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Kushwah AS, Dixit H, Upadhyay V, Verma SK, Prasad R. The study of iron- and copper-binding proteome of Fusarium oxysporum and its effector candidates. Proteins 2024; 92:1097-1112. [PMID: 38666709 DOI: 10.1002/prot.26696] [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: 07/05/2023] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron-binding proteins (IBPs) and copper-binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high-throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron-binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate-binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen-host interactions. The insights gained from this report on the role of metal ions in plant-pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.
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Affiliation(s)
- Ankita Singh Kushwah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi, North Campus, Delhi, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Hu M, Yu Z, Griffis TJ, Yang WH, Mohn J, Millet DB, Baker JM, Wang D. Hydrologic Connectivity Regulates Riverine N 2O Sources and Dynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9701-9713. [PMID: 38780660 DOI: 10.1021/acs.est.4c01285] [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: 05/25/2024]
Abstract
Indirect nitrous oxide (N2O) emissions from streams and rivers are a poorly constrained term in the global N2O budget. Current models of riverine N2O emissions place a strong focus on denitrification in groundwater and riverine environments as a dominant source of riverine N2O, but do not explicitly consider direct N2O input from terrestrial ecosystems. Here, we combine N2O isotope measurements and spatial stream network modeling to show that terrestrial-aquatic interactions, driven by changing hydrologic connectivity, control the sources and dynamics of riverine N2O in a mesoscale river network within the U.S. Corn Belt. We find that N2O produced from nitrification constituted a substantial fraction (i.e., >30%) of riverine N2O across the entire river network. The delivery of soil-produced N2O to streams was identified as a key mechanism for the high nitrification contribution and potentially accounted for more than 40% of the total riverine emission. This revealed large terrestrial N2O input implies an important climate-N2O feedback mechanism that may enhance riverine N2O emissions under a wetter and warmer climate. Inadequate representation of hydrologic connectivity in observations and modeling of riverine N2O emissions may result in significant underestimations.
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Affiliation(s)
- Minpeng Hu
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Zhongjie Yu
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Timothy J Griffis
- Department of Soil, Water, and Climate, University of Minnesota─Twin Cities, St. Paul, Minnesota 55108, United States
| | - Wendy H Yang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Joachim Mohn
- Laboratory for Air Pollution & Environmental Technology, Empa, Dübendorf CH-8600, Switzerland
| | - Dylan B Millet
- Department of Soil, Water, and Climate, University of Minnesota─Twin Cities, St. Paul, Minnesota 55108, United States
| | - John M Baker
- Department of Soil, Water, and Climate, University of Minnesota─Twin Cities, St. Paul, Minnesota 55108, United States
- Agricultural Research Service, United States Department of Agriculture, St. Paul, Minnesota 55108, United States
| | - Dongqi Wang
- School of Geographical Sciences, Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, People's Republic of China
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3
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Lourenço KS, Suleiman AKA, Pijl A, Dimitrov MR, Cantarella H, Kuramae EE. Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments. MethodsX 2024; 12:102699. [PMID: 38660030 PMCID: PMC11041840 DOI: 10.1016/j.mex.2024.102699] [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: 01/30/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).
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Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas 13020-902, SP, Brazil
| | - Afnan Khalil Ahmad Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
- Soil Health group, Bioclear Earth B.V., Rozenburglaan 13, Groningen 9727 DL, The Netherlands
| | - Agata Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
| | - Mauricio R. Dimitrov
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas 13020-902, SP, Brazil
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, Wageningen 6708, PB, The Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
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4
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Yousif NM, Gomaa OM. Screen-printed biosensor based on electro-polymerization of bio-composite for nitrate detection in aqueous media. ENVIRONMENTAL TECHNOLOGY 2024; 45:2363-2374. [PMID: 36689460 DOI: 10.1080/09593330.2023.2172618] [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: 08/09/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Bacillus sp. possessing a periplasmic nitrate reductase was used as a recognition element to develop a nitrate biosensor. The bacteria was embedded within a polyaniline (PANI) electro-conductive matrix via electro-polymerization on miniaturized carbon screen-printed electrodes (SPE) at 100 mV/s and scan rate from -0.35 V to + 1.7 V. Surface medication of SPE was verified via Fourier Transform Infrared spectroscopy (FTIR) and Scanning Electron Microscopy (SEM). The optimal bacterial density was OD600 1.2. To enhance the biosensors performance, Bacillus sp. was (1) grown in riboflavin (RF) inducing media as an endogenous redox mediator and (2) exposed to different gamma radiation doses as a physical method to increase electron transfer. Results show a link between exposing cells to gamma irradiation stress, this was evident by electron spin resonance (ESR) and changes in FTIR spectrum, in addition to the increase in catalase enzyme. The nitrate limit of detection (LOD) was 0.5-25 mg/L for non-irradiated RF induced immobilized cells and LOD was 0.5-75 mg/L nitrate for 2 kGy gamma irradiated cells. The prepared biosensor showed acceptable reproducibility and multiple usages after storage at 4°C over 3 months. Low cost and simple preparation allow the biosensor to be mass-produced as a disposable device. Bacillus sp. and its endogenous redox mediator immobilized within polyaniline are good candidates for the improvement of amperometric biosensors for the quantification of nitrate in aqueous solutions.
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Affiliation(s)
- Nashwa M Yousif
- Solid State Physics and Accelerators Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Ola M Gomaa
- Radiation Microbiology Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
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5
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Matsuda K, Nakahara Y, Choirunnisa AR, Arima K, Wakimoto T. Phylogeny-guided Characterization of Bacterial Hydrazine Biosynthesis Mediated by Cupin/methionyl tRNA Synthetase-like Enzymes. Chembiochem 2024; 25:e202300838. [PMID: 38403952 DOI: 10.1002/cbic.202300838] [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: 12/12/2023] [Revised: 01/27/2024] [Accepted: 02/25/2024] [Indexed: 02/27/2024]
Abstract
Cupin/methionyl-tRNA synthetase (MetRS)-like didomain enzymes catalyze nitrogen-nitrogen (N-N) bond formation between Nω-hydroxylamines and amino acids to generate hydrazines, key biosynthetic intermediates of various natural products containing N-N bonds. While the combination of these two building blocks leads to the creation of diverse hydrazine products, the full extent of their structural diversity remains largely unknown. To explore this, we herein conducted phylogeny-guided genome-mining of related hydrazine biosynthetic pathways consisting of two enzymes: flavin-dependent Nω-hydroxylating monooxygenases (NMOs) that produce Nω-hydroxylamine precursors and cupin/MetRS-like enzymes that couple the Nω-hydroxylamines with amino acids via N-N bonds. A phylogenetic analysis identified the largely unexplored sequence spaces of these enzyme families. The biochemical characterization of NMOs demonstrated their capabilities to produce various Nω-hydroxylamines, including those previously not known as precursors of N-N bonds. Furthermore, the characterization of cupin/MetRS-like enzymes identified five new hydrazine products with novel combinations of building blocks, including one containing non-amino acid building blocks: 1,3-diaminopropane and putrescine. This study substantially expanded the variety of N-N bond forming pathways mediated by cupin/MetRS-like enzymes.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuto Nakahara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Atina Rizkiya Choirunnisa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kuga Arima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
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6
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Shaaban M. Microbial pathways of nitrous oxide emissions and mitigation approaches in drylands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120393. [PMID: 38364533 DOI: 10.1016/j.jenvman.2024.120393] [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: 11/10/2023] [Revised: 01/07/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Drylands refer to water scarcity and low nutrient levels, and their plant and biocrust distribution is highly diverse, making the microbial processes that shape dryland functionality particularly unique compared to other ecosystems. Drylands are constraint for sustainable agriculture and risk for food security, and expected to increase over time. Nitrous oxide (N2O), a potent greenhouse gas with ozone reduction potential, is significantly influenced by microbial communities in drylands. However, our understanding of the biological mechanisms and processes behind N2O emissions in these areas is limited, despite the fact that they highly account for total gaseous nitrogen (N) emissions on Earth. This review aims to illustrate the important biological pathways and microbial players that regulate N2O emissions in drylands, and explores how these pathways might be influenced by global changes for example N deposition, extreme weather events, and climate warming. Additionally, we propose a theoretical framework for manipulating the dryland microbial community to effectively reduce N2O emissions using evolving techniques that offer inordinate specificity and efficacy. By combining expertise from different disciplines, these exertions will facilitate the advancement of innovative and environmentally friendly microbiome-based solutions for future climate change vindication approaches.
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Affiliation(s)
- Muhammad Shaaban
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.
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7
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Lin Z, Shi L, Wei X, Han B, Peng C, Yao Z, He Y, Xiao Q, Lu X, Deng Y, Zhou H, Liu K, Shao X. Soil properties and fungal community jointly explain N 2O emissions following N and P enrichment in an alpine meadow. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123344. [PMID: 38215869 DOI: 10.1016/j.envpol.2024.123344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Nutrient enrichment, such as nitrogen (N) and phosphorus (P), typically affects nitrous oxide (N2O) emissions in terrestrial ecosystems, predominantly via microbial nitrification and denitrification processes in the soil. However, the specific impact of soil property and microbial community alterations under N and P enrichment on grassland N2O emissions remains unclear. To address this, a field experiment was conducted in an alpine meadow of the northeastern Qinghai-Tibetan Plateau. This study aimed to unravel the mechanisms underlying N and P enrichment effects on N2O emissions by monitoring N2O fluxes, along with analyzing associated microbial communities and soil physicochemical properties. We observed that N enrichment individually or in combination with P enrichment, escalated N2O emissions. P enrichment dampened the stimulatory effect of N enrichment on N2O emissions, indicative of an antagonistic effect. Structural equation modeling (SEM) revealed that N enrichment enhanced N2O emissions through alterations in fungal community composition and key soil physicochemical properties such as pH, ammonium nitrogen (NH4+-N), available phosphorus (AP), microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN)). Notably, our findings demonstrated that N2O emissions were significantly more influenced by fungal activities, particularly genera like Fusarium, rather than bacterial processes in response to N enrichment. Overall, the study highlights that N enrichment intensifies the role of fungal attributes and soil properties in driving N2O emissions. In contrast, P enrichment exhibited a non-significant effect on N2O emissions, which highlights the critical role of the fungal community in N2O emissions responses to nutrient enrichments in alpine grassland ecosystems.
