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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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2
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Katayama T, Maruyama JI. Trace copper-mediated asexual development via a superoxide dismutase and induction of AobrlA in Aspergillus oryzae. Front Microbiol 2023; 14:1135012. [PMID: 36970664 PMCID: PMC10030727 DOI: 10.3389/fmicb.2023.1135012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
The filamentous fungus Aspergillus oryzae, in which sexual reproduction remains to be discovered, proliferates mainly via asexual spores (conidia). Therefore, despite its industrial importance in food fermentation and recombinant protein production, breeding beneficial strains by genetic crosses is difficult. In Aspergillus flavus, which is genetically close to A. oryzae, structures known as sclerotia are formed asexually, but they are also related to sexual development. Sclerotia are observed in some A. oryzae strains, although no sclerotia formation has been reported in most strains. A better understanding of the regulatory mechanisms underlying sclerotia formation in A. oryzae may contribute to discover its sexual development. Some factors involved in sclerotia formation have been previously identified, but their regulatory mechanisms have not been well studied in A. oryzae. In this study, we found that copper strongly inhibited sclerotia formation and induced conidiation. Deletion of AobrlA encoding a core regulator of conidiation and ecdR involved in transcriptional induction of AobrlA suppressed the copper-mediated inhibition of sclerotia formation, suggesting that AobrlA induction in response to copper leads not only to conidiation but also to inhibition of sclerotia formation. In addition, deletion of the copper-dependent superoxide dismutase (SOD) gene and its copper chaperone gene partially suppressed such copper-mediated induction of conidiation and inhibition of sclerotia formation, indicating that copper regulates asexual development via the copper-dependent SOD. Taken together, our results demonstrate that copper regulates asexual development, such as sclerotia formation and conidiation, via the copper-dependent SOD and transcriptional induction of AobrlA in A. oryzae.
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Affiliation(s)
- Takuya Katayama
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Jun-ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
- *Correspondence: Jun-ichi Maruyama,
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3
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Németh A, Ainsworth J, Ravishankar H, Lens PNL, Heffernan B. Temperature dependence of nitrification in a membrane-aerated biofilm reactor. Front Microbiol 2023; 14:1114647. [PMID: 37168114 PMCID: PMC10165249 DOI: 10.3389/fmicb.2023.1114647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/20/2023] [Indexed: 05/13/2023] Open
Abstract
The membrane-aerated biofilm reactor (MABR) is a novel method for the biological treatment of wastewaters and has been successfully applied for nitrification. To improve the design and adaptation of MABR processes for colder climates and varying temperatures, the temperature dependence of a counter-diffusional biofilm's nitrification performance was investigated. A lab-scale MABR system with silicone hollow fibre membranes was operated at various temperatures between 8 and 30°C, and batch tests were performed to determine the ammonia oxidation kinetics. Biofilm samples were taken at 8 and 24°C and analysed with 16S rRNA sequencing to monitor changes in the microbial community composition, and a mathematical model was used to study the temperature dependence of mass transfer. A high nitrification rate (3.08 g N m-2 d-1) was achieved at 8°C, and temperature dependence was found to be low (θ = 1.024-1.026) compared to suspended growth processes. Changes in the community composition were moderate, Nitrospira defluvii remaining the most dominant species. Mass transfer limitations were shown to be largely responsible for the observed trends, consistent with other biofilm processes. The results show that the MABR is a promising technology for low temperature nitrification, and appropriate management of the mass transfer resistance can optimise the process for both low and high temperature operation.
