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Sennett LB, Roco CA, Lim NYN, Yavitt JB, Dörsch P, Bakken LR, Shapleigh JP, Frostegård Å. Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N 2O emissions. Nat Commun 2024; 15:7298. [PMID: 39181870 PMCID: PMC11344836 DOI: 10.1038/s41467-024-51688-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N2O - is intricately controlled by O2. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N2O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O2 legacy for accurately predicting N2O emissions originating from denitrification.
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Affiliation(s)
- Louise B Sennett
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Constance A Roco
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Natalie Y N Lim
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
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2
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Zhou J, Deng W, Wu J, Xiang H, Shen X, Lin JG, Hong Y. Respiration and growth of Paracoccus denitrificans R-1 with nitrous oxide as an electron acceptor. Microbiol Spectr 2024; 12:e0381123. [PMID: 38647341 PMCID: PMC11237620 DOI: 10.1128/spectrum.03811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
In the nitrogen biogeochemical cycle, the reduction of nitrous oxide (N2O) to N2 by N2O reductase, which is encoded by nosZ gene, is the only biological pathway for N2O consumption. In this study, we successfully isolated a strain of denitrifying Paracoccus denitrificans R-1 from sewage treatment plant sludge. This strain has strong N2O reduction capability, and the average N2O reduction rate was 5.10 ± 0.11 × 10-9 µmol·h-1·cell-1 under anaerobic condition in a defined medium. This reduction was accompanied by the stoichiometric consumption of acetate over time when N2O served as the sole electron acceptor and the reduction can yield energy to support microbial growth, suggesting that microbial N2O reduction is related to the energy generation process. Genomic analysis showed that the gene cluster encoding N2O reductase of P. denitrificans R-1 was composed of nosR, nosZ, nosD, nosF, nosY, nosL, and nosZ, which was identified as that in other strains in clade I. Respiratory inhibitors test indicated that the pathway of electron transport for N2O reduction was different from that of the traditional electron transport chain for aerobic respiration. Cu2+, silver nanoparticles, O2, and acidic conditions can strongly inhibit the reduction, whereas NO3- or NH4+ can promote it. These findings suggest that modular N2O reduction of P. denitrificans R-1 is linked to the electron transport and energy conservation, and dissimilatory N2O reduction is a form of microbial anaerobic respiration. IMPORTANCE Nitrous oxide (N2O) is a potent greenhouse gas and contributor to ozone layer destruction, and atmospheric N2O has increased steadily over the past century due to human activities. The release of N2O from fixed N is almost entirely controlled by microbial N2O reductase activities. Here, we investigated the ability to obtain energy for the growth of Paracoccus denitrificans R-1 by coupling the oxidation of various electron donors to N2O reduction. The modular N2O reduction process of denitrifying microorganism not only can consume N2O produced by itself but also can consume the external N2O generated from biological or abiotic pathways under suitable condition, which should be critical for controlling the release of N2O from ecosystems into the atmosphere.
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Affiliation(s)
- Jiaxian Zhou
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Wenfang Deng
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Hua Xiang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Xiaomei Shen
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Yangming Chiao Tung University, Hsinchu City, Taiwan
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
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3
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Hiis EG, Vick SHW, Molstad L, Røsdal K, Jonassen KR, Winiwarter W, Bakken LR. Unlocking bacterial potential to reduce farmland N 2O emissions. Nature 2024; 630:421-428. [PMID: 38811724 PMCID: PMC11168931 DOI: 10.1038/s41586-024-07464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.
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Affiliation(s)
- Elisabeth G Hiis
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Molstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kristine Røsdal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Wilfried Winiwarter
- International Institute for Applied Systems Analysis, Laxenburg, Austria
- Institute of Environmental Engineering, University of Zielona Góra, Zielona Góra, Poland
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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4
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Roothans N, Gabriëls M, Abeel T, Pabst M, van Loosdrecht MCM, Laureni M. Aerobic denitrification as an N2O source from microbial communities. THE ISME JOURNAL 2024; 18:wrae116. [PMID: 38913498 PMCID: PMC11272060 DOI: 10.1093/ismejo/wrae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.
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Affiliation(s)
- Nina Roothans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Minke Gabriëls
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, van Mourik Broekmanweg 6, Delft 2628 XE, the Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, United States
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Michele Laureni
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
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5
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Liu C, Yue Y, Zheng S, Liu X, Pang L, Yang Z. Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:120930-120944. [PMID: 37945964 DOI: 10.1007/s11356-023-30818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.
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Affiliation(s)
- Caiqiong Liu
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
| | - Yao Yue
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, Wuhan University, Wuhan, 430072, China
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Shan Zheng
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
| | - Xuna Liu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Zhonghua Yang
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China.
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6
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Wang X, Sun T, Yan S, Chen S, Zhang Y. Sediment microbial community characteristics in sea cucumber restocking area. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106233. [PMID: 37866200 DOI: 10.1016/j.marenvres.2023.106233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.
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Affiliation(s)
- Xiaoling Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Tao Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Shengjun Yan
- National Marine Environmental Monitoring Center, Dalian, 116021, China
| | - Shangyi Chen
- Comprehensive Administrative Law Enforcement Bureau, Qingdao, 266011, China
| | - Yue Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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7
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McGuire PM, Butkevich N, Saksena AV, Walter MT, Shapleigh JP, Reid MC. Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors. Environ Microbiol 2023; 25:1696-1712. [PMID: 37105180 DOI: 10.1111/1462-2920.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 - removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.