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Affiliation(s)
- Zhenrong Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Lina Shi
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Xiaoting Wei
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Bing Han
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Cuoji Peng
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Zeying Yao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China; College of Practaculture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Yicheng He
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Qing Xiao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Xinmin Lu
- Tianshui Institute of Pomology, Tianshui, 741002, PR China
| | - Yanfang Deng
- Qilian Mountain National Park Qinghai Service Guarantee Center, Xining, 810001, PR China
| | - Huakun Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Science, Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Xining, 810001, PR China
| | - Kesi Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Xinqing Shao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
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Gan X, Hu H, Fu Q, Zhu J. Nitrate reduction coupling with As(III) oxidation in neutral As-contaminated paddy soil preserves nitrogen, reduces N 2O emissions and alleviates As toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169360. [PMID: 38104836 DOI: 10.1016/j.scitotenv.2023.169360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
In arsenic (As)-contaminated paddy soil, microbial-driven nitrate (NO3-) reduction coupled with arsenite (As(III)) oxidation can reduce As toxicity, but the whereabouts of NO3- remain unclear. In this study, the experiments were established using selective streptomycin (STP) and cyclohexylamine to inhibit bacterial and fungal functional responses, respectively, and metagenomic sequencing techniques were used to explain the biological mechanisms of NO3- reduction coupled with As(III) oxidation in neutral As-contaminated paddy soil. The results indicated that fungal denitrification resulted in stronger nitrous oxide (N2O) emissions (321.6 μg kg-1) than bacterial denitrification (175.9 μg kg-1) in neutral As-contaminated paddy soil, but NO3- reduction coupled with As(III) oxidation reduced the N2O emissions. Only adding STP led to ammonium (NH4+) generation (17.7 mg kg-1), and simultaneously more NH4+ appeared in NO3- reduction coupled with As(III) oxidation; this may be because it improved the electron transfer efficiency by 18.2 %. Achromobacter was involved in denitrification coupled with As(III) oxidation. Burkholderiales was responsible for NO3- reduction to NH4+ coupled with As(III) oxidation. This study provided a theoretical basis for NO3- reduction coupled with As(III) oxidation reducing N2O emissions, promoting the reduction of NO3- to NH4+, and reducing As toxicity in paddy soil.
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Affiliation(s)
- Xuelian Gan
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongqing Hu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingling Fu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jun Zhu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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Yu NN, Park G. Nitric Oxide in Fungi: Production and Function. J Fungi (Basel) 2024; 10:155. [PMID: 38392826 PMCID: PMC10889981 DOI: 10.3390/jof10020155] [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: 12/15/2023] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Nitric oxide (NO) is synthesized in all kingdoms of life, where it plays a role in the regulation of various physiological and developmental processes. In terms of endogenous NO biology, fungi have been less well researched than mammals, plants, and bacteria. In this review, we summarize and discuss the studies to date on intracellular NO biosynthesis and function in fungi. Two mechanisms for NO biosynthesis, NO synthase (NOS)-mediated arginine oxidation and nitrate- and nitrite-reductase-mediated nitrite reduction, are the most frequently reported. Furthermore, we summarize the multifaceted functions of NO in fungi as well as its role as a signaling molecule in fungal growth regulation, development, abiotic stress, virulence regulation, and metabolism. Finally, we present potential directions for future research on fungal NO biology.
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Affiliation(s)
- Nan-Nan Yu
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Gyungsoon Park
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Republic of Korea
- Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
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10
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Kanematsu Y, Kondo HX, Takano Y. Computational Exploration of Minimum Energy Reaction Pathway of N 2O Formation from Intermediate I of P450nor Using an Active Center Model. Int J Mol Sci 2023; 24:17172. [PMID: 38139001 PMCID: PMC10743073 DOI: 10.3390/ijms242417172] [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: 11/03/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention in chemistry, biology, and environmental engineering. The catalytic cycle of P450nor is proposed to consist of three major steps. The reaction mechanism for the last step, N2O generation, remains unknown. In this study, the reaction pathway of the N2O generation from the intermediate I was explored with the B3LYP calculations using an active center model after the examination of the validity of the model. In the validation, we compared the heme distortions between P450nor and other oxidoreductases, suggesting a small effect of protein environment on the N2O generation reaction in P450nor. We then evaluated the electrostatic environment effect of P450nor on the hydride affinity to the active site with quantum mechanics/molecular mechanics (QM/MM) calculations, confirming that the affinity was unchanged with or without the protein environment. The active center model for P450nor showed that the N2O generation process in the enzymatic reaction undergoes a reasonable barrier height without protein environment. Consequently, our findings strongly suggest that the N2O generation reaction from the intermediate I depends sorely on the intrinsic reactivity of the heme cofactor bound on cysteine residue.
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Affiliation(s)
- Yusuke Kanematsu
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
| | - Hiroko X. Kondo
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
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11
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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.
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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.
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12
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Stanfill SB, Hecht SS, Joerger AC, González PJ, Maia LB, Rivas MG, Moura JJG, Gupta AK, Le Brun NE, Crack JC, Hainaut P, Sparacino-Watkins C, Tyx RE, Pillai SD, Zaatari GS, Henley SJ, Blount BC, Watson CH, Kaina B, Mehrotra R. From cultivation to cancer: formation of N-nitrosamines and other carcinogens in smokeless tobacco and their mutagenic implications. Crit Rev Toxicol 2023; 53:658-701. [PMID: 38050998 DOI: 10.1080/10408444.2023.2264327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/20/2023] [Indexed: 12/07/2023]
Abstract
Tobacco use is a major cause of preventable morbidity and mortality globally. Tobacco products, including smokeless tobacco (ST), generally contain tobacco-specific N-nitrosamines (TSNAs), such as N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-butanone (NNK), which are potent carcinogens that cause mutations in critical genes in human DNA. This review covers the series of biochemical and chemical transformations, related to TSNAs, leading from tobacco cultivation to cancer initiation. A key aim of this review is to provide a greater understanding of TSNAs: their precursors, the microbial and chemical mechanisms that contribute to their formation in ST, their mutagenicity leading to cancer due to ST use, and potential means of lowering TSNA levels in tobacco products. TSNAs are not present in harvested tobacco but can form due to nitrosating agents reacting with tobacco alkaloids present in tobacco during certain types of curing. TSNAs can also form during or following ST production when certain microorganisms perform nitrate metabolism, with dissimilatory nitrate reductases converting nitrate to nitrite that is then released into tobacco and reacts chemically with tobacco alkaloids. When ST usage occurs, TSNAs are absorbed and metabolized to reactive compounds that form DNA adducts leading to mutations in critical target genes, including the RAS oncogenes and the p53 tumor suppressor gene. DNA repair mechanisms remove most adducts induced by carcinogens, thus preventing many but not all mutations. Lastly, because TSNAs and other agents cause cancer, previously documented strategies for lowering their levels in ST products are discussed, including using tobacco with lower nornicotine levels, pasteurization and other means of eliminating microorganisms, omitting fermentation and fire-curing, refrigerating ST products, and including nitrite scavenging chemicals as ST ingredients.
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Affiliation(s)
- Stephen B Stanfill
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andreas C Joerger
- Structural Genomics Consortium (SGC), Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pablo J González
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - Luisa B Maia
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | - Maria G Rivas
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - José J G Moura
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | | | - Nick E Le Brun
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Jason C Crack
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Grenoble Alpes University, Grenoble, France
| | - Courtney Sparacino-Watkins
- University of Pittsburgh, School of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, PA, USA
| | - Robert E Tyx
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suresh D Pillai
- Department of Food Science & Technology, National Center for Electron Beam Research, Texas A&M University, College Station, TX, USA
| | - Ghazi S Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - S Jane Henley
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin C Blount
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clifford H Watson
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Ravi Mehrotra
- Centre for Health, Innovation and Policy Foundation, Noida, India
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13
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Zuo X, Xu W, Wei S, Jiang S, Luo Y, Ling M, Zhang K, Gao Y, Wang Z, Hu J, Grossart HP, Luo Z. Aerobic denitrifying bacterial-fungal consortium mediating nitrate removal: Dynamics, network patterns and interactions. iScience 2023; 26:106824. [PMID: 37250796 PMCID: PMC10212969 DOI: 10.1016/j.isci.2023.106824] [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: 03/24/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
In recent years, nitrogen removal by mixed microbial cultures has received increasing attention owing to cooperative metabolism. A natural bacterial-fungal consortium was isolated from mariculture, which exhibited an excellent aerobic denitrification capacity. Under aerobic conditions, nitrate removal and denitrification efficiencies were up to 100% and 44.27%, respectively. High-throughput sequencing and network analysis suggested that aerobic denitrification was potentially driven by the co-occurrence of the following bacterial and fungal genera: Vibrio, Fusarium, Gibberella, Meyerozyma, Exophiala and Pseudoalteromonas, with the dominance of Vibrio and Fusarium in bacterial and fungal communities, respectively. In addition, the isolated consortium had a high steady aerobic denitrification performance in our sub-culturing experiments. Our results provide new insights on the dynamics, network patterns and interactions of aerobic denitrifying microbial consortia with a high potential for new biotechnology applications.