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Affiliation(s)
- András Németh
- OxyMem Ltd., Athlone, Ireland
- *Correspondence: András Németh,
| | | | | | - Piet N. L. Lens
- Department of Microbiology, University of Galway, Galway, Ireland
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4
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Gago JF, Viver T, Urdiain M, Pastor S, Kämpfer P, Robledo PA, Ferreira E, Rosselló-Móra R. Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island, Spain. Syst Appl Microbiol 2021; 44:126277. [PMID: 34788687 DOI: 10.1016/j.syapm.2021.126277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/07/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022]
Abstract
From a collection of > 140 strains isolated from groundwater with thermal anomalies for the purpose of obtaining good candidates with applications in the cosmetic industry, two strains were selected because of their taxonomic novelty. Among the isolates, strains TMF_100T and TFM_099 stood out for their potential biotechnological relevance, and a comparative analysis of 16S rRNA gene sequences indicated that these strains represented a new species of the genus Hydrotalea. In addition, from the public genomic databases, metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) could be retrieved that affiliated with this genus. These MAGs and SAGs had been obtained from different environmental samples, such as acid mine drainage or marine sediments. In addition to the description of the new species, the ecological relevance of the members of this genus was demonstrated by means of denitrification, CRISPR-Cas system diversity and heavy metal resistance, as well as their wide geographical distribution and environmental versatility. Supported by the taxonomic study, together with physiological and morphological differences and ecological features, we concluded that strain TMF_100T represented a novel species within the genus Hydrotalea, for which we propose the name Hydrotalea lipotrueae sp. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | - Pedro A Robledo
- Delegation of Geological and Mining Institute of Spain (IGME-CSIC) in Balearic Islands, Palma de Mallorca, Spain
| | | | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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5
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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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6
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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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7
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Wu L, Chen X, Wei W, Liu Y, Wang D, Ni BJ. A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9175-9190. [PMID: 32657581 DOI: 10.1021/acs.est.0c03948] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The continuous increase of nitrous oxide (N2O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N2O production, a clear understanding of the knowledge on archaeal N2O production is necessary for global N2O mitigation. Compared to bacterial N2O production by ammonia-oxidizing bacteria (AOB), AOA-driven N2O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N2O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N2O production pathways, discussed the relative contribution of AOA to N2O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N2O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N2O production. We, then, put forward perspectives for archaeal N2O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N2O mitigations.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Xueming Chen
- College of Environment and Resources, Fuzhou University, Fujian 350116, PR China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Dongbo Wang
- Key Laboratory of Environmental Biology and Pollution Control, College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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8
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Wise BR, Roane TM, Mosier AC. Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment. MICROBIAL ECOLOGY 2020; 79:562-575. [PMID: 31446448 DOI: 10.1007/s00248-019-01420-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.
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Affiliation(s)
- Ben R Wise
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Timberley M Roane
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA.
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9
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Keuschnig C, Gorfer M, Li G, Mania D, Frostegård Å, Bakken L, Larose C. NO and N 2 O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains. Environ Microbiol 2020; 22:2182-2195. [PMID: 32157782 DOI: 10.1111/1462-2920.14980] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 02/21/2020] [Accepted: 03/07/2020] [Indexed: 11/30/2022]
Abstract
Fungal denitrification is claimed to produce non-negligible amounts of N2 O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with NO 2 - . Enzymatic reduction of NO 2 - (NIR) and NO (NOR) was assessed by correcting measured NO- and N2 O-kinetics for abiotic NO- and N2 O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N2 O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N2 O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2 O as a response to an abiotic NO production from the medium.
