed: 03/17/2023] Open
Abstract
One of the major challenges for the bioremediation application of microbial nitrous oxide (N2O) reduction is its oxygen sensitivity. While a few strains were reported capable of reducing N2O under aerobic conditions, the N2O reduction kinetics of phylogenetically diverse N2O reducers are not well understood. Here, we analyzed and compared the kinetics of clade I and clade II N2O-reducing bacteria in the presence or absence of oxygen (O2) by using a whole-cell assay with N2O and O2 microsensors. Among the seven strains tested, N2O reduction of Stutzerimonas stutzeri TR2 and ZoBell was not inhibited by oxygen (i.e., oxygen tolerant). Paracoccus denitrificans, Azospirillum brasilense, and Gemmatimonas aurantiaca reduced N2O in the presence of O2 but slower than in the absence of O2 (i.e., oxygen sensitive). N2O reduction of Pseudomonas aeruginosa and Dechloromonas aromatica did not occur when O2 was present (i.e., oxygen intolerant). Amino acid sequences and predicted structures of NosZ were highly similar among these strains, whereas oxygen-tolerant N2O reducers had higher oxygen consumption rates. The results suggest that the mechanism of O2 tolerance is not directly related to NosZ structure but is rather related to the scavenging of O2 in the cells and/or accessory proteins encoded by the nos cluster. IMPORTANCE Some bacteria can reduce N2O in the presence of O2, whereas others cannot. It is unclear whether this trait of aerobic N2O reduction is related to the phylogeny and structure of N2O reductase. The understanding of aerobic N2O reduction is critical for guiding emission control, due to the common concurrence of N2O and O2 in natural and engineered systems. This study provided the N2O reduction kinetics of various bacteria under aerobic and anaerobic conditions and classified the bacteria into oxygen-tolerant, -sensitive, and -intolerant N2O reducers. Oxygen-tolerant N2O reducers rapidly consumed O2, which could help maintain the low O2 concentration in the cells and keep their N2O reductase active. These findings are important and useful when selecting N2O reducers for bioremediation applications.
Collapse
Affiliation(s)
- Zhiyue Wang
- Department of Civil and Environmental Engineering, University of Hawai'i, Honolulu, Hawai'i, USA
- Water Resources Research Center, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Nisha Vishwanathan
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Sophie Kowaliczko
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
44
|
Han H, Kim DD, Song MJ, Yun T, Yoon H, Lee HW, Kim YM, Laureni M, Yoon S. Biotrickling Filtration for the Reduction of N 2O Emitted during Wastewater Treatment: Results from a Long-Term In Situ Pilot-Scale Testing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3883-3892. [PMID: 36809918 DOI: 10.1021/acs.est.2c08818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Wastewater treatment plants (WWTPs) are a major source of N2O, a potent greenhouse gas with 300 times higher global warming potential than CO2. Several approaches have been proposed for mitigation of N2O emissions from WWTPs and have shown promising yet only site-specific results. Here, self-sustaining biotrickling filtration, an end-of-the-pipe treatment technology, was tested in situ at a full-scale WWTP under realistic operational conditions. Temporally varying untreated wastewater was used as trickling medium, and no temperature control was applied. The off-gas from the covered WWTP aerated section was conveyed through the pilot-scale reactor, and an average removal efficiency of 57.9 ± 29.1% was achieved during 165 days of operation despite the generally low and largely fluctuating influent N2O concentrations (ranging between 4.8 and 96.4 ppmv). For the following 60-day period, the continuously operated reactor system removed 43.0 ± 21.2% of the periodically augmented N2O, exhibiting elimination capacities as high as 5.25 g N2O m-3·h-1. Additionally, the bench-scale experiments performed abreast corroborated the resilience of the system to short-term N2O starvations. Our results corroborate the feasibility of biotrickling filtration for mitigating N2O emitted from WWTPs and demonstrate its robustness toward suboptimal field operating conditions and N2O starvation, as also supported by analyses of the microbial compositions and nosZ gene profiles.
Collapse
Affiliation(s)
- Heejoo Han
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Daehyun D Kim
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Taeho Yun
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Hyun Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
- School of Civil & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | | | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Michele Laureni
- Department of Geoscience and Engineering, Delft University of Technology, 2628 CN Delft, The Netherlands
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| |
Collapse
|
45
|
Yang Z, Lou Y, Pan H, Wang H, Yang Q, Zhuge Y, Hu J. Improved Denitrification Performance of Polybutylene Succinate/Corncob Composite Carbon Source by Proper Pretreatment: Performance, Functional Genes and Microbial Community Structure. Polymers (Basel) 2023; 15:polym15040801. [PMID: 36850087 PMCID: PMC9958998 DOI: 10.3390/polym15040801] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Blending biodegradable polymers with plant materials is an effective method to improve the biodegradability of solid carbon sources and save denitrification costs, but the recalcitrant lignin in plant materials hinders the microbial decomposition of available carbon sources. In the present study, corncob pretreated by different methods was used to prepare polybutylene succinate/corncob (PBS/corncob) composites for biological denitrification. The PBS/corncob composite with alkaline pretreatment achieved the optimal NO3--N removal rate (0.13 kg NO3--N m-3 day-1) with less adverse effects. The pretreatment degree, temperature, and their interaction distinctly impacted the nitrogen removal performance and dissolved organic carbon (DOC) release, while the N2O emission was mainly affected by the temperature and the interaction of temperature and pretreatment degree. Microbial community analysis showed that the bacterial community was responsible for both denitrification and lignocellulose degradation, while the fungal community was primarily in charge of lignocellulose degradation. The outcomes of this study provide an effective strategy for improving the denitrification performance of composite carbon sources.