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Affiliation(s)
- Xiaotian Zuo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing 100083, China
| | - Shuangcheng Jiang
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China
| | - Yu Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Minghuang Ling
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Kai Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yuanhao Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zhichao Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Jiege Hu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin 16775, Germany
- Institute of Biochemistry and Biology, Postdam University, Potsdam 14469, Germany
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing 210044, China
- Marine Biology College, Xiamen Ocean Vocational College, Xiamen 361012, China
- Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang 222005, China
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14
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Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Hirai MY. An agroecological structure model of compost-soil-plant interactions for sustainable organic farming. ISME COMMUNICATIONS 2023; 3:28. [PMID: 37002405 PMCID: PMC10066230 DOI: 10.1038/s43705-023-00233-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan.
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan.
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan.
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan.
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Naoto Nihei
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Fukushima, 960-1296, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | | | | | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shunya Taguchi
- Center for Frontier Medical Engineering, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Teruo Matsushita
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshiaki Ito
- Keiyo Gas Energy Solution Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Sankichi Horiuchi
- Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa, Chiba, 277-8567, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kenichi Mori
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Takumi Nishiuchi
- Division of Integrated Omics research, Bioscience Core Facility, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Miroku Co., Ltd., Kitsuki, Oita, 873-0021, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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15
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Brimberry M, Corrigan P, Silakov A, Lanzilotta WN. Evidence for Porphyrin-Mediated Electron Transfer in the Radical SAM Enzyme HutW. Biochemistry 2023; 62:1191-1196. [PMID: 36877586 PMCID: PMC10035031 DOI: 10.1021/acs.biochem.2c00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Bacteria that infect the human gut must compete for essential nutrients, including iron, under a variety of different metabolic conditions. Several enteric pathogens, including Vibrio cholerae and Escherichia coli O157:H7, have evolved mechanisms to obtain iron from heme in an anaerobic environment. Our laboratory has demonstrated that a radical S-adenosylmethionine (SAM) methyltransferase is responsible for the opening of the heme porphyrin ring and release of iron under anaerobic conditions. Furthermore, the enzyme in V. cholerae, HutW, has recently been shown to accept electrons from NADPH directly when SAM is utilized to initiate the reaction. However, how NADPH, a hydride donor, catalyzes the single electron reduction of a [4Fe-4S] cluster, and/or subsequent electron/proton transfer reactions, was not addressed. In this work, we provide evidence that the substrate, in this case, heme, facilitates electron transfer from NADPH to the [4Fe-4S] cluster. This study uncovers a new electron transfer pathway adopted by radical SAM enzymes and further expands our understanding of these enzymes in bacterial pathogens.
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Affiliation(s)
- Marley Brimberry
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602, United States
| | - Patrick Corrigan
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - William N Lanzilotta
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602, United States
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16
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Li X, Gao D, Li Y, Zheng Y, Dong H, Liang X, Liu M, Hou L. Increased Nitrogen Loading Facilitates Nitrous Oxide Production through Fungal and Chemodenitrification in Estuarine and Coastal Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2660-2671. [PMID: 36734984 DOI: 10.1021/acs.est.2c06602] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Estuarine and coastal environments are assumed to contribute to nitrous oxide (N2O) emissions under increasing nitrogen loading. However, isotopic and molecular mechanisms underlying N2O production pathways under elevated nitrogen concentration remain poorly understood. Here we used microbial inhibition, isotope mass balance, and molecular approaches to investigate N2O production mechanisms in estuarine and coastal sediments through a series of anoxic incubations. Site preference of the N2O molecule increased due to increasing nitrate concentration, suggesting the changes in N2O production pathways. Enhanced N2O production under high nitrate concentration was not mediated by bacterial denitrification, but instead was mainly regulated by fungal denitrification. Elevated nitrate concentration increased the contribution of fungal denitrification to N2O production by 11-25%, whereas it decreased bacterial N2O production by 16-33%. Chemodenitrification was also enhanced by high nitrate concentration, contributing to 13-28% of N2O production. Elevated nitrate concentration significantly mediated nirK-type denitrifiers structure and abundance, which are the keystone taxa driving N2O production. Collectively, these results suggest that increasing nitrate concentration can shift N2O production pathways from bacterial to fungal and chemodenitrification, which are mainly responsible for the enhanced N2O production and have widespread implications for N2O projections under ongoing nitrogen pollution in estuarine and coastal ecosystems.
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Affiliation(s)
- Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai200241, China
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai200241, China
| | - Ye Li
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai200241, China
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17
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Bhadra M, Albert T, Franke A, Josef V, Ivanović-Burmazović I, Swart M, Moënne-Loccoz P, Karlin KD. Reductive Coupling of Nitric Oxide by Cu(I): Stepwise Formation of Mono- and Dinitrosyl Species En Route to a Cupric Hyponitrite Intermediate. J Am Chem Soc 2023; 145:2230-2242. [PMID: 36652374 PMCID: PMC10122266 DOI: 10.1021/jacs.2c09874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Transition-metal-mediated reductive coupling of nitric oxide (NO(g)) to nitrous oxide (N2O(g)) has significance across the fields of industrial chemistry, biochemistry, medicine, and environmental health. Herein, we elucidate a density functional theory (DFT)-supplemented mechanism of NO(g) reductive coupling at a copper-ion center, [(tmpa)CuI(MeCN)]+ (1) {tmpa = tris(2-pyridylmethyl)amine}. At -110 °C in EtOH (<-90 °C in MeOH), exposing 1 to NO(g) leads to a new binuclear hyponitrite intermediate [{(tmpa)CuII}2(μ-N2O22-)]2+ (2), exhibiting temperature-dependent irreversible isomerization to the previously characterized κ2-O,O'-trans-[(tmpa)2Cu2II(μ-N2O22-)]2+ (OOXray) complex. Complementary stopped-flow kinetic analysis of the reaction in MeOH reveals an initial mononitrosyl species [(tmpa)Cu(NO)]+ (1-(NO)) that binds a second NO molecule, forming a dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2). The decay of 1-(NO)2 requires an available starting complex 1 to form a dicopper-dinitrosyl species hypothesized to be [{(tmpa)Cu}2(μ-NO)2]2+ (D) bearing a diamond-core motif, en route to the formation of hyponitrite intermediate 2. In contrast, exposing 1 to NO(g) in 2-MeTHF/THF (v/v 4:1) at <-80 °C leads to the newly observed transient metastable dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2) prior to its disproportionation-mediated transformation to the nitrite product [(tmpa)CuII(NO2)]+. Our study furnishes a near-complete profile of NO(g) activation at a reduced Cu site with tripodal tetradentate ligation in two distinctly different solvents, aided by detailed spectroscopic characterization of metastable intermediates, including resonance Raman characterization of the new dinitrosyl and hyponitrite species detected.
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Affiliation(s)
- Mayukh Bhadra
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Alicja Franke
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians University, Munich, 81377 Munich, Germany
| | - Verena Josef
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians University, Munich, 81377 Munich, Germany
| | - Marcel Swart
- IQCC & Departament de Química, Universitat de Girona, Campus Montilivi (Ciencies), 17003 Girona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Kenneth D Karlin
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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18
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Liu H, Wu M, Gao H, Gao J, Wang S. Application of 15N tracing and bioinformatics for estimating microbial-mediated nitrogen cycle processes in oil-contaminated soils. ENVIRONMENTAL RESEARCH 2023; 217:114799. [PMID: 36384190 DOI: 10.1016/j.envres.2022.114799] [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: 09/01/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Crude oil pollution can profoundly alter the nitrogen (N) cycle in the soil. Here, a 30-day incubation with 15N tracer approach was performed to assess the impacts of crude oil concentrations (medium: 10,000 mg kg-1; heavy: 50,000 mg kg-1) on soil N cycling based on a numerical model. Results showed that crude oil pollution significantly increased the gross N-transformation rates, but the rates of oxidation of recalcitrant organic N, the immbolization of NO3- and the adsorption of NH4+ changed differently as a function of hydrocarbon concentrations. There was no significant difference of the oxidation rate of recalcitrant organic N between the medium and heavy oil-contaminated soils (medium: 0.1149 mmol N kg-1 d-1; heavy: 0.1299 mmol N kg-1 d-1), but the rates of NO3- immobilization (0.1135 mmol N kg-1 d-1) and NH4+ adsorption were the highest (0.1148 mmol N kg-1 d-1) in the moderately oil-contaminated soils than those in the heavy polluted soil (0.0849 mmol N kg-1 d-1 and 0.0034 mmol N kg-1 d-1, respectively). The NO3- immobilization rate was 2.5-fold higher than its reduction rate, indicating that NO3- immobilization played a more important role during the process of NO3- transformation. Microbial community structure analysis indicated that phyla of Actinobacteria and Ascomycota respectively promoted the immobilization of NO3- to recalcitrant organic N and the reduction of NO3- to NH4+. The genus of Aspergillus was related to net NH4+ production, and the genera of Penicillium and Acremonium were responsible for oxidation of recalcitrant organic N to NO3-.