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Affiliation(s)
- Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully Cedex, France
| | - Markus Gorfer
- Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Guofen Li
- Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Lars Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1432, Aas, Norway
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134, Ecully Cedex, France
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10
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Zou D, Pan J, Liu Z, Zhang C, Liu H, Li M. The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient. Front Microbiol 2020; 11:285. [PMID: 32174899 PMCID: PMC7056671 DOI: 10.3389/fmicb.2020.00285] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/07/2020] [Indexed: 01/05/2023] Open
Abstract
Bathyarchaeota, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. Metabolic pathways of the Bathyarchaeota members are diverse and, hence, this phylum has been proposed to play an important role in global biogeochemical cycles. Bathyarchaeota members are distributed in the estuarine environments. However, limited information is available about their detailed community structure, abundance, and functions in the Pearl River estuary (PRE). In the current study, we performed a comprehensive investigation of the archaeal community in the PRE surface sediments along a salinity gradient, with a focus on Bathyarchaeota. Bathyarchaeota was the dominant archaeal phylum, with the abundance of the bathyarchaeotal 16S rRNA gene ranging from 1.43 × 108 to 1.22 × 109 copies/g sediment dry weight (d.w.), and Bathy-8 was the dominant subgroup. Thaumarchaeota, Lokiarchaeota, and Euryarchaeota, including Thermoprofundales (MBG-D archaea), were the other major archaeal groups in the PRE. The differences of community distributions in the high- and low-salinity sediments were hence investigated. Statistical analysis revealed that besides salinity, ammonium, and total organic carbon were the most important environmental factors influencing the archaea community structure, including that of Bathyarchaeota, in the PRE. The archaeal network indicated the cooccurrence among Bathyarchaeota, Lokiarchaeota, and Euryarchaeota, while Bathy-6 presented unique correlations compared with other bathyarchaeotal subgroups. These observations indicate that Bathyarchaeota may play a role in ecosystem function through microbe-microbe interactions, revealing a possible different lifestyle for Bathy-6 in eutrophic estuarine sediments.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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11
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Yoon S, Song B, Phillips RL, Chang J, Song MJ. Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems. FEMS Microbiol Ecol 2019; 95:5488431. [DOI: 10.1093/femsec/fiz066] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/10/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.
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Affiliation(s)
- Sukhwan Yoon
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Sciences, College of William and Mary, 1375 Greate Rd, Gloucester Point, VA 23062, USA
| | - Rebecca L Phillips
- Ecological Insights Corporation, 130 69th Street SE, Hazelton, ND 58544, USA
| | - Jin Chang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
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12
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Multicopper oxidases: Biocatalysts in microbial pathogenesis and stress management. Microbiol Res 2019; 222:1-13. [DOI: 10.1016/j.micres.2019.02.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/03/2019] [Accepted: 02/14/2019] [Indexed: 02/08/2023]
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13
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Copper Utilization, Regulation, and Acquisition by Aspergillus fumigatus. Int J Mol Sci 2019; 20:ijms20081980. [PMID: 31018527 PMCID: PMC6514546 DOI: 10.3390/ijms20081980] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
Copper is an essential micronutrient for the opportunistic human pathogen, Aspergillus fumigatus. Maintaining copper homeostasis is critical for survival and pathogenesis. Copper-responsive transcription factors, AceA and MacA, coordinate a complex network responsible for responding to copper in the environment and determining which response is necessary to maintain homeostasis. For example, A. fumigatus uses copper exporters to mitigate the toxic effects of copper while simultaneously encoding copper importers and small molecules to ensure proper supply of the metal for copper-dependent processes such a nitrogen acquisition and respiration. Small molecules called isocyanides recently found to be produced by A. fumigatus may bind copper and partake in copper homeostasis similarly to isocyanide copper chelators in bacteria. Considering that the host uses copper as a microbial toxin and copper availability fluctuates in various environmental niches, understanding how A. fumigatus maintains copper homeostasis will give insights into mechanisms that facilitate the development of invasive aspergillosis and its survival in nature.
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Ma Y, Zilles JL, Kent AD. An evaluation of primers for detecting denitrifiers via their functional genes. Environ Microbiol 2019; 21:1196-1210. [PMID: 30724437 DOI: 10.1111/1462-2920.14555] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022]
Abstract
Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.