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Affiliation(s)
- Philip M McGuire
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Natalie Butkevich
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Aryaman V Saksena
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Matthew C Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
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8
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Hu Y, Wu J, Ye J, Liu X, Wang Y, Ye F, Hong Y. The imbalance between N 2O production and reduction by multi-microbial communities determines sedimentary N 2O emission potential in the Pearl River Estuary. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106119. [PMID: 37535997 DOI: 10.1016/j.marenvres.2023.106119] [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: 05/22/2023] [Revised: 07/04/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
Denitrification is the dominant process of nitrogen removal and nitrous oxide (N2O) emissions in estuarine ecosystems. However, little is known regarding the microbial mechanism of the production and reduction of N2O in estuaries. We investigated in situ dissolved N2O as well as potential N2O production rate (NPR), reduction rate (NRR), and emission rate (NER), and key functional genes related to N2O transformation of denitrification in the Pearl River Estuary. Higher N2O emission potential was found in the upstream and midstream regions with higher NPR and lower NRR values. In contrast, higher NRR values were detected in downstream. Notably, nirS and nirK type N2O producers dominated the upstream zone, whereas abundant N2O reducers, especially nosZ II type N2O reducers, were observed in downstream. Most importantly, the gene abundance ratio (Rnir/nosZ) was significantly correlated with the N2O emission potential (Re). Niche differentiation between N2O producers and N2O reducers from upstream to downstream affected N2O emission potential. This study highlights the N2O emission potential in estuarine sediments is determined by an imbalance between N2O production and the reduction of multi-bacterial communities.
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Affiliation(s)
- Yaohao Hu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, PR China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, PR China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, PR China
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, PR China
| | - Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, PR China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, PR China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, PR China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, PR China.
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9
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Ciccarese D, Tantawi O, Zhang IH, Plata D, Babbin AR. Microscale dynamics promote segregated denitrification in diatom aggregates sinking slowly in bulk oxygenated seawater. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:275. [PMID: 38665198 PMCID: PMC11041763 DOI: 10.1038/s43247-023-00935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/18/2023] [Indexed: 04/28/2024]
Abstract
Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms-important primary producers for global carbon export-support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle's boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification.
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Affiliation(s)
- Davide Ciccarese
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Omar Tantawi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Irene H. Zhang
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Desiree Plata
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
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10
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Miralles-Robledillo JM, Martínez-Espinosa RM, Pire C. Analysis of the external signals driving the transcriptional regulation of the main genes involved in denitrification in Haloferax mediterranei. Front Microbiol 2023; 14:1109550. [PMID: 37007523 PMCID: PMC10062603 DOI: 10.3389/fmicb.2023.1109550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
Haloferax mediterranei is the model microorganism for the study of the nitrogen cycle in haloarchaea. This archaeon not only assimilate N-species such as nitrate, nitrite, or ammonia, but also it can perform denitrification under low oxygen conditions, using nitrate or nitrite as alternative electron acceptors. However, the information currently available on the regulation of this alternative respiration in this kind of microorganism is scarce. Therefore, in this research, the study of haloarchaeal denitrification using H. mediterranei has been addressed by analyzing the promoter regions of the four main genes of denitrification (narGH, nirK, nor, and nosZ) through bioinformatics, reporter gene assays under oxic and anoxic conditions and by site-directed mutagenesis of the promoter regions. The results have shown that these four promoter regions share a common semi-palindromic motif that plays a role in the control of the expression levels of nor and nosZ (and probably nirK) genes. Regarding the regulation of the genes under study, it has been concluded that nirK, nor, and nosZ genes share some expression patterns, and therefore their transcription could be under the control of the same regulator whereas nar operon expression displays differences, such as the activation by dimethyl sulfoxide with respect to the expression in the absence of an electron acceptor, which is almost null under anoxic conditions. Finally, the study with different electron acceptors demonstrated that this haloarchaea does not need complete anoxia to perform denitrification. Oxygen concentrations around 100 μM trigger the activation of the four promoters. However, a low oxygen concentration per se is not a strong signal to activate the promoters of the main genes involved in this pathway; high activation also requires the presence of nitrate or nitrite as final electron acceptors.
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Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- *Correspondence: Carmen Pire,
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Singh AK, Nakhate SP, Gupta RK, Chavan AR, Poddar BJ, Prakash O, Shouche YS, Purohit HJ, Khardenavis AA. Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm. ENVIRONMENTAL RESEARCH 2022; 215:114199. [PMID: 36058281 DOI: 10.1016/j.envres.2022.114199] [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: 05/17/2021] [Revised: 05/21/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50-60 cm) and, active process of aerobic denitrification in the top soil (0-10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.
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Affiliation(s)
- Ashish Kumar Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suraj Prabhakarrao Nakhate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Atul Rajkumar Chavan
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhagyashri Jagdishprasad Poddar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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12
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Preparation for Denitrification and Phenotypic Diversification at the Cusp of Anoxia: a Purpose for N 2O Reductase Vis-à-Vis Multiple Roles of O 2. Appl Environ Microbiol 2022; 88:e0105322. [PMID: 36250705 PMCID: PMC9642011 DOI: 10.1128/aem.01053-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic respiration. This implies a selective advantage of the stringent O2 repression of denitrification gene transcription, which is found in most denitrifying bacteria. In some bacteria, the metabolic burden of adaptation can be minimized further by phenotypic diversification, colloquially termed "bet-hedging," where all cells synthesize the N2O reductase (NosZ) but only a minority synthesize nitrite reductase (NirS), as demonstrated for the model strain Paracoccus denitrificans. We hypothesized that the cells lacking NirS would be entrapped in anoxia but with the possibility of escape if supplied with O2 or N2O. To test this, cells were exposed to gradual O2 depletion or sudden anoxia and subsequent spikes of O2 and N2O. The synthesis of NirS in single cells was monitored by using an mCherry-nirS fusion replacing the native nirS, and their growth was detected as dilution of green, fluorescent fluorescein isothiocyanate (FITC) stain. We demonstrate anoxic entrapment due to e--acceptor deprivation and show that O2 spiking leads to bet-hedging, while N2O spiking promotes NirS synthesis and growth in all cells carrying NosZ. The cells rescued by the N2O spike had much lower respiration rates than those rescued by the O2 spike, however, which could indicate that the well-known autocatalytic synthesis of NirS via NO production requires O2. Our results bring into relief a fitness advantage of pairing restrictive nirS expression with universal NosZ synthesis in energy-limited systems. IMPORTANCE Denitrifying bacteria have evolved elaborate regulatory networks securing their respiratory metabolism in environments with fluctuating oxygen concentrations. Here, we provide new insight regarding their bet-hedging in response to hypoxia, which minimizes their N2O emissions because all cells express NosZ, reducing N2O to N2, while a minority express NirS + Nor, reducing NO2- to N2O. We hypothesized that the cells without Nir were entrapped in anoxia, without energy to synthesize Nir, and that they could be rescued by short spikes of O2 or N2O. We confirm such entrapment and the rescue of all cells by an N2O spike but only a fraction by an O2 spike. The results shed light on the role of O2 repression in bet-hedging and generated a novel hypothesis regarding the autocatalytic nirS expression via NO production. Insight into the regulation of denitrification, including bet-hedging, holds a clue to understanding, and ultimately curbing, the escalating emissions of N2O, which contribute to anthropogenic climate forcing.