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Affiliation(s)
- Heng Liu
- Key Laboratory of Environmental Engineering of Shaanxi Province, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Manli Wu
- Key Laboratory of Environmental Engineering of Shaanxi Province, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China; Key Laboratory of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an, 710055, China.
| | - Huan Gao
- Key Laboratory of Environmental Engineering of Shaanxi Province, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Jinghua Gao
- Key Laboratory of Environmental Engineering of Shaanxi Province, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - ShiJie Wang
- Key Laboratory of Environmental Engineering of Shaanxi Province, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
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19
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Miyamoto H, Kikuchi J. An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach. Comput Struct Biotechnol J 2023; 21:869-878. [PMID: 36698969 PMCID: PMC9860287 DOI: 10.1016/j.csbj.2023.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
The natural world is constantly changing, and planetary boundaries are issuing severe warnings about biodiversity and cycles of carbon, nitrogen, and phosphorus. In other views, social problems such as global warming and food shortages are spreading to various fields. These seemingly unrelated issues are closely related, but it can be said that understanding them in an integrated manner is still a step away. However, progress in analytical technologies has been recognized in various fields and, from a microscopic perspective, with the development of instruments including next-generation sequencers (NGS), nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC/MS), and liquid chromatography-mass spectrometry (LC/MS), various forms of molecular information such as genome data, microflora structure, metabolome, proteome, and lipidome can be obtained. The development of new technology has made it possible to obtain molecular information in a variety of forms. From a macroscopic perspective, the development of environmental analytical instruments and environmental measurement facilities such as satellites, drones, observation ships, and semiconductor censors has increased the data availability for various environmental factors. Based on these background, the role of computational science is to provide a mechanism for integrating and understanding these seemingly disparate data sets. This review describes machine learning and the need for structural equations and statistical causal inference of these data to solve these problems. In addition to introducing actual examples of how these technologies can be utilized, we will discuss how to use these technologies to implement environmentally friendly technologies in society.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co. Ltd., Chiba, Chiba 260-0034, Japan
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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20
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Mancia A, Chadwick DR, Waters SM, Krol DJ. Low N 2O emissions associated with sheep excreta deposition in temperate managed lowland grassland and extensively grazed hill pasture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158070. [PMID: 35981583 DOI: 10.1016/j.scitotenv.2022.158070] [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: 05/06/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas (GHG) whose emission from soil can be enhanced by ruminant excretal returns in grasslands. The default (Tier 1) emission factors (EF3PRP; i.e. proportion of deposited nitrogen emitted as N2O) for ruminant excreta deposition are associated with a wide range of uncertainties and the development of country-specific (Tier 2) EF3PRP is encouraged. In Ireland, a Tier 2 EF3PRP has been developed for cattle excreta but no data are available for sheep. The aim of this study was to generate data to contribute to the derivation of a Tier 2 EF3PRP for sheep excreta, while assessing the effect of excreta type, grassland type and season of deposition on N2O emissions. An experiment was carried out on two sites in the west of Ireland: a managed lowland grassland (LOW) and an extensively grazed hill pasture (HILL), characterised by mineral and acid peat soils, respectively. For each season, four treatments were applied to the soil in a fully randomized block design: control (C), sheep urine (U), sheep dung (D), and artificial urine (AU). Nitrous oxide fluxes were assessed over a full year following each application of treatments, using a static chambers methodology. Results showed a brief initial peak following each application of U/AU in LOW but not in HILL. Cumulative N2O emissions were significantly higher from the lowland site. Average EF3PRP for combined excreta was negligible on both sites, thus lower than the IPCC Tier 1 EF3PRP. Causes of low emissions are likely to depend on site characteristics (e.g. soil acidity in HILL) and season of application (i.e. ammonia volatilisation in summer). This study showed very low N2O emissions from sheep excretal returns in Irish grasslands and highlighted the importance of developing Tier 2, animal-specific EF3PRP. More experimental grasslands should be assessed to confirm these results.
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Affiliation(s)
- Aude Mancia
- Teagasc, Crops, Land Use and Environment Programme, Johnstown Castle, Co. Wexford, Ireland; School of Natural Sciences, Bangor University, Bangor, UK; Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | | | - Sinéad M Waters
- Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Dominika J Krol
- Teagasc, Crops, Land Use and Environment Programme, Johnstown Castle, Co. Wexford, Ireland.
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21
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Su X, Cui L, Tang Y, Wen T, Yang K, Wang Y, Zhang J, Zhu G, Yang X, Hou L, Zhu YG. Denitrification and N 2O Emission in Estuarine Sediments in Response to Ocean Acidification: From Process to Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14828-14839. [PMID: 36194569 DOI: 10.1021/acs.est.2c03550] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Global estuarine ecosystems are experiencing severe nitrogen pollution and ocean acidification (OA) simultaneously. Sedimentary denitrification is an important way of reactive nitrogen removal but at the same time leads to the emission of large amounts of nitrous oxide (N2O), a potent greenhouse gas. It is known that OA in estuarine regions could impact denitrification and N2O production; however, the underlying mechanism is still underexplored. Here, sediment incubation and pure culture experiments were conducted to explore the OA impacts on microbial denitrification and the associated N2O emissions in estuarine sediments. Under neutral (in situ) conditions, fungal N2O emission dominated in the sediment, while the bacterial and fungal sources had a similar role under acidification. This indicated that acidification decreased the sedimentary fungal denitrification and likely inhibited the activity of fungal denitrifiers. To explore molecular mechanisms, a denitrifying fungal strain of Penicillium janthinellum was isolated from the sediments. By using deuterium-labeled single-cell Raman spectroscopy and isobaric tags for relative and absolute quantitation proteomics, we found that acidification inhibited electron transfers in P. janthinellum and downregulated expressions of the proteins related to energy production and conservation. Two collaborative pathways of energy generation in the P. janthinellum were further revealed, that is, aerobic oxidative phosphorylation and TCA cycle and anoxic pyruvate fermentation. This indicated a distinct energy supply strategy from bacterial denitrification. Our study provides insights into fungi-mediated nitrogen cycle in acidifying aquatic ecosystems.
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Affiliation(s)
- Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment; Key Laboratory of Low-Carbon Green Agriculture in Southwestern China, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing400715, China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Yijia Tang
- School of Life and Environmental Sciences, The University of Sydney, Biomedical Building (C81), Sydney, New South Wales2015, Australia
| | - Teng Wen
- School of Geography, Nanjing Normal University, Nanjing210023, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, Nanjing210023, China
| | - Kai Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Yingmu Wang
- College of Civil Engineering, Fuzhou University, Fuzhou350116, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing210023, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, Nanjing210023, China
| | - Guibing Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai200062, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- University of the Chinese Academy of Sciences, Beijing100049, China
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22
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Dey A, Albert T, Kong RY, Macmillan SN, Moënne-Loccoz P, Lancaster KM, Goldberg DP. Direct Reduction of NO to N 2O by a Mononuclear Nonheme Thiolate Ligated Iron(II) Complex via Formation of a Metastable {FeNO} 7 Complex. Inorg Chem 2022; 61:14909-14917. [PMID: 36107151 PMCID: PMC9555345 DOI: 10.1021/acs.inorgchem.2c02383] [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] [Indexed: 11/30/2022]
Abstract
Addition of NO to a nonheme dithiolate-ligated iron(II) complex, FeII(Me3TACN)(S2SiMe2) (1), results in the generation of N2O. Low-temperature spectroscopic studies reveal a metastable six-coordinate {FeNO}7 intermediate (S = 3/2) that was trapped at -135 °C and was characterized by low-temperature UV-vis, resonance Raman, EPR, Mössbauer, XAS, and DFT studies. Thermal decay of the {FeNO}7 species leads to the evolution of N2O, providing a rare example of a mononuclear thiolate-ligated {FeNO}7 that mediates NO reduction to N2O without the requirement of any exogenous electron or proton sources.
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Affiliation(s)
- Aniruddha Dey
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, Unites States
| | - Richard Y. Kong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, Unites States
| | - Samantha N. Macmillan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, Unites States
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, Unites States
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, Unites States
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, United States
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23
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Nitrous Oxide Emissions from Nitrite Are Highly Dependent on Nitrate Reductase in the Microalga Chlamydomonas reinhardtii. Int J Mol Sci 2022; 23:ijms23169412. [PMID: 36012676 PMCID: PMC9409008 DOI: 10.3390/ijms23169412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 12/11/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and an ozone-depleting compound whose synthesis and release have traditionally been ascribed to bacteria and fungi. Although plants and microalgae have been proposed as N2O producers in recent decades, the proteins involved in this process have been only recently unveiled. In the green microalga Chlamydomonas reinhardtii, flavodiiron proteins (FLVs) and cytochrome P450 (CYP55) are two nitric oxide (NO) reductases responsible for N2O synthesis in the chloroplast and mitochondria, respectively. However, the molecular mechanisms feeding these NO reductases are unknown. In this work, we use cavity ring-down spectroscopy to monitor N2O and CO2 in cultures of nitrite reductase mutants, which cannot grow on nitrate or nitrite and exhibit enhanced N2O emissions. We show that these mutants constitute a very useful tool to study the rates and kinetics of N2O release under different conditions and the metabolism of this greenhouse gas. Our results indicate that N2O production, which was higher in the light than in the dark, requires nitrate reductase as the major provider of NO as substrate. Finally, we show that the presence of nitrate reductase impacts CO2 emissions in both light and dark conditions, and we discuss the role of NO in the balance between CO2 fixation and release.