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Affiliation(s)
- Yanjun Ma
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julie L Zilles
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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15
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Xu H, Sheng R, Xing X, Zhang W, Hou H, Liu Y, Qin H, Chen C, Wei W. Characterization of Fungal nirK-Containing Communities and N 2O Emission From Fungal Denitrification in Arable Soils. Front Microbiol 2019; 10:117. [PMID: 30778342 PMCID: PMC6369356 DOI: 10.3389/fmicb.2019.00117] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/18/2019] [Indexed: 11/25/2022] Open
Abstract
Fungal denitrifiers play important roles in soil nitrogen cycling, but we have very limited knowledge about their distribution and functions in ecosystems. In this study, three types of arable soils were collected across different climate zones in China, including quaternary red clay soils, alluvial soils, and black soils. The composition and abundance of fungal nirK-containing denitrifiers was determined by MiSeq high-throughput sequencing and qPCR, respectively. Furthermore, a substrate-induced inhibition approach was used to explore N2O emissions from fungal denitrification. The results showed that the arable soils contained a wide range of nirK-containing fungal denitrifiers, with four orders and eight genera. Additionally, approximately 57.30% of operational taxonomic unit (OTUs) belonged to unclassified nirK-containing fungi. Hypocreales was the most predominant order, with approximately 40.51% of the total number of OTUs, followed by Sordariales, Eurotiales, and Mucorales. It was further indicated that 53% of fungal nirK OTUs were shared by the three types of soils (common), and this group of fungi comprised about 98% of the total relative abundance of the nirK-containing population, indicating that the distribution of fungal nirK-containing denitrifiers was quite homogenous among the soil types. These common OTUs were determined by multiple soil characteristics, while the composition of unique OTUs was manipulated by the specific properties of each soil type. Furthermore, fungal N2O emissions were significantly and positively correlated with fungal nirK abundance in the soils, whereas it was not clearly related to fungal nirK compositions. In conclusion, although the arable soils hosted diverse nirK-containing fungal denitrifiers, fungal nirK compositions were highly homogenous among the soil types, which could be a consequence of enduring agricultural practices. The abundance of fungal nirK-containing denitrifiers, rather than their composition, may play more significant roles in relation to N2O emission from fungal denitrification.
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Affiliation(s)
- Huifang Xu
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Sheng
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xiaoyi Xing
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Haijun Hou
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yi Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hongling Qin
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Chunlan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Wenxue Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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16
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Duan P, Zhang X, Zhang Q, Wu Z, Xiong Z. Field-aged biochar stimulated N 2O production from greenhouse vegetable production soils by nitrification and denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1303-1310. [PMID: 30045510 DOI: 10.1016/j.scitotenv.2018.06.166] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Evidence suggests that biochar is among ideal strategies for climate change mitigation and sustainable agriculture. However, the effects of soil aging on the physicochemical characteristics of biochar and nitrous oxide (N2O) production remain elusive. We set up a microcosm experiment with two greenhouse vegetable production (GVP) (alkaline and acid) soils by using the 15N tracing technique and quantitative polymerase chain reaction (qPCR) to investigate the mechanisms of N2O production as affected by fresh (FB) and aged biochar (AB) amendment. The results showed that AB increased the specific surface area, organic C, ammonium sorption capacity and cation exchange capacity, whereas decreased the pore size and pH relative to the FB. Results also demonstrated that FB effectively decreased N2O emissions from both soils while it enhanced the abundance of nirK and nosZI genes in alkaline soil and reduced the abundance of ammonia-oxidizing bacteria (AOB) amoA and increased nirK and nosZII genes in acid soil. In contrast, AB significantly stimulated nitrification and denitrification in both soils and thus significantly increased the N2O emissions by 43-78%. Furthermore, AB induced increases in ammonia-oxidizing archaeal (AOA) amoA and nirK gene abundances in alkaline soil and fungal nirK gene abundances in acid soil. These results suggest that AB may not be suitable for the mitigation of soil N2O emissions in GVP soils thus improving our understanding of the potential mechanism of biochar in N2O emissions.