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13
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Oba K, Suenaga T, Kuroiwa M, Riya S, Terada A. Exploring the Functions of Efficient Canonical Denitrifying Bacteria as N 2O Sinks: Implications from 15N Tracer and Transcriptome Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11694-11706. [PMID: 35917165 DOI: 10.1021/acs.est.2c02119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In denitrifying reactors, canonical complete denitrifying bacteria reduce nitrate (NO3-) to nitrogen via N2O. However, they can also produce N2O under certain conditions. We used a 15N tracer method, in which 15N-labeled NO3-/nitrite (NO2-) and nonlabeled N2O were simultaneously supplied with organic electron donors to five canonical complete denitrifying bacteria affiliated with either Clade I or Clade II nosZ. We calculated their NO3-, NO2-, and N2O consumption rates. The Clade II nosZ bacterium Azospira sp. strain I13 had the highest N2O consumption rate (3.47 ± 0.07 fmol/cell/h) and the second lowest NO3- consumption rate (0.20 ± 0.03 fmol/cell/h); hence, it is a N2O sink. A change from peptone- to acetate/citrate-based organic electron donors increased the NO3- consumption rate by 4.8 fold but barely affected the N2O consumption rate. Electron flow was directed to N2O rather than NO3- in Azospira sp. strain I13 and Az. oryzae strain PS only exerting a N2O sink but to NO3- in the Clade I nosZ N2O-reducing bacteria Pseudomonas stutzeri strain JCM 5965 and Alicycliphilus denitrificans strain I51. Transcriptome analyses revealed that the genotype could not fully describe the phenotype. The results show that N2O production and consumption differ among canonical denitrifying bacteria and will be useful for developing N2O mitigation strategies.
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Affiliation(s)
- Kohei Oba
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Toshikazu Suenaga
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
- Department of Chemical Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-8527, Japan
| | - Megumi Kuroiwa
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Shohei Riya
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
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14
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Identification of nosZ-expressing microorganisms consuming trace N 2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales. THE ISME JOURNAL 2022; 16:2087-2098. [PMID: 35676322 PMCID: PMC9381517 DOI: 10.1038/s41396-022-01260-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 12/12/2022]
Abstract
Microorganisms possessing N2O reductases (NosZ) are the only known environmental sink of N2O. While oxygen inhibition of NosZ activity is widely known, environments where N2O reduction occurs are often not devoid of O2. However, little is known regarding N2O reduction in microoxic systems. Here, 1.6-L chemostat cultures inoculated with activated sludge samples were sustained for ca. 100 days with low concentration (<2 ppmv) and feed rate (<1.44 µmoles h−1) of N2O, and the resulting microbial consortia were analyzed via quantitative PCR (qPCR) and metagenomic/metatranscriptomic analyses. Unintended but quantified intrusion of O2 sustained dissolved oxygen concentration above 4 µM; however, complete N2O reduction of influent N2O persisted throughout incubation. Metagenomic investigations indicated that the microbiomes were dominated by an uncultured taxon affiliated to Burkholderiales, and, along with the qPCR results, suggested coexistence of clade I and II N2O reducers. Contrastingly, metatranscriptomic nosZ pools were dominated by the Dechloromonas-like nosZ subclade, suggesting the importance of the microorganisms possessing this nosZ subclade in reduction of trace N2O. Further, co-expression of nosZ and ccoNO/cydAB genes found in the metagenome-assembled genomes representing these putative N2O-reducers implies a survival strategy to maximize utilization of scarcely available electron acceptors in microoxic environmental niches.
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15
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Evaluation of Non-Biodegradable Organic Matter and Microbial Community’s Effects on Achievement of Partial Nitrification Coupled with ANAMMOX for Treating Low-Carbon Livestock Wastewater. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
After the anaerobic digestion of livestock manure, high concentrations of nutrients still remain. Treatment of livestock wastewater through partial nitrification coupled with anaerobic ammonium oxidation (ANAMMOX) could be a useful technology depending on the investigation of microorganism enrichment and partial nitrification coupled with achievement of the ANAMMOX process. The results show 78.4% and 64.7% nitrite accumulation efficiency was successfully obtained in an intermittent aeration sequencing batch reactor and a continuous aeration sequencing batch reactor, respectively, at a loading rate of 0.93 kg ammonium/(m3·d). The main reason for the high nitrite accumulation efficiency was the intermittent aeration strategy which generated a 20–30 min lag reaction for nitrite oxidation and promoted the growth of the dominant ammonium oxidation bacteria (Nitrosomonas). Non-biodegradable organic matter in the effluents of partial nitrification did not have obvious influence on ANAMMOX activity at low loading rates (118 ± 13 mg COD/L and 168 ± 9 mg COD/L), and up to 87.4% average nitrite removal rate was observed. However, with the influent COD concentration increasing to 242 ± 17 mg/L, the potential inhibition of ANAMMOX activity was exerted by non-biodegradable organic matter.