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24
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Microbiogeochemical Traits to Identify Nitrogen Hotspots in Permafrost Regions. NITROGEN 2022. [DOI: 10.3390/nitrogen3030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Permafrost-affected tundra soils are large carbon (C) and nitrogen (N) reservoirs. However, N is largely bound in soil organic matter (SOM), and ecosystems generally have low N availability. Therefore, microbial induced N-cycling processes and N losses were considered negligible. Recent studies show that microbial N processing rates, inorganic N availability, and lateral N losses from thawing permafrost increase when vegetation cover is disturbed, resulting in reduced N uptake or increased N input from thawing permafrost. In this review, we describe currently known N hotspots, particularly bare patches in permafrost peatland or permafrost soils affected by thermokarst, and their microbiogeochemical characteristics, and present evidence for previously unrecorded N hotspots in the tundra. We summarize the current understanding of microbial N cycling processes that promote the release of the potent greenhouse gas (GHG) nitrous oxide (N2O) and the translocation of inorganic N from terrestrial into aquatic ecosystems. We suggest that certain soil characteristics and microbial traits can be used as indicators of N availability and N losses. Identifying N hotspots in permafrost soils is key to assessing the potential for N release from permafrost-affected soils under global warming, as well as the impact of increased N availability on emissions of carbon-containing GHGs.
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25
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Yang K, Bu H, Zhang Y, Yu H, Huang S, Ke L, Hong P. Efficacy of simultaneous hexavalent chromium biosorption and nitrogen removal by the aerobic denitrifying bacterium Pseudomonas stutzeri YC-34 from chromium-rich wastewater. Front Microbiol 2022; 13:961815. [PMID: 35992714 PMCID: PMC9389319 DOI: 10.3389/fmicb.2022.961815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/11/2022] [Indexed: 12/03/2022] Open
Abstract
The impact of high concentrations of heavy metals and the loss of functional microorganisms usually affect the nitrogen removal process in wastewater treatment systems. In the study, a unique auto-aggregating aerobic denitrifier (Pseudomonas stutzeri strain YC-34) was isolated with potential applications for Cr(VI) biosorption and reduction. The nitrogen removal efficiency and denitrification pathway of the strain were determined by measuring the concentration changes of inorganic nitrogen during the culture of the strain and amplifying key denitrification functional genes. The changes in auto-aggregation index, hydrophobicity index, and extracellular polymeric substances (EPS) characteristic index were used to evaluate the auto-aggregation capacity of the strain. Further studies on the biosorption ability and mechanism of cadmium in the process of denitrification were carried out. The changes in tolerance and adsorption index of cadmium were measured and the micro-characteristic changes on the cell surface were analyzed. The strain exhibited excellent denitrification ability, achieving 90.58% nitrogen removal efficiency with 54 mg/L nitrate-nitrogen as the initial nitrogen source and no accumulation of ammonia and nitrite-nitrogen. Thirty percentage of the initial nitrate-nitrogen was converted to N2, and only a small amount of N2O was produced. The successful amplification of the denitrification functional genes, norS, norB, norR, and nosZ, further suggested a complete denitrification pathway from nitrate to nitrogen. Furthermore, the strain showed efficient aggregation capacity, with the auto-aggregation and hydrophobicity indices reaching 78.4 and 75.5%, respectively. A large amount of protein-containing EPS was produced. In addition, the strain effectively removed 48.75, 46.67, 44.53, and 39.84% of Cr(VI) with the initial concentrations of 3, 5, 7, and 10 mg/L, respectively, from the nitrogen-containing synthetic wastewater. It also could reduce Cr(VI) to the less toxic Cr(III). FTIR measurements and characteristic peak deconvolution analysis demonstrated that the strain had a robust hydrogen-bonded structure with strong intermolecular forces under the stress of high Cr(VI) concentrations. The current results confirm that the novel denitrifier can simultaneously remove nitrogen and chromium and has potential applications in advanced wastewater treatment for the removal of multiple pollutants from sewage.
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26
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Su X, Yang L, Yang K, Tang Y, Wen T, Wang Y, Rillig MC, Rohe L, Pan J, Li H, Zhu YG. Estuarine plastisphere as an overlooked source of N2O production. Nat Commun 2022; 13:3884. [PMID: 35794126 PMCID: PMC9259610 DOI: 10.1038/s41467-022-31584-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/22/2022] [Indexed: 12/13/2022] Open
Abstract
“Plastisphere”, microbial communities colonizing plastic debris, has sparked global concern for marine ecosystems. Microbiome inhabiting this novel human-made niche has been increasingly characterized; however, whether the plastisphere holds crucial roles in biogeochemical cycling remains largely unknown. Here we evaluate the potential of plastisphere in biotic and abiotic denitrification and nitrous oxide (N2O) production in estuaries. Biofilm formation provides anoxic conditions favoring denitrifiers. Comparing with surrounding bulk water, plastisphere exhibits a higher denitrifying activity and N2O production, suggesting an overlooked N2O source. Regardless of plastisphere and bulk water, bacterial and fungal denitrifications are the main regulators for N2O production instead of chemodenitrification. However, the contributions of bacteria and fungi in the plastisphere are different from those in bulk water, indicating a distinct N2O production pattern in the plastisphere. These findings pinpoint plastisphere as a N2O source, and provide insights into roles of the new biotope in biogeochemical cycling in the Anthropocene. The roles of marine plastisphere in global nitrogen cycling are largely unknown. Here, the authors indicate that the plastisphere could act as a potential source of N2O production, which is mainly regulated by the biotic denitrification
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27
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Lin Z, Ma K, Yang Y. Nitrous Oxide Emission from Full-Scale Anammox-Driven Wastewater Treatment Systems. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070971. [PMID: 35888061 PMCID: PMC9317218 DOI: 10.3390/life12070971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022]
Abstract
Wastewater treatment plants (WWTPs) are important contributors to global greenhouse gas (GHG) emissions, partly due to their huge emission of nitrous oxide (N2O), which has a global warming potential of 298 CO2 equivalents. Anaerobic ammonium-oxidizing (anammox) bacteria provide a shortcut in the nitrogen removal pathway by directly transforming ammonium and nitrite to nitrogen gas (N2). Due to its energy efficiency, the anammox-driven treatment has been applied worldwide for the removal of inorganic nitrogen from ammonium-rich wastewater. Although direct evidence of the metabolic production of N2O by anammox bacteria is lacking, the microorganisms coexisting in anammox-driven WWTPs could produce a considerable amount of N2O and hence affect the sustainability of wastewater treatment. Thus, N2O emission is still one of the downsides of anammox-driven wastewater treatment, and efforts are required to understand the mechanisms of N2O emission from anammox-driven WWTPs using different nitrogen removal strategies and develop effective mitigation strategies. Here, three main N2O production processes, namely, hydroxylamine oxidation, nitrifier denitrification, and heterotrophic denitrification, and the unique N2O consumption process termed nosZ-dominated N2O degradation, occurring in anammox-driven wastewater treatment systems, are summarized and discussed. The key factors influencing N2O emission and mitigation strategies are discussed in detail, and areas in which further research is urgently required are identified.
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28
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Kaushal R, Hsueh YH, Chen CL, Lan YP, Wu PY, Chen YC, Liang MC. Isotopic assessment of soil N 2O emission from a sub-tropical agricultural soil under varying N-inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154311. [PMID: 35257756 DOI: 10.1016/j.scitotenv.2022.154311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/12/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen fertilizers result in high crop productivity but also enhance the emission of N2O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N2O and N2 via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N2O production. Here, we report the results of N2O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N2O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N2O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N2O during the entire course of the incubation experiments. Peak N2O emissions of 122 ± 98 μg N2O-N m-2 h-1, 338 ± 49 μg N2O-N m-2 h-1 and 739 ± 296 μg N2O-N m-2 h-1 were observed for urea application rate of 40, 80, and 120 μg N g-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ15N, δ18O, and 15N site preference, we inferred co-occurrence of several microbial N2O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N2O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N2O emission pulse in intermediate urea-N levels. Signature of N2O consumption by reduction could be traced during declining emissions in treatment with high urea level.
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Affiliation(s)
- Ritika Kaushal
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsin Hsueh
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan; Taiwan International Graduate Program-Earth Systems Science, Academia Sinica, Taipei, Taiwan
| | - Chi-Ling Chen
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Yi-Ping Lan
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan
| | - Ping-Yu Wu
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Yi-Chun Chen
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Mao-Chang Liang
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan.
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29
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Metagenomic analysis of microbial community structure and function in a improved biofilter with odorous gases. Sci Rep 2022; 12:1731. [PMID: 35110663 PMCID: PMC8810771 DOI: 10.1038/s41598-022-05858-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/19/2022] [Indexed: 11/09/2022] Open
Abstract
Biofilters have been broadly applied to degrade the odorous gases from industrial emissions. A industrial scale biofilter was set up to treat the odorous gases. To explore biofilter potentials, the microbial community structure and function must be well defined. Using of improved biofilter, the differences in microbial community structures and functions in biofilters before and after treatment were investigated by metagenomic analysis. Odorous gases have the potential to alter the microbial community structure in the sludge of biofilter. A total of 90,016 genes assigned into various functional metabolic pathways were identified. In the improved biofilter, the dominant phyla were Proteobacteria, Planctomycetes, and Chloroflexi, and the dominant genera were Thioalkalivibrio, Thauera, and Pseudomonas. Several xenobiotic biodegradation-related pathways showed significant changes during the treatment process. Compared with the original biofilter, Thermotogae and Crenarchaeota phyla were significantly enriched in the improved biofilter, suggesting their important role in nitrogen-fixing. Furthermore, several nitrogen metabolic pathway-related genes, such as nirA and nifA, and sulfur metabolic pathway-related genes, such as fccB and phsA, were considered to be efficient genes that were involved in removing odorous gases. Our findings can be used for improving the efficiency of biofilter and helping the industrial enterprises to reduce the emission of waste gases.