Collapse
|
46
|
Castellano-Hinojosa A, Bedmar EJ, Medina-Sánchez JM. Efficiency of reactive nitrogen removal in a model Mediterranean high-mountain lake and its downwater river ecosystem: Biotic and abiotic controls. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159901. [PMID: 36334677 DOI: 10.1016/j.scitotenv.2022.159901] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
High-mountain lakes and rivers are usually oligotrophic and strongly influenced by atmospheric transport processes. Thus, wet deposition of reactive N species (Nr), mainly in the form of nitrate (NO3-), is a major source of N input in these high-mountain ecosystems. Bacterial denitrifiers are thought to be largely responsible for reduction of NO3- to nitrous oxide (N2O) and molecular dinitrogen (N2) as main biological pathway of N removal in these ecosystems. Nitrifiers, through the oxidation of ammonium to NO3-, can also be a source of NO3- and N2O. However, there is uncertainty regarding the abiotic and biotic factors controlling Nr elimination from aquatic ecosystems at different altitudes and seasons. We examined the efficiency of Nr removal as N2O and N2 (total removal) or N2 only (clean removal) in a model lake and its downwater river ecosystem (Sierra Nevada, Spain) representative of Mediterranean high-mountain freshwater ecosystems along an altitudinal gradient during the warm period of the year. Denitrification activity and the abundance of nitrifiers and denitrifiers in sediments were measured at thaw, mid ice-free and late ice-free periods. We found the efficiency of total and clean removal of Nr increased from the downwater river to the high-mountain lake. Regardless of the location, the efficiency of total removal of Nr decreased over the ice-free period whereas that of clean removal of Nr peaked at mid ice-free period. The efficiency of total removal of Nr was mainly controlled by the abundance of archaeal nitrifiers and bacterial denitrifiers. Abiotic (ammonium and NO3- concentration) and biotic (mainly nosZI-type denitrifiers) factors drove changes in the efficiency of clean removal of Nr. Our results suggest that abiotic and biotic factors can control the efficiencies of Nr removal in Mediterranean high-mountain lakes and their downwater rivers, and that these efficiencies increase with altitude and vary over the ice-free period.
Collapse
Affiliation(s)
- Antonio Castellano-Hinojosa
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; Instituto Universitario de Investigación del Agua, Universidad de Granada, Granada, Spain.
| | - Eulogio J Bedmar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan M Medina-Sánchez
- Instituto Universitario de Investigación del Agua, Universidad de Granada, Granada, Spain; Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| |
Collapse
|
47
|
Hou K, Cheng C, Shi B, Liu W, Du Z, Li B, Wang J, Wang J. New insights into the effects of chlorpyrifos on soil microbes: Carbon and nitrogen cycle related microbes in wheat/maize rotation agricultural field. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120908. [PMID: 36549448 DOI: 10.1016/j.envpol.2022.120908] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Chlorpyrifos, a broad-spectrum organophosphorus insecticide, has been widely detected worldwide and is a potential neurotoxin and endocrine disruptor. Besides, chlorpyrifos has been proven that have a negative effect on soil microbes. In the present study, chlorpyrifos formulation (LORSBAN®, 45% emulsifiable concentrate) was applied in an agricultural field at the recommended dose (R dose, 270.0 and 337.5 g a.i. ha-1 for wheat and maize respectively) and double recommended (DR) dose. Chlorpyrifos residue level and effect on soil microbes related to soil carbon and nitrogen cycle function were analyzed. Results showed that the half-lives of chlorpyrifos in wheat and maize field soil were 7.23-8.23 and 1.45-1.77 d, respectively. Application of chlorpyrifos at even DR dose did not result in unacceptable residual chlorpyrifos, where the final residual chlorpyrifos in wheat/maize (leaf, stem, and grain) was meet the requirement of the maximum residual limit (0.5 mg kg-1 for wheat and 0.05 mg kg-1 for maize) in China. Chlorpyrifos enhanced the activity of β-glucosidase by increasing the relative abundance of Sphingosinicella and promoted the carbon cycle in wheat field. The changes of cbbLR and cbbLG gene abundance also confirmed that chlorpyrifos could affect the import and export of soil carbon pool. The effect of chlorpyrifos on soil N cycle was determined by changes in the abundance of the bacterial genus Gemmatimonas, which is associated with denitrification. Further analysis of N-cycle functional genes and urease activity showed that chlorpyrifos inhibited nitrogen fixation in wheat field, but promoted nitrogen fixation in maize field. In general, bacterial abundance, urease, and AOA-amoA gene could be early warning markers of chlorpyrifos contamination. The results demonstrated the negative effects of chlorpyrifos on soil microbes especially on soil C and N cycle in actual agricultural field. It provides new insights about chlorpyrifos environmental pollution and its effect on soil ecosystems.