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16
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Huang L, Luo J, Li L, Jiang H, Sun X, Yang J, She W, Liu W, Li L, Davis AP. Unconventional microbial mechanisms for the key factors influencing inorganic nitrogen removal in stormwater bioretention columns. WATER RESEARCH 2022; 209:117895. [PMID: 34864344 DOI: 10.1016/j.watres.2021.117895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Bioretention systems are environmentally friendly measures to control the amount of water and pollutants in urban stormwater runoff, and their treatment performance for inorganic N strongly depends on various microbial processes. However, microbial responses to variations of N mass reduction in bioretention systems are complex and poorly understood, which is not conducive to management designs. In the present study, a series of bioretention columns were established to monitor their fate performance for inorganic N (NH4+and NO3-) by using different configurations and by dosing with simulated stormwater events. The results showed that NH4+ was efficiently oxidized to NO3-, mainly by ammonia- and nitrite-oxidizing bacteria in the oxic media, regardless of the configurations of the bioretention systems or stormwater conditions. In contrast, NO3- removal pathways varied greatly in different columns. The presence of vegetation efficiently improved NO3-mass reduction through root assimilation and enhancement of microbial NO3- reduction in the rhizosphere. The construction of an organic-rich saturation zone can make the redox potential too low for heterotrophic denitrification to occur, so as to ensure high NO3- mass reduction mainly via stimulating chemolithotrophic NO3- reduction coupled with oxidation of reductive sulfur compounds derived from the bio-reduction of sulfate. In contrast, in the organic-poor saturation zone, multiple oligotrophic NO3- reduction pathways may be responsible for the high NO3- mass reduction. These findings highlight the necessity of considering the variation of N bio-transformation pathways for inorganic N removal in the configuration of bioretention systems.
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Affiliation(s)
- Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China
| | - Junyue Luo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Linxin Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Weiyu She
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Wen Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Liqing Li
- School of Environmental Science, China University of Geosciences, Wuhan 430074, China.
| | - Allen P Davis
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20742, USA
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17
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Lin X, McNichol J, Chu X, Qian Y, Luo H. Cryptic niche differentiation of novel sediment ecotypes of Rugeria pomeroyi correlates with nitrate respiration. Environ Microbiol 2021; 24:390-403. [PMID: 34964547 DOI: 10.1111/1462-2920.15882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 10/19/2022]
Abstract
Marine intertidal sediments fluctuate in redox conditions and nutrient availability, and they are also known as an important sink of nitrogen mainly through denitrification, yet how denitrifying bacteria adapt to this dynamic habitat remains largely untapped. Here, we investigated novel intertidal benthic ecotypes of the model pelagic marine bacterium Ruegeria pomeroyi DSS-3 with a population genomic approach. While differing by only 1.3% at the 16S rRNA gene level, members of the intertidal benthic ecotypes are complete denitrifiers whereas the pelagic ecotype representative (DSS-3) is a partial denitrifier lacking a nitrate reductase. The intertidal benthic ecotypes are further differentiated by using non-homologous nitrate reductases and a different set of genes that allow alleviating oxidative stress and acquiring organic substrates. In the presence of nitrate, the two ecotypes showed contrasting growth patterns under initial oxygen concentrations at 1 vol% versus 7 vol% and supplemented with different carbon sources abundant in intertidal sediments. Collectively, this combination of evidence indicates that there are cryptic niches in coastal intertidal sediments that support divergent evolution of denitrifying bacteria. This knowledge will in turn help understand how these benthic environments operate to effectively remove nitrogen.
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Affiliation(s)
- Xingqin Lin
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Jesse McNichol
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Xiao Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Yang Qian
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Haiwei Luo
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China.,Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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18
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Jonassen KR, Hagen LH, Vick SHW, Arntzen MØ, Eijsink VGH, Frostegård Å, Lycus P, Molstad L, Pope PB, Bakken LR. Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions. ISME JOURNAL 2021; 16:580-590. [PMID: 34489539 PMCID: PMC8776835 DOI: 10.1038/s41396-021-01101-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022]
Abstract
Inoculating agricultural soils with nitrous oxide respiring bacteria (NRB) can reduce N2O-emission, but would be impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production are suitable substrates and vectors for NRB. We show that indigenous NRB in digestates grew to high abundance during anaerobic enrichment under N2O. Gas-kinetics and meta-omic analyses showed that these NRB’s, recovered as metagenome-assembled genomes (MAGs), grew by harvesting fermentation intermediates of the methanogenic consortium. Three NRB’s were isolated, one of which matched the recovered MAG of a Dechloromonas, deemed by proteomics to be the dominant producer of N2O-reductase in the enrichment. While the isolates harbored genes required for a full denitrification pathway and could thus both produce and sequester N2O, their regulatory traits predicted that they act as N2O sinks in soil, which was confirmed experimentally. The isolates were grown by aerobic respiration in digestates, and fertilization with these NRB-enriched digestates reduced N2O emissions from soil. Our use of digestates for low-cost and large-scale inoculation with NRB in soil can be taken as a blueprint for future applications of this powerful instrument to engineer the soil microbiome, be it for enhancing plant growth, bioremediation, or any other desirable function.
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Affiliation(s)
- Kjell Rune Jonassen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.,VEAS WWTP, Slemmestad, Norway
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Lars Molstad
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
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19
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Wang M, Zhou T, Liang Y, Li G, Sun Y. Response characteristics of nirS-type denitrifier Paracoccus denitrificans under florfenicol stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 219:112355. [PMID: 34049225 DOI: 10.1016/j.ecoenv.2021.112355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Florfenicol (FF) is widely used in aquaculture and can interfere with denitrification when released into natural ecosystems. The aim of this study was to analyze the response characteristics of nirS-type denitrifier Paracoccus denitrificans under FF stress and further mine antibiotic-responsive factors in aquatic environment. Phenotypic analysis revealed that FF delayed the nitrate removal with a maximum inhibition value of 82.4% at exponential growth phase, leading to nitrite accumulation reached to 21.9-fold and biofilm biomass decreased by ~38.6%, which were due to the lower bacterial population count (P < 0.01). RNA-seq transcriptome analyses indicated that FF treatment decreased the expression of nirS, norB, nosD and nosZ genes that encoded enzymes required for NO2- to N2 conversion from 1.02- to 2.21-fold (P < 0.001). Furthermore, gene associated with the flagellar system FlgL was also down-regulated by 1.03-fold (P < 0.001). Moreover, 10 confirmed sRNAs were significantly induced, which regulated a wide range of metabolic pathways and protein expression. Interestingly, different bacteria contained the same sRNAs means that sRNAs can spread between them. Overall, this study suggests that the denitrification of nirS-type denitrifiers can be hampered widely by FF and the key sRNAs have great potential to be antibiotic-responsive factors.