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30
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Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
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Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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31
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Novinscak A, Goyer C, Wilson C, Zebarth BJ, Burton DL, Chantigny MH, Filion M. Seasonal changes in the abundance and activity of bacterial and fungal denitrifying communities associated with different compost amendments. Can J Microbiol 2021; 68:91-102. [PMID: 34762539 DOI: 10.1139/cjm-2021-0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Composts can be efficient organic amendments in potato culture as they can supply carbon and nutrients to the soil. However, more information is required to the effects of composts on denitrification and nitrous oxide emissions (N2O) and the emission-producing denitrifying communities. The effect of three compost amendments (municipal source separated organic waste compost (SSOC), forestry waste mixed with poultry manure compost (FPMC), and forestry residues compost (FRC)) on fungal and bacterial denitrifying communities and activity was examined in an agricultural field cropped to potatoes in during the fall, spring and summer seasons. The denitrification enzyme activity (DEA), N2O emissions and respiration were measured in parallel. N2O emission rates were greater in FRC-amended soils in the fall and summer, while soil respiration was highest in SSOC-amended soil in the fall. A large number of nirK denitrifying fungal transcripts was detected in the fall, coinciding with compost application while the greatest nirK bacterial transcripts were measured in the summer when plants were actively growing. Denitrifying community and transcript levels were poor predictors of DEA, N2O emissions or respiration rates in compost-amended soil. Overall, the sampling date was driving the population and activity levels of the three denitrifying communities under study.
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Affiliation(s)
- Amy Novinscak
- Université de Moncton, 5568, Moncton, New Brunswick, Canada;
| | - Claudia Goyer
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, New Brunswick, Canada;
| | - Carolyn Wilson
- Dalhousie University, 3688, Biology Department, Truro, Nova Scotia, Canada;
| | - Bernie J Zebarth
- Fredericton Research and Development Centre, 98656, Fredericton, New Brunswick, Canada;
| | - David L Burton
- Dalhousie University, 3688, Biology Department, Truro, Nova Scotia, Canada;
| | | | - Martin Filion
- Saint-Jean-sur-Richelieu Research and Development Centre, 98683, Saint-Jean-sur-Richelieu, Quebec, Canada;
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32
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Bright Side of Fusarium oxysporum: Secondary Metabolites Bioactivities and Industrial Relevance in Biotechnology and Nanotechnology. J Fungi (Basel) 2021; 7:jof7110943. [PMID: 34829230 PMCID: PMC8625159 DOI: 10.3390/jof7110943] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/31/2022] Open
Abstract
Fungi have been assured to be one of the wealthiest pools of bio-metabolites with remarkable potential for discovering new drugs. The pathogenic fungi, Fusarium oxysporum affects many valuable trees and crops all over the world, producing wilt. This fungus is a source of different enzymes that have variable industrial and biotechnological applications. Additionally, it is widely employed for the synthesis of different types of metal nanoparticles with various biotechnological, pharmaceutical, industrial, and medicinal applications. Moreover, it possesses a mysterious capacity to produce a wide array of metabolites with a broad spectrum of bioactivities such as alkaloids, jasmonates, anthranilates, cyclic peptides, cyclic depsipeptides, xanthones, quinones, and terpenoids. Therefore, this review will cover the previously reported data on F. oxysporum, especially its metabolites and their bioactivities, as well as industrial relevance in biotechnology and nanotechnology in the period from 1967 to 2021. In this work, 180 metabolites have been listed and 203 references have been cited.
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Su X, Wen T, Wang Y, Xu J, Cui L, Zhang J, Xue X, Ding K, Tang Y, Zhu YG. Stimulation of N 2 O emission via bacterial denitrification driven by acidification in estuarine sediments. GLOBAL CHANGE BIOLOGY 2021; 27:5564-5579. [PMID: 34453365 DOI: 10.1111/gcb.15863] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 05/02/2023]
Abstract
Ocean acidification in nitrogen-enriched estuaries has raised global concerns. For decades, biotic and abiotic denitrification in estuarine sediments has been regarded as the major ways to remove reactive nitrogen, but they occur at the expense of releasing greenhouse gas nitrous oxide (N2 O). However, how these pathways respond to acidification remains poorly understood. Here we performed a N2 O isotopocules analysis coupled with respiration inhibition and molecular approaches to investigate the impacts of acidification on bacterial, fungal, and chemo-denitrification, as well as N2 O emission, in estuarine sediments through a series of anoxic incubations. Results showed that acidification stimulated N2 O release from sediments, which was mainly mediated by the activity of bacterial denitrifiers, whereas in neutral environments, N2 O production was dominated by fungi. We also found that the contribution of chemo-denitrification to N2 O production cannot be ignored, but was not significantly affected by acidification. The mechanistic investigation further demonstrated that acidification changed the keystone taxa of sedimentary denitrifiers from N2 O-reducing to N2 O-producing ones and reduced microbial electron-transfer efficiency during denitrification. These findings provide novel insights into how acidification stimulates N2 O emission and modulates its pathways in estuarine sediments, and how it may contribute to the acceleration of global climate change in the Anthropocene.
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Affiliation(s)
- Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Teng Wen
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Yingmu Wang
- College of Civil Engineering, Fuzhou University, Fuzhou, China
| | - Junshi Xu
- Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, Nanjing, China
| | - Ximei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yijia Tang
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Institute of Agriculture, Sydney, New South Wales, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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34
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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Soil Redox Controls CO 2, CH 4 and N 2O Efflux from White-Rot Fungi in Temperate Forest Ecosystems. J Fungi (Basel) 2021; 7:jof7080621. [PMID: 34436159 PMCID: PMC8398011 DOI: 10.3390/jof7080621] [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: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Microaerophilic white-rot fungi (WRF) are impacted by oxygen depletion because of fluctuating redox occurrence in southern temperate forest soils of Chile (1500-5000 mm year-1). How these conditions influence WRF survival has been scarcely examined. We explored the contributions of WRF to greenhouse gas (GHG) emissions of N2O and CH4 and soil organic C oxidation (CO2) in five sterilized and inoculated forest soils derived from various parent materials and climates. The soil was incubated for 20 days following (i) oxic, (ii) anoxic, and (iii) fluctuating redox conditions. Fungi contributed to 45% of the total GHG under redox fluctuating conditions, including the contribution of bacteria, while the opposite (26%) was valid for oxic treatment. On average, the highest gas emission (62%) was N2O for WRF under redox treatment, followed by anoxic (22%) and oxic (16%) treatments, while CO2 and CH4 emissions followed oxic > redox > anoxic. These data suggest that indigenous microbial WRF communities are well adapted to fluctuating redox milieu with a significant release of GHG emissions in humid temperate forests of the southern cone.
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Ganasamurthy S, Rex D, Samad MS, Richards KG, Lanigan GJ, Grelet GA, Clough TJ, Morales SE. Competition and community succession link N transformation and greenhouse gas emissions in urine patches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146318. [PMID: 34030223 DOI: 10.1016/j.scitotenv.2021.146318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/28/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) is a strong greenhouse gas produced by biotic/abiotic processes directly linked to both fungal and prokaryotic communities that produce, consume or create conditions leading to its emission. In soils exposed to nitrogen (N) in the form of urea, an ecological succession is triggered resulting in a dynamic turnover of microbial populations. However, knowledge of the mechanisms controlling this succession and the repercussions for N2O emissions remain incomplete. Here, we monitored N2O production and fungal/prokaryotic community changes (via 16S and 18S amplicon sequencing) in soil microcosms exposed to urea. Contributions of microbes to emissions were determined using biological inhibitors. Results confirmed that urea leads to shifts in microbial community assemblages by selecting for certain microbial groups (fast growers) as dictated through life history strategies. Urea reduced overall community diversity by conferring dominance to specific groups at different stages in the succession. The diversity lost under urea was recovered with inhibitor addition through the removal of groups that were actively growing under urea indicating that species replacement is mediated in part by competition. Results also identified fungi as significant contributors to N2O emissions, and demonstrate that dominant fungal populations are consistently replaced at different stages of the succession. These successions were affected by addition of inhibitors which resulted in strong decreases in N2O emissions, suggesting that fungal contributions to N2O emissions are larger than that of prokaryotes.
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Affiliation(s)
- Syaliny Ganasamurthy
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - David Rex
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand
| | - Md Sainur Samad
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand; Heinrich von Thünen-Institute, Institute for Biodiversity, Braunschweig, Germany
| | - Karl G Richards
- Teagasc, Environmental Research Centre, Johnstown Castle, Wexford, Ireland
| | - Gary J Lanigan
- Teagasc, Environmental Research Centre, Johnstown Castle, Wexford, Ireland
| | - Gwen-Aëlle Grelet
- Manaaki Whenua- Landcare Research, Land Use & Ecosystems Team, Gerald Street, PO, Box 69040, Lincoln 7640, New Zealand
| | - Timothy J Clough
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand.
| | - Sergio E Morales
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand.