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Affiliation(s)
- Pengpeng Duan
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qianqian Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Wu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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17
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Paranychianakis NV, Tsiknia M, Kalogerakis N. Pathways regulating the removal of nitrogen in planted and unplanted subsurface flow constructed wetlands. WATER RESEARCH 2016; 102:321-329. [PMID: 27379728 DOI: 10.1016/j.watres.2016.06.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Single-stage constructed wetlands (CWs) are characterized by a low potential for N removal. Understanding the pathways regulating N cycling as well as their dependence on environmental variables might improve the potential of CWs for N removal and results in more accurate simulation tools. In this study we employed qPCR targeting marker functional genes (amoA, nirK, nirS, clade I and II nosZ) or microorganisms (anammox) regulating key pathways of N cycling to unravel their relative importance. Furthermore, the influence of plant species on treatment performance was studied. Our findings indicated nitrification-denitrification as the principal route of N removal in CWs, while anammox did not have a strong contribution. Evidence was also arisen that ammonia oxidizing archaea (AOA) contributed on NH3 oxidation. Overall, plant species had a weak effect on the abundance of N functional genes (amoA of AOA), but it strongly affected the performance of CWs in terms of N removal in the following order: unplanted < Phragmites communis < Typha latifolia. These findings suggest that plant species stimulate N removal by upregulating the rates that the responsible biochemical pathways operate, probably by increasing O2 supply. In addition, our study revealed differences in indicators linked to N2O emissions. The abundance of clade II nosZ genes remained low across the season scaling down a strong contribution in the reduction of the emitted N2O. The increasing ratios of nosZ/Σnir and nirS/nirK with the progress of season indicate a shift in the composition of denitrifiers towards strains with a lower genetic potential for N2O release. Similar trends were observed among the treatments but the mechanisms differed. The planted treatments stimulated an increase in the ΣnosZ/Σnir ratio, while the unplanted an increase in the nirS/nirK ratio.
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Affiliation(s)
- Nikolaos V Paranychianakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece.
| | - Myrto Tsiknia
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece
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18
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Chen H, Yu F, Shi W. Detection of N 2O-producing fungi in environment using nitrite reductase gene (nirK)-targeting primers. Fungal Biol 2016; 120:1479-1492. [PMID: 27890085 DOI: 10.1016/j.funbio.2016.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/19/2023]
Abstract
Fungal denitrification has been increasingly investigated, but its community ecology is poorly understood due to the lack of culture-independent tools. In this work, four pairs of nirK-targeting primers were designed and evaluated for primer specificity and efficiency using thirty N2O-producing fungal cultures and an agricultural soil. All primers amplified nirK from fungi and soil, but their efficiency and specificity were different. A primer set, FnirK_F3/R2 amplified ∼80 % of tested fungi, including Aspergillus, Fusarium, Penicillium, and Trichoderma, as compared to ∼40-70 % for other three primers. The nirK fragments of fungal and soil DNA amplified by FnirK_F3/R2 were phylogenetically related to denitrifying fungi in the orders Eurotiales, Hypocreales, and Sordariales; and clone sequences were also distributed in the clusters of Chaetomium, Metarhizium, and Myceliophthora that were uncultured from soil in our previous work. This proved the wide-range capability of primers for amplifying diverse denitrifying fungi from environment. However, our primers and recently-developed other primers amplified bacterial nirK from soil and this co-amplification of fungal and bacterial nirK was theoretically discussed. The FnirK_F3/R2 was further compared with published primers; results from clone libraries demonstrated that FnirK_F3/R2 was more specifically targeted on fungi and had broader taxonomical coverage than some others.
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Affiliation(s)
- Huaihai Chen
- Department of Soil Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Fangbo Yu
- Department of Soil Science, North Carolina State University, Raleigh, NC 27695, USA; School of Environment and Resource Sciences, Zhejiang Agriculture and Forestry University, Linan, Zhejiang 311300, China
| | - Wei Shi
- Department of Soil Science, North Carolina State University, Raleigh, NC 27695, USA.