Collapse
Affiliation(s)
- Kaixuan Hou
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Chao Cheng
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Baihui Shi
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Wei Liu
- Experiment Management Centre, Dezhou University, No. 566 University West Road, Dezhou, 253023, PR China.
| | - Zhongkun Du
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Bing Li
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| |
Collapse
|
48
|
Vineis JH, Bulseco AN, Bowen JL. Microbial chemolithoautotrophs are abundant in salt marsh sediment following long-term experimental nitrate enrichment. FEMS Microbiol Lett 2023; 370:fnad082. [PMID: 37541957 DOI: 10.1093/femsle/fnad082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Long-term anthropogenic nitrate (NO3-) enrichment is a serious threat to many coastal systems. Nitrate reduction coupled with the oxidation of reduced forms of sulfur is conducted by chemolithoautotrophic microbial populations in a process that decreases nitrogen (N) pollution. However, little is known about the diversity and distribution of microbes capable of carbon fixation within salt marsh sediment and how they respond to long-term NO3- loading. We used genome-resolved metagenomics to characterize the distribution, phylogenetic relationships, and adaptations important to microbial communities within NO3--enriched sediment. We found NO3- reducing sulfur oxidizers became dominant members of the microbial community throughout the top 25 cm of the sediment following long-term NO3- enrichment. We also found that most of the chemolithoautotrophic genomes recovered contained striking metabolic versatility, including the potential for complete denitrification and evidence of mixotrophy. Phylogenetic reconstruction indicated that similar carbon fixation strategies and metabolic versatility can be found in several phylogenetic groups, but the genomes recovered here represent novel organisms. Our results suggest that the role of chemolithoautotrophy within NO3--enriched salt marsh sediments may be quantitatively more important for retaining carbon and filtering NO3- than previously indicated and further inquiry is needed to explicitly measure their contribution to carbon turnover and removal of N pollution.
Collapse
Affiliation(s)
- Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Ashley N Bulseco
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 30 Nahant Road, Nahant, MA 01908, United States
| |
Collapse
|
49
|
Pizarro L, Magalhães C, Almeida CMR, Carvalho MDF, Semedo M. Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4. FEMS Microbiol Lett 2023; 370:fnad047. [PMID: 37279908 PMCID: PMC10337742 DOI: 10.1093/femsle/fnad047] [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: 01/31/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.
Collapse
Affiliation(s)
- Leonor Pizarro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Faculty of Biotechnology, Catholic University of Portugal, Porto 4169-005, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Biology, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - Maria de Fátima Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
| |
Collapse
|
50
|
Zheng CW, Zhou C, Luo YH, Long M, Long X, Zhou D, Bi Y, Yang S, Rittmann BE. Coremoval of Energetics and Oxyanions via the In Situ Coupling of Catalytic and Enzymatic Destructions: A Solution to Ammunition Wastewater Treatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:666-673. [PMID: 36445010 DOI: 10.1021/acs.est.2c05675] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ammunition wastewater contains toxic nitrated explosives like RDX and oxyanions like nitrate and perchlorate. Its treatment is challenged by low efficiency due to contaminant recalcitrance and high cost due to multiple processes needed for separately removing different contaminant types. This paper reports a H2-based low-energy strategy featuring the treatment of explosives via catalytic denitration followed by microbial mineralization coupled with oxyanion reduction. After a nitrate- and perchlorate-reducing biofilm incapable of RDX biodegradation was coated with palladium nanoparticles (Pd0NPs), RDX was rapidly denitrated with a specific catalytic activity of 8.7 gcat-1 min-1, while biological reductions of nitrate and perchlorate remained efficient. In the subsequent 30-day continuous test, >99% of RDX, nitrate, and perchlorate were coremoved, and their effluent concentrations were below their respective regulation levels. Detected intermediates and shallow metagenome analysis suggest that the intermediates after Pd-catalytic denitration of RDX ultimately were enzymatically utilized by the nitrate- and perchlorate-reducing bacteria as additional electron donor sources.
Collapse
Affiliation(s)
- Chen-Wei Zheng
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85281, United States
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85281, United States
| | - Yi-Hao Luo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85281, United States
| | - Min Long
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85281, United States
| | - Xiangxing Long
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85281, United States
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, Arizona85281, United States
| | - Dandan Zhou
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun130024, China
| | - Yuqiang Bi
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, Arizona85281, United States
| | - Shize Yang
- Eyring Materials Center, Arizona State University, Tempe, Arizona85281, United States
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85281, United States
| |
Collapse
|