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37
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Ou SN, Liang JL, Jiang XM, Liao B, Jia P, Shu WS, Li JT. Physiological, Genomic and Transcriptomic Analyses Reveal the Adaptation Mechanisms of Acidiella bohemica to Extreme Acid Mine Drainage Environments. Front Microbiol 2021; 12:705839. [PMID: 34305876 PMCID: PMC8298002 DOI: 10.3389/fmicb.2021.705839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Fungi in acid mine drainage (AMD) environments are of great concern due to their potentials of decomposing organic carbon, absorbing heavy metals and reducing AMD acidity. Based on morphological analysis and ITS/18S high-throughput sequencing technology, previous studies have provided deep insights into the diversity and community composition of fungi in AMD environments. However, knowledge about physiology, metabolic potential and transcriptome profiles of fungi inhabiting AMD environments is still scarce. Here, we reported the physiological, genomic, and transcriptomic characterization of Acidiella bohemica SYSU C17045 to improve our understanding of the physiological, genomic, and transcriptomic mechanisms underlying fungal adaptation to AMD environments. A. bohemica was isolated from an AMD environment, which has been proved to be an acidophilic fungus in this study. The surface of A. bohemica cultured in AMD solutions was covered with a large number of minerals such as jarosite. We thus inferred that the A. bohemica might have the potential of biologically induced mineralization. Taking advantage of PacBio single-molecule real-time sequencing, we obtained the high-quality genome sequences of A. bohemica (50 Mbp). To our knowledge, this was the first attempt to employ a third-generation sequencing technology to explore the genomic traits of fungi isolated from AMD environments. Moreover, our transcriptomic analysis revealed that a series of genes in the A. bohemica genome were related to its metabolic pathways of C, N, S, and Fe as well as its adaptation mechanisms, including the response to acid stress and the resistance to heavy metals. Overall, our physiological, genomic, and transcriptomic data provide a foundation for understanding the metabolic potential and adaptation mechanisms of fungi in AMD environments.
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Affiliation(s)
- Shu-Ning Ou
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiao-Min Jiang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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38
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Muñoz-Gómez SA, Kreutz M, Hess S. A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts. SCIENCE ADVANCES 2021; 7:eabg4102. [PMID: 34117067 PMCID: PMC8195481 DOI: 10.1126/sciadv.abg4102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/27/2021] [Indexed: 05/08/2023]
Abstract
Oxygenic photosynthesizers (cyanobacteria and eukaryotic algae) have repeatedly become endosymbionts throughout evolution. In contrast, anoxygenic photosynthesizers (e.g., purple bacteria) are exceedingly rare as intracellular symbionts. Here, we report on the morphology, ultrastructure, lifestyle, and metagenome of the only "purple-green" eukaryote known. The ciliate Pseudoblepharisma tenue harbors green algae and hundreds of genetically reduced purple bacteria. The latter represent a new candidate species of the Chromatiaceae that lost known genes for sulfur dissimilation. The tripartite consortium is physiologically complex because of the versatile energy metabolism of each partner but appears to be ecologically specialized as it prefers hypoxic sediments. The emergent niche of this complex symbiosis is predicted to be a partial overlap of each partners' niches and may be largely defined by anoxygenic photosynthesis and possibly phagotrophy. This purple-green ciliate thus represents an extraordinary example of how symbiosis merges disparate physiologies and allows emergent consortia to create novel ecological niches.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Institute for Zoology, Cologne Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany.
- Center for Mechanism of Evolution, The Biodesign Institute, School of Life Sciences, Arizona State University, 727 E. Tyler St., Tempe, AZ 85281-5001, USA
| | - Martin Kreutz
- Private Laboratory, Am See 27, 78465 Constance, Germany
| | - Sebastian Hess
- Institute for Zoology, Cologne Biocenter, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany.
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39
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Short-lived intermediate in N 2O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography. Proc Natl Acad Sci U S A 2021; 118:2101481118. [PMID: 34001620 DOI: 10.1073/pnas.2101481118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitric oxide (NO) reductase from the fungus Fusarium oxysporum is a P450-type enzyme (P450nor) that catalyzes the reduction of NO to nitrous oxide (N2O) in the global nitrogen cycle. In this enzymatic reaction, the heme-bound NO is activated by the direct hydride transfer from NADH to generate a short-lived intermediate ( I ), a key state to promote N-N bond formation and N-O bond cleavage. This study applied time-resolved (TR) techniques in conjunction with photolabile-caged NO to gain direct experimental results for the characterization of the coordination and electronic structures of I TR freeze-trap crystallography using an X-ray free electron laser (XFEL) reveals highly bent Fe-NO coordination in I , with an elongated Fe-NO bond length (Fe-NO = 1.91 Å, Fe-N-O = 138°) in the absence of NAD+ TR-infrared (IR) spectroscopy detects the formation of I with an N-O stretching frequency of 1,290 cm-1 upon hydride transfer from NADH to the Fe3+-NO enzyme via the dissociation of NAD+ from a transient state, with an N-O stretching of 1,330 cm-1 and a lifetime of ca. 16 ms. Quantum mechanics/molecular mechanics calculations, based on these crystallographic and IR spectroscopic results, demonstrate that the electronic structure of I is characterized by a singly protonated Fe3+-NHO•- radical. The current findings provide conclusive evidence for the N2O generation mechanism via a radical-radical coupling of the heme nitroxyl complex with the second NO molecule.
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40
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Reed CJ, Lam QN, Mirts EN, Lu Y. Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chem Soc Rev 2021; 50:2486-2539. [PMID: 33475096 PMCID: PMC7920998 DOI: 10.1039/d0cs01297a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
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Affiliation(s)
- Christopher J Reed
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA.
| | - Quan N Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA
| | - Evan N Mirts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA. and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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41
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Dawar K, Khan A, Sardar K, Fahad S, Saud S, Datta R, Danish S. Effects of the nitrification inhibitor nitrapyrin and mulch on N 2O emission and fertilizer use efficiency using 15N tracing techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143739. [PMID: 33229088 DOI: 10.1016/j.scitotenv.2020.143739] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
Nitrous oxide (N2O), is a potent greenhouse gas (GHG) that shares 7% of global warming around the world. Among different sources, agricultural systems account for approx. 60% of global anthropogenic N2O emissions. These N2O emissions are associated with the activity of nitrifiers and denitrifiers that contribute to >4 Tg (teragrams) N2O-N emission per year. Application of nitrogen (N) fertilizers and manures in agricultural fields plays an imperative role in this regard. On the other hand nitrification inhibitors are an effective approach to minimize N2O-N emissions from agricultural fields. Here we examined the effects of applying urea with a nitrification inhibitor (Ni) nitrapyrin and mulch (Mu) on urea transformation, nitrous oxide (N2O) emissions, grain yield and nitrogen (N) uptake efficiency. The treatments include a control (zero N), urea (U) applied at 200 kg N ha-1, U + Ni (Ni applied at 700 g ha-1), U+ Mu (Mu applied at 4 t ha-1) and U + Ni + Mu. The N2O emission factor (EF) was 66% and 75% when U and Mu were applied, respectively. Yield-scaled N2O emissions were lower in U and Mu by 45% and 55%, respectively. The Ni coupled with Mu enhanced urea-15N recovery by 58% and wheat grain yield by 23% and total N uptake by 30% compared with U alone. In conclusion, Ni usage is an effective strategy to mitigate N2O emissions under field conditions.
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Affiliation(s)
- Khadim Dawar
- Department of Soil and Environmental Science, the University of Agriculture Peshawar, Pakistan.
| | - Aamir Khan
- Department of Soil and Environmental Science, the University of Agriculture Peshawar, Pakistan
| | - Kamil Sardar
- Department of Soil and Environmental Science, the University of Agriculture Peshawar, Pakistan
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan 570228, China; Department of Agronomy, The University of Haripur, Haripur, Khyber Pakhtunkhwa 22620, Pakistan.
| | - Shah Saud
- Department of Horticulture, Northeast Agriculture University, Harbin, China
| | - Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Czech Republic
| | - Subhan Danish
- Department of Soil Science, Bahauddin Zakariya University, Multan, 60800, Punjab, Pakistan
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42
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Huang Y, Jing J, Yan M, Hazard C, Chen Y, Guo C, Xiao X, Lin J. Contribution of pathogenic fungi to N 2O emissions increases temporally in intensively managed strawberry cropping soil. Appl Microbiol Biotechnol 2021; 105:2043-2056. [PMID: 33555364 DOI: 10.1007/s00253-021-11163-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/26/2022]
Abstract
Intensively managed agriculture land is a significant contributor to nitrous oxide (N2O) emissions, which adds to global warming and the depletion of the ozone layer. Recent studies have suggested that fungal dominant N2O production may be promoted by pathogenic fungi under high nitrogen fertilization and continuous cropping. Here, we measured the contribution of fungal communities to N2O production under intensively managed strawberry fields of three continuous cropping years (1, 5, and 10 years) and compared this adjacent bare soil. Higher N2O emission was observed from the 10-year field, of which fungi and prokaryotes accounted for 79.7% and 21.3%, respectively. Fungal population density in the 10-year field soil (4.25 × 105 colony forming units per g (CFU/g) of air-dried soil) was greater than the other cropping years. Illumina MiSeq sequencing of the nirK gene showed that long-term continuous cropping decreased the diversity of the fungal denitrifier community, but increased the abundance of Fusarium oxysporum. Additionally, F. oxysporum produced large amounts of N2O in culture and in sterile 10-year field soil. A systemic infection displayed by bioassay strawberry plants after inoculation demonstrated that F. oxysporum was a pathogenic fungus. Together, results suggest that long-term intensively managed monocropping significantly influenced the denitrifying fungal community and increased their biomass, which increased fungal contribution to N2O emissions and specifically by pathogenic fungi. KEY POINTS: • Distinguishing the role of fungi in long-term continuous cropping field. • Identifying the abundant fungal species with denitrifying ability.