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Affiliation(s)
- Mei Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Tong Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yi Liang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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20
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Bernabeu E, Miralles-Robledillo JM, Giani M, Valdés E, Martínez-Espinosa RM, Pire C. In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification. Biomolecules 2021; 11:biom11071043. [PMID: 34356667 PMCID: PMC8301774 DOI: 10.3390/biom11071043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Affiliation(s)
- Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Elena Valdés
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
- Correspondence: ; Tel.: +34-965903400 (ext. 2064)
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21
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Störiko A, Pagel H, Mellage A, Cirpka OA. Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models? Front Microbiol 2021; 12:684146. [PMID: 34220770 PMCID: PMC8250433 DOI: 10.3389/fmicb.2021.684146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.
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Affiliation(s)
- Anna Störiko
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Holger Pagel
- Biogeophysics, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Adrian Mellage
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Olaf A. Cirpka
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
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22
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Schutte CA, Huanca-Valenzuela P, Lavik G, Marchant HK, de Beer D. Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification. Front Microbiol 2021; 12:556268. [PMID: 34220727 PMCID: PMC8250833 DOI: 10.3389/fmicb.2021.556268] [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: 04/27/2020] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NOx (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NOx consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NOx uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NOx supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NOx always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NOx uptake by the MPB and drives water column NOx to the depths of maximum denitrification potential.
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Affiliation(s)
- Charles A Schutte
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Gaute Lavik
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dirk de Beer
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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23
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Zhou Y, Suenaga T, Qi C, Riya S, Hosomi M, Terada A. Temperature and oxygen level determine N 2 O respiration activities of heterotrophic N 2 O-reducing bacteria: Biokinetic study. Biotechnol Bioeng 2020; 118:1330-1341. [PMID: 33305820 DOI: 10.1002/bit.27654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
Nitrous oxide (N2 O), a potent greenhouse gas, is reduced to N2 gas by N2 O-reducing bacteria (N2 ORB), a process which represents an N2 O sink in natural and engineered ecosystems. The N2 O sink activity by N2 ORB depends on temperature and O2 exposure, yet the specifics are not yet understood. This study explores the effects of temperature and oxygen exposure on biokinetics of pure culture N2 ORB. Four N2 ORB, representing either clade I type nosZ (Pseudomonas stutzeri JCM5965 and Paracoccus denitrificans NBRC102528) or clade II type nosZ (Azospira sp. strains I09 and I13), were individually tested. The higher activation energy for N2 O by Azospira sp. strain I13 (114.0 ± 22.6 kJ mol-1 ) compared with the other tested N2 ORB (38.3-60.1 kJ mol-1 ) indicates that N2 ORB can adapt to different temperatures. The O2 inhibition constants (KI ) of Azospira sp. strain I09 and Ps. stutzeri JCM5965 increased from 0.06 ± 0.05 and 0.05 ± 0.02 μmol L-1 to 0.92 ± 0.24 and 0.84 ± 0.31 μmol L-1 , respectively, as the temperature increased from 15°C to 35°C, while that of Azospira sp. strain I13 was temperature-independent (p = 0.106). Within the range of temperatures examined, Azospira sp. strain I13 had a faster recovery after O2 exposure compared with Azospira sp. strain I09 and Ps. stutzeri JCM5965 (p < 0.05). These results suggest that temperature and O2 exposure result in the growth of ecophysiologically distinct N2 ORB as N2 O sinks. This knowledge can help develop a suitable N2 O mitigation strategy according to the physiologies of the predominant N2 ORB.
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Affiliation(s)
- Yiwen Zhou
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Toshikazu Suenaga
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Chuang Qi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.,School of Environment, Nanjing Normal University, Nanjing, China
| | - Shohei Riya
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Masaaki Hosomi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Global Innovation Research Institute, Tokyo University of Agriculture and Technology, Tokyo, Japan
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24
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Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW. Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Front Microbiol 2020; 11:587127. [PMID: 33193240 PMCID: PMC7604516 DOI: 10.3389/fmicb.2020.587127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
A nitrate- and metal-contaminated site at the Oak Ridge Reservation (ORR) was previously shown to contain the metal molybdenum (Mo) at picomolar concentrations. This potentially limits microbial nitrate reduction, as Mo is required by the enzyme nitrate reductase, which catalyzes the first step of nitrate removal. Enrichment for anaerobic nitrate-reducing microbes from contaminated sediment at the ORR yielded Bacillus strain EB106-08-02-XG196. This bacterium grows in the presence of multiple metals (Cd, Ni, Cu, Co, Mn, and U) but also exhibits better growth compared to control strains, including Pseudomonas fluorescens N2E2 isolated from a pristine ORR environment under low molybdate concentrations (<1 nM). Molybdate is taken up by the molybdate binding protein, ModA, of the molybdate ATP-binding cassette transporter. ModA of XG196 is phylogenetically distinct from those of other characterized ModA proteins. The genes encoding ModA from XG196, P. fluorescens N2E2 and Escherichia coli K12 were expressed in E. coli and the recombinant proteins were purified. Isothermal titration calorimetry analysis showed that XG196 ModA has a higher affinity for molybdate than other ModA proteins with a molybdate binding constant (KD) of 2.2 nM, about one order of magnitude lower than those of P. fluorescens N2E2 (27.0 nM) and E. coli K12 (25.0 nM). XG196 ModA also showed a fivefold higher affinity for molybdate than for tungstate (11 nM), whereas the ModA proteins from P. fluorescens N2E2 [KD (Mo) 27.0 nM, KD (W) 26.7 nM] and E. coli K12[(KD (Mo) 25.0 nM, KD (W) 23.8 nM] had similar affinities for the two oxyanions. We propose that high molybdate affinity coupled with resistance to multiple metals gives strain XG196 a competitive advantage in Mo-limited environments contaminated with high concentrations of metals and nitrate, as found at ORR.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Torben Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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25
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Involvement of NO 3 - in Ecophysiological Regulation of Dissimilatory Nitrate/Nitrite Reduction to Ammonium (DNRA) Is Implied by Physiological Characterization of Soil DNRA Bacteria Isolated via a Colorimetric Screening Method. Appl Environ Microbiol 2020; 86:AEM.01054-20. [PMID: 32631862 DOI: 10.1128/aem.01054-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) has recently regained attention as a nitrogen retention pathway that may potentially be harnessed to alleviate nitrogen loss resulting from denitrification. Until recently, the ecophysiology of DNRA bacteria inhabiting agricultural soils has remained largely unexplored, due to the difficulty in targeted enrichment and isolation of DNRA microorganisms. In this study, >100 DNRA bacteria were isolated from NO3 --reducing anoxic enrichment cultures established with rice paddy soils using a newly developed colorimetric screening method. Six of these isolates, each assigned to a different genus, were characterized to improve the understanding of DNRA physiology. All the isolates carried nrfA and/or nirB, and the Bacillus sp. strain possessed a clade II nosZ gene conferring the capacity for N2O reduction. A common prominent physiological feature observed in the isolates was NO2 - accumulation before NH4 + production, which was further examined with Citrobacter sp. strain DNRA3 (possessing nrfA and nirB) and Enterobacter sp. strain DNRA5 (possessing only nirB). Both isolates showed inhibition of NO2 --to-NH4 + reduction at submillimolar NO3 - concentrations and downregulation of nrfA or nirB transcription when NO3 - was being reduced to NO2 - In batch and chemostat experiments, both isolates produced NH4 + from NO3 - reduction when incubated with excess organic electron donors, while incubation with excess NO3 - resulted in NO2 - buildup but no substantial NH4 + production, presumably due to inhibitory NO3 - concentrations. This previously overlooked link between NO3 - repression of NO2 --to-NH4 + reduction and the C-to-N ratio regulation of DNRA activity may be a key mechanism underpinning denitrification-versus-DNRA competition in soil.IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is an anaerobic microbial pathway that competes with denitrification for common substrates NO3 - and NO2 - Unlike denitrification, which leads to nitrogen loss and N2O emission, DNRA reduces NO3 - and NO2 - to NH4 +, a reactive nitrogen compound with a higher tendency to be retained in the soil matrix. Therefore, stimulation of DNRA has often been proposed as a strategy to improve fertilizer efficiency and reduce greenhouse gas emissions. Such attempts have been hampered by lack of insights into soil DNRA bacterial ecophysiology. Here, we have developed a new screening method for isolating DNRA-catalyzing organisms from agricultural soils without apparent DNRA activity. Physiological characteristics of six DNRA isolates were closely examined, disclosing a previously overlooked link between NO3 - repression of NO2 --to-NH4 + reduction and the C-to-N ratio regulation of DNRA activity, which may be a key to understanding why DNRA activity is rarely observed at substantial levels in nitrogen-rich agricultural soils.
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26
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Involvement of the cbb3-Type Terminal Oxidase in Growth Competition of Bacteria, Biofilm Formation, and in Switching between Denitrification and Aerobic Respiration. Microorganisms 2020; 8:microorganisms8081230. [PMID: 32806683 PMCID: PMC7464135 DOI: 10.3390/microorganisms8081230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
Paracoccus denitrificans has a branched electron transport chain with three terminal oxidases transferring electrons to molecular oxygen, namely aa3-type and cbb3-type cytochrome c oxidases and ba3-type ubiquinol oxidase. In the present study, we focused on strains expressing only one of these enzymes. The competition experiments showed that possession of cbb3-type oxidase confers significant fitness advantage during oxygen-limited growth and supports the biofilm lifestyle. The aa3-type oxidase was shown to allow rapid aerobic growth at a high oxygen supply. Activity of the denitrification pathway that had been expressed in cells grown anaerobically with nitrate was fully inhibitable by oxygen only in wild-type and cbb3 strains, while in strains aa3 and ba3 dinitrogen production from nitrate and oxygen consumption occurred simultaneously. Together, the results highlight the importance of the cbb3-type oxidase for the denitrification phenotype and suggest a way of obtaining novel bacterial strains capable of aerobic denitrification.
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27
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Albina P, Durban N, Bertron A, Schiettekatte M, Albrecht A, Robinet JC, Erable B. Adaptation of neutrophilic Paracoccus denitrificans to denitrification at highly alkaline pH. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:22112-22119. [PMID: 32285397 DOI: 10.1007/s11356-020-08360-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/09/2020] [Indexed: 06/11/2023]
Abstract
Bacterial denitrification is widely documented at neutral pH in order to improve the removal of nitrate in wastewater treatment processes. However, certain industrial contexts generate alkaline waste and effluent containing nitrate that must be denitrified. To obtain more information on denitrification at alkaline pH, this study evaluated the possibility of adapting a neutrophilic denitrifying strain, Paracoccus denitrificans, to alkaline pH. Firstly, P. denitrificans' denitrifying activity was evaluated without acclimation in batch bioreactors at pH 7.0, 8.0, 9.0 and 10.0. Then, two acclimation methods using successive batch bioreactors and a continuous bioreactor allowed P. denitrificans to be gradually exposed to alkaline pH: from 8.5 to 11.2 in 26 and 72 days respectively. Results showed that P. denitrificans could grow and catalyse nitrate reduction (i) at pH 9.0 without acclimation, (ii) at pH 10.5 in successive batch cultures with progressively increasing pH and (iii) at pH 10.8 in continuously fed culture with a hydraulic retention time (HRT) of 8 days. It was shown that denitrification affected the pH despite the presence of carbonate buffering of the P. denitrificans growth medium. With acetate as an electron donor, the pH of a carbonate buffered medium tends towards pH 10 during the process of denitrification. Graphical abstract.
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Affiliation(s)
- Pierre Albina
- LGC, CNRS, INPT, UPS, Université de Toulouse, Toulouse, France.
- LMDC, INSA/UPS Génie Civil, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse Cedex 04, France.
| | - Nadège Durban
- LGC, CNRS, INPT, UPS, Université de Toulouse, Toulouse, France
- LMDC, INSA/UPS Génie Civil, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Alexandra Bertron
- LMDC, INSA/UPS Génie Civil, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Maud Schiettekatte
- LMDC, INSA/UPS Génie Civil, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Achim Albrecht
- Andra, 1-7 rue Jean-Monet, Châtenay-Malabry, 62298, France
| | | | - Benjamin Erable
- LGC, CNRS, INPT, UPS, Université de Toulouse, Toulouse, France
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28
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Torregrosa-Crespo J, Pire C, Bergaust L, Martínez-Espinosa RM. Haloferax mediterranei, an Archaeal Model for Denitrification in Saline Systems, Characterized Through Integrated Physiological and Transcriptional Analyses. Front Microbiol 2020; 11:768. [PMID: 32390995 PMCID: PMC7188791 DOI: 10.3389/fmicb.2020.00768] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Haloferax mediterranei (R4) belongs to the group of halophilic archaea, one of the predominant microbial populations in hypersaline environments. In these ecosystems, the low availability of oxygen pushes the microbial inhabitants toward anaerobic pathways and the presence of N-oxyanions favor denitrification. In a recent study comparing three Haloferax species carrying dissimilatory N-oxide reductases, H. mediterranei showed promise as a future model for archaeal denitrification. This work further explores the respiratory physiology of this haloarchaeon when challenged with ranges of nitrite and nitrate concentrations and at neutral or sub-neutral pH during the transition to anoxia. Moreover, to begin to understand the transcriptional regulation of N-oxide reductases, detailed gas kinetics was combined with gene expression analyses at high resolution. The results show that H. mediterranei has an expression pattern similar to that observed in the bacterial Domain, well-coordinated at low concentrations of N-oxyanions. However, it could only sustain a few generations of exponential anaerobic growth, apparently requiring micro-oxic conditions for de novo synthesis of denitrification enzymes. This is the first integrated study within this field of knowledge in haloarchaea and Archaea in general, and it sheds lights on denitrification in salty environments.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Linda Bergaust
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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29
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Chen M, Zhou X, Chen X, Cai Q, Zeng RJ, Zhou S. Mechanisms of nitrous oxide emission during photoelectrotrophic denitrification by self-photosensitized Thiobacillus denitrificans. WATER RESEARCH 2020; 172:115501. [PMID: 31954933 DOI: 10.1016/j.watres.2020.115501] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/31/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Photoelectrotrophic denitrification (PEDeN) using bio-hybrids has the potential to remove nitrate (NO3-) from wastewater in an economical and sustainable way. As a gas of global concern, the mechanisms of nitrous oxide (N2O) emissions during this novel process remain unclear. Herein, a self-photosensitized bio-hybrid, i. e., Thiobacillus denitrificans-cadmium sulfide, was constructed and the factors affecting N2O emissions during PEDeN by the bio-hybrids were investigated. The system was sensitive to the input NO3--N and NO2--N, resulting in changes in the N2O/(N2+N2O) ratio from 1% to 95%. In addition to free nitrous acid (FNA), reactive oxidative species (ROS) were a unique factor affecting N2O emission during PEDeN. Importantly, the N2O reduction step exhibited greater susceptibility to the ROS than nitrate reduction step. The contributions of hydrogen peroxide (H2O2), superoxides (O2-•), hydroxyl radicals (•OH) and FNA to the inhibition of N2O reduction were >15.0%, >5.4%, 1.3%, and <70.2%, respectively for a reduction of 13.5 mg/L NO3--N. A significant down-regulation of the relative transcription of the gene nosZ demonstrated that the inhibition of N2O reductase occurred at the gene level. This finding has important implications not only for mitigating N2O emissions during the PEDeN process but also for encouraging a reexamination process of N2O emissions in nature, particularly in systems in which ROS are present during the denitrification process.
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Affiliation(s)
- Man Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaofang Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiangyu Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Quanhua Cai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Raymond Jianxiong Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
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30
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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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31
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Ge X, Vaccaro BJ, Thorgersen MP, Poole FL, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW. Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle. Environ Microbiol 2018; 21:152-163. [PMID: 30289197 DOI: 10.1111/1462-2920.14435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/24/2018] [Accepted: 09/27/2018] [Indexed: 11/25/2022]
Abstract
Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO4 2- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Erica L Majumder
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Kara B De León
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Ji Won Moon
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Charles J Paradis
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - Paul D Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
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Lycus P, Soriano-Laguna MJ, Kjos M, Richardson DJ, Gates AJ, Milligan DA, Frostegård Å, Bergaust L, Bakken LR. A bet-hedging strategy for denitrifying bacteria curtails their release of N 2O. Proc Natl Acad Sci U S A 2018; 115:11820-11825. [PMID: 30385636 PMCID: PMC6243289 DOI: 10.1073/pnas.1805000115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
When oxygen becomes limiting, denitrifying bacteria must prepare for anaerobic respiration by synthesizing the reductases NAR (NO3- → NO2-), NIR (NO2- → NO), NOR (2NO → N2O), and NOS (N2O → N2), either en bloc or sequentially, to avoid entrapment in anoxia without energy. Minimizing the metabolic burden of this precaution is a plausible fitness trait, and we show that the model denitrifier Paracoccus denitrificans achieves this by synthesizing NOS in all cells, while only a minority synthesize NIR. Phenotypic diversification with regards to NIR is ascribed to stochastic initiation of gene transcription, which becomes autocatalytic via NO production. Observed gas kinetics suggest that such bet hedging is widespread among denitrifying bacteria. Moreover, in response to oxygenation, P. denitrificans preserves NIR in the poles of nongrowing persister cells, ready to switch to anaerobic respiration in response to sudden anoxia. Our findings add dimensions to the regulatory biology of denitrification and identify regulatory traits that decrease N2O emissions.
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Affiliation(s)
- Pawel Lycus
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | | | - Morten Kjos
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - David John Richardson
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, United Kingdom
| | - Andrew James Gates
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, United Kingdom
| | - Daniel Aleksanteri Milligan
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Linda Bergaust
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway;
| | - Lars Reier Bakken
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway;
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Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS. Systems biology approaches towards predictive microbial ecology. Environ Microbiol 2018; 20:4197-4209. [DOI: 10.1111/1462-2920.14378] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 01/17/2023]
Affiliation(s)
| | | | - Sean M. Gibbons
- Institute for Systems Biology Seattle WA USA
- eScience Institute, University of Washington Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
| | - Mónica V. Orellana
- Institute for Systems Biology Seattle WA USA
- Polar Science Center Applied Physics Lab, University of Washington Seattle WA
| | - Nitin S. Baliga
- Institute for Systems Biology Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
- Departments of Biology and Microbiology University of Washington Seattle WA USA
- Lawrence Berkeley National Lab Berkeley CA USA
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34
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Moisander PH, Shoemaker KM, Daley MC, McCliment E, Larkum J, Altabet MA. Copepod-Associated Gammaproteobacteria Respire Nitrate in the Open Ocean Surface Layers. Front Microbiol 2018; 9:2390. [PMID: 30369912 PMCID: PMC6194322 DOI: 10.3389/fmicb.2018.02390] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022] Open
Abstract
Microbial dissimilatory nitrate reduction to nitrite, or nitrate respiration, was detected in association with copepods in the oxygenated water column of the North Atlantic subtropical waters. These unexpected rates correspond to up to 0.09 nmol N copepod-1 d-1 and demonstrate a previously unaccounted nitrogen transformation in the oceanic pelagic surface layers. Genes and transcripts for both the periplasmic and membrane associated dissimilatory nitrate reduction pathways (Nap and Nar, respectively) were detected. The napA genes and transcripts were closely related with sequences from several clades of Vibrio sp., while the closest relatives of the narG sequences were Pseudoalteromonas spp. and Alteromonas spp., many of them representing clades only distantly related to previously described cultivated bacteria. The discovered activity demonstrates a novel Gammaproteobacterial respiratory role in copepod association, presumably providing energy for these facultatively anaerobic bacteria, while supporting a reductive path of nitrogen in the oxygenated water column of the open ocean.
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Affiliation(s)
- Pia H. Moisander
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, United States
| | - Katyanne M. Shoemaker
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, United States
| | - Meaghan C. Daley
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, United States
| | - Elizabeth McCliment
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, United States
| | - Jennifer Larkum
- School of Marine Science and Technology, University of Massachusetts Dartmouth, New Bedford, MA, United States
| | - Mark A. Altabet
- School of Marine Science and Technology, University of Massachusetts Dartmouth, New Bedford, MA, United States
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35
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Wang Y, Wang Z, Duo Y, Wang X, Chen J, Chen J. Gene cloning, expression, and reducing property enhancement of nitrous oxide reductase from Alcaligenes denitrificans strain TB. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:43-52. [PMID: 29649759 DOI: 10.1016/j.envpol.2018.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/14/2018] [Accepted: 04/01/2018] [Indexed: 06/08/2023]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and tends to accumulate as an intermediate in the process of bacteria denitrification. To achieve complete reduction of nitrogen oxide (NOx) in bacteria denitrification, the structural gene nosZ encoding nitrous oxide reductase (N2OR) was cloned from Alcaligenes denitrificans strain TB (GenBank JQ044686). The recombinant plasmid containing the nosZ gene was built, and the expression of nosZ gene in Escherichia coli was determined. Results show that the nosZ gene consisting of 1917 nucleotides achieves heterologous expression successfully by codon optimization strategy under optimal conditions (pre-induction inoculum OD600 of 0.67, final IPTG concentration of 0.5 mM, inducing time of 6 h, and inducing temperature of 28 °C). Determination result of gas chromatography confirms that N2O degradation efficiency of recombinant E. coli is strengthened by at least 1.92 times compared with that of original strain TB when treated with N2O as substrate. Moreover, N2OR activity in recombinant strain is 2.09 times higher than that in wild strain TB, which validates the aforementioned result and implies that the recombinant E. coli BL21 (DE3)-pET28b-nosZ is a potential candidate to control N2O accumulation and alleviate greenhouse effect. In addition, the N2OR structure and the possible N2O binding site in Alcaligenes sp. TB are predicted, which open an avenue for further research on the relationship between N2OR activity and its structure.
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Affiliation(s)
- Yu Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zeyu Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yankai Duo
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiaoping Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jianmeng Chen
- Engineering Research Center of the Ministry of Education for Bioconversion and Biopurification, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jun Chen
- Engineering Research Center of the Ministry of Education for Bioconversion and Biopurification, Zhejiang University of Technology, Hangzhou 310014, PR China.
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36
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O 2 versus N 2O respiration in a continuous microbial enrichment. Appl Microbiol Biotechnol 2018; 102:8943-8950. [PMID: 30054702 PMCID: PMC6153640 DOI: 10.1007/s00253-018-9247-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 11/15/2022]
Abstract
Despite its ecological importance, essential aspects of microbial N2O reduction—such as the effect of O2 availability on the N2O sink capacity of a community—remain unclear. We studied N2O vs. aerobic