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Novel P450nor Gene Detection Assay Used To Characterize the Prevalence and Diversity of Soil Fungal Denitrifiers. Appl Environ Microbiol 2016; 82:4560-4569. [PMID: 27208113 DOI: 10.1128/aem.00231-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/16/2016] [Indexed: 02/03/2023] Open
Abstract
UNLABELLED Denitrifying fungi produce nitrous oxide (N2O), a potent greenhouse gas, as they generally lack the ability to convert N2O to dinitrogen. Contrary to the case for bacterial denitrifiers, the prevalence and diversity of denitrifying fungi found in the environment are not well characterized. In this study, denitrifying fungi were isolated from various soil ecosystems, and novel PCR primers targeting the P450nor gene, encoding the enzyme responsible for the conversion of nitric oxide to N2O, were developed, validated, and used to study the diversity of cultivable fungal denitrifiers. This PCR assay was also used to detect P450nor genes directly from environmental soil samples. Fungal denitrification capabilities were further validated using an N2O gas detection assay and a PCR assay targeting the nirK gene. A collection of 492 facultative anaerobic fungi was isolated from 15 soil ecosystems and taxonomically identified by sequencing the internal transcribed spacer sequence. Twenty-seven fungal denitrifiers belonging to 10 genera had the P450nor and the nirK genes and produced N2O from nitrite. N2O production is reported in strains not commonly known as denitrifiers, such as Byssochlamys nivea, Volutella ciliata, Chloridium spp., and Trichocladium spp. The prevalence of fungal denitrifiers did not follow a soil ecosystem distribution; however, a higher diversity was observed in compost and agricultural soils. The phylogenetic trees constructed using partial P450nor and nirK gene sequences revealed that both genes clustered taxonomically closely related strains together. IMPORTANCE A PCR assay targeting the P450nor gene involved in fungal denitrification was developed and validated. The newly developed P450nor primers were used on fungal DNA extracted from a collection of fungi isolated from various soil environments and on DNA directly extracted from soil. The results indicated that approximatively 25% of all isolated fungi possessed this gene and were able to convert nitrite to N2O. All soil samples from which denitrifying fungi were isolated also tested positive for the presence of P450nor The P450nor gene detection assay was reliable in detecting a large diversity of fungal denitrifiers. Due to the lack of homology existing between P450nor and bacterial denitrification genes, it is expected that this assay will become a tool of choice for studying fungal denitrifiers.
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20
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Higgins SA, Welsh A, Orellana LH, Konstantinidis KT, Chee-Sanford JC, Sanford RA, Schadt CW, Löffler FE. Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils. Appl Environ Microbiol 2016; 82:2919-2928. [PMID: 26969694 PMCID: PMC4959062 DOI: 10.1128/aem.00243-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Members of the Fungi convert nitrate (NO3 (-)) and nitrite (NO2 (-)) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3 (-) or NO2 (-) in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2 (-) Novel PCR primers targeting the p450nor gene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylum Ascomycota and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N2O from NO2 (-), whereas nirK (encoding the NO-forming NO2 (-) reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separate nirK primer sets. Collectively, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation. IMPORTANCE A comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungal p450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.
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Affiliation(s)
- Steven A Higgins
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Allana Welsh
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Robert A Sanford
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Christopher W Schadt
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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21
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Kamp A, Høgslund S, Risgaard-Petersen N, Stief P. Nitrate Storage and Dissimilatory Nitrate Reduction by Eukaryotic Microbes. Front Microbiol 2015; 6:1492. [PMID: 26734001 PMCID: PMC4686598 DOI: 10.3389/fmicb.2015.01492] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/10/2015] [Indexed: 11/13/2022] Open
Abstract
The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described. A first compilation of intracellular nitrate inventories in various marine sediments is presented, indicating that intracellular nitrate pools vastly exceed porewater nitrate pools. The relative contribution by foraminifers to total sedimentary denitrification is estimated for different marine settings, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies Aarhus University Aarhus, Denmark
| | - Signe Høgslund
- Department of Bioscience, Aarhus University Aarhus, Denmark
| | | | - Peter Stief
- Department of Biology, Nordic Center for Earth Evolution, University of Southern Denmark Odense, Denmark
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