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Affiliation(s)
- Ying Huang
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Jinquan Jing
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Meiling Yan
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, 36 Avenue Guy de Collongue, 69134, Ecully, France
| | - Yuehong Chen
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China.
| | - Chengbao Guo
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Xu Xiao
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Jiujun Lin
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
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Aldossari N, Ishii S. Isolation of cold-adapted nitrate-reducing fungi that have potential to increase nitrate removal in woodchip bioreactors. J Appl Microbiol 2020; 131:197-207. [PMID: 33222401 DOI: 10.1111/jam.14939] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 11/27/2022]
Abstract
AIMS The aim of this study was to obtain cold-adapted denitrifying fungi that could be used for bioaugmentation in woodchip bioreactors to remove nitrate from agricultural subsurface drainage water. METHODS AND RESULTS We isolated a total of 91 nitrate-reducing fungal strains belonging to Ascomycota and Mucoromycota from agricultural soil and a woodchip bioreactor under relatively cold conditions (5 and 15°C). When these strains were incubated with 15 N-labelled nitrate, 29 N2 was frequently produced, suggesting the occurrence of co-denitrification (microbially mediated nitrosation). Two strains also produced 30 N2 , indicating their ability to reduce N2 O. Of the 91 nitrate-reducing fungal strains, fungal nitrite reductase gene (nirK) and cytochrome P450 nitric oxide reductase gene (p450nor) were detected by PCR in 34 (37%) and 11 (12%) strains, respectively. Eight strains possessed both nirK and p450nor, further verifying their denitrification capability. In addition, most strains degraded cellulose under denitrification condition. CONCLUSIONS Diverse nitrate-reducing fungi were isolated from soil and a woodchip bioreactor. These fungi reduced nitrate to gaseous N forms at relatively low temperatures. These cold-adapted, cellulose-degrading and nitrate-reducing fungi could support themselves and other denitrifiers in woodchip bioreactors. SIGNIFICANCE AND IMPACT OF THE STUDY The cold-adapted, cellulose-degrading and nitrate-reducing fungi isolated in this study could be useful to enhance nitrate removal in woodchip bioreactors under low-temperature conditions.
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Affiliation(s)
- N Aldossari
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, USA
| | - S Ishii
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, USA.,BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
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Manivel G, Raj DML, Prathiviraj R, Senthilraja P. Distribution of phylogenetic proximity upon species-rich marine Ascomycetes with reference to Pichavaram mangrove soil sediment of southern India. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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He Z, Deng H, Wang Q, Li Y, Liang X, Liu D, Wu Y. Electrochemical and spectroscopic characteristics of cytochrome P450 55A3 and its interaction with nitric oxide. Int J Biol Macromol 2020; 167:1406-1413. [PMID: 33202279 DOI: 10.1016/j.ijbiomac.2020.11.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/17/2020] [Accepted: 11/12/2020] [Indexed: 11/30/2022]
Abstract
Cytochrome P450 55A3 (CYP55A3) is an enzyme with the catalytic activity of nitric oxide (NO) to nitrous oxide using NADH or NADPH as the electron donor. Herein CYP55A3 has been expressed in E. coli and purified by His-tag columns. The electrochemical and spectroscopic characteristic of CYP55A3 and its interaction with NO has been studied. The direct electrochemistry of Fe3+/Fe2+ redox peaks in CYP55A3 was realized on the pyrolitic graphite electrode with the redox potential of -475 mV in pH 7.0 phosphate buffer. With the addition of NO a ferric nitroxyl complex (Fe3+-NO) formed with a new reduction peak at -0.78 V. The reduction peak current increased with the concentration of NO and showed typical Michaelis-Menten kinetic characteristics with the apparent Michaelis constant Kmapp 9.78 μM. The binding constant K calculated to be 3.93 × 104 M by UV-vis method. The fluorescence emission spectra of iron porphyrin in CYP55A3 showed with the peak wavelength 633 nm, and its fluorescence intensity increased after binding with NO. The fluorescence analysis demonstrated that NADH can relay electrons to iron porphyrin and reduce NO. The reductive product of NO released and the iron porphyrin in CYP55A3 turned back to the original form.
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Affiliation(s)
- Zheng He
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Huan Deng
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Qiang Wang
- College of Pharmacy, South Central University for Nationalities, Wuhan 430074, PR China
| | - Yong Li
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Xiaosheng Liang
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China
| | - Deli Liu
- College of Life Science, Central China Normal University, Wuhan 430079, PR China
| | - Yunhua Wu
- College of Life Science, South Central University for Nationalities, Wuhan 430074, PR China.
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Zheng N, Yu Y, Wang J, Chapman SJ, Yao H, Zhang Y. The conversion of subtropical forest to tea plantation changes the fungal community and the contribution of fungi to N 2O production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:115106. [PMID: 32806403 DOI: 10.1016/j.envpol.2020.115106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The conversion of natural forests to tea plantations largely affects soil nitrous oxide (N2O) emissions and soil microbial communities. However, the impacts of this conversion on the contribution of fungi to N2O emission and on fungal community structure remain unclear. In this study, we determined the soil N2O emission rate, N2O production by fungi, associated fungal community diversity, and related ecological factors in chronological changes of tea crop systems (3, 36 and 105 years old tea orchards named T3, T36 and T105, respectively), and in an adjacent soil from a natural forest. The results indicate that the tea plantations significantly enhanced soil N2O production compared with the forest soil. Tea plantations significantly decreased soil pH and C/N ratio, but increased soil inorganic nitrogen (N). Furthermore, they increased the fungal contribution to the production of soil N2O, but decreased the bacterial counterpart. We also observed that fungal community and functional composition differed distinctly between tea plantations and forest. Additionally, most of the fungal groups in high N2O emission soils (T36 and T105) were identified as the genus Fusarium, which were positively correlated with soil N2O emissions. The variation in N2O emission response could be well explained by NO3--N, soil organic carbon (SOC), C/N, and Fusarium, which contributed to up to 97% of the observed variance. Altogether, these findings provide significant direct evidence that the increase of soil N2O emissions and fungal communities be attributed to the conversion of natural forest to tea plantations.
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Affiliation(s)
- Ningguo Zheng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China; Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo, 315800, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yongxiang Yu
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan, 430205, People's Republic of China
| | - Juan Wang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China; Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo, 315800, People's Republic of China
| | | | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China; Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo, 315800, People's Republic of China; Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan, 430205, People's Republic of China.
| | - Yingying Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China; Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo, 315800, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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Kantnerová K, Yu L, Zindel D, Zahniser MS, Nelson DD, Tuzson B, Nakagawa M, Toyoda S, Yoshida N, Emmenegger L, Bernasconi SM, Mohn J. First investigation and absolute calibration of clumped isotopes in N 2 O by mid-infrared laser spectroscopy. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8836. [PMID: 32430945 DOI: 10.1002/rcm.8836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Unravelling the biogeochemical cycle of the potent greenhouse gas nitrous oxide (N2 O) is an underdetermined problem in environmental sciences due to the multiple source and sink processes involved, which complicate mitigation of its emissions. Measuring the doubly isotopically substituted molecules (isotopocules) of N2 O can add new opportunities to fingerprint and constrain its cycle. METHODS We present a laser spectroscopic technique to selectively and simultaneously measure the eight most abundant isotopocules of N2 O, including three doubly substituted species - so called "clumped isotopes". For the absolute quantification of individual isotopocule abundances, we propose a new calibration scheme that combines thermal equilibration of a working standard gas with a direct mole fraction-based approach. RESULTS The method is validated for a large range of isotopic composition values by comparison with other established methods (laser spectroscopy using conventional isotopic scale and isotope ratio mass spectrometry). Direct intercomparison with recently developed ultrahigh-resolution mass spectrometry shows clearly the advantages of the new laser technique, especially with respect to site specificity of isotopic substitution in the N2 O molecule. CONCLUSIONS Our study represents a new methodological basis for the measurements of both singly substituted and clumped N2 O isotopes. It has a high potential to stimulate future research in the N2 O community by establishing a new class of reservoir-insensitive tracers and molecular-scale insights.
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Affiliation(s)
- Kristýna Kantnerová
- Empa, Laboratory for Air Pollution/Environmental Technology, Dübendorf, 8600, Switzerland
- ETH Zürich, Department of Earth Sciences, Zürich, 8092, Switzerland
| | - Longfei Yu
- Empa, Laboratory for Air Pollution/Environmental Technology, Dübendorf, 8600, Switzerland
| | - Daniel Zindel
- ETH Zurich, Laboratory of Physical Chemistry, Zürich, 8093, Switzerland
| | - Mark S Zahniser
- Aerodyne Research Inc., Center for Atmospheric and Environmental Chemistry, Billerica, MA, 01821, USA
| | - David D Nelson
- Aerodyne Research Inc., Center for Atmospheric and Environmental Chemistry, Billerica, MA, 01821, USA
| | - Béla Tuzson
- Empa, Laboratory for Air Pollution/Environmental Technology, Dübendorf, 8600, Switzerland
| | - Mayuko Nakagawa
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo, 152-8550, Japan
| | - Sakae Toyoda
- Tokyo Institute of Technology, Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Yokohama, 226-8503, Japan
| | - Naohiro Yoshida
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo, 152-8550, Japan
- Tokyo Institute of Technology, Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Yokohama, 226-8503, Japan
| | - Lukas Emmenegger
- Empa, Laboratory for Air Pollution/Environmental Technology, Dübendorf, 8600, Switzerland
| | | | - Joachim Mohn
- Empa, Laboratory for Air Pollution/Environmental Technology, Dübendorf, 8600, Switzerland
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Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle. PLANTS 2020; 9:plants9070903. [PMID: 32708782 PMCID: PMC7412212 DOI: 10.3390/plants9070903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH4+) and nitrate (NO3−) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N2O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N2O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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50
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Stein LY. The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases. Trends Microbiol 2020; 28:500-511. [DOI: 10.1016/j.tim.2020.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 11/26/2022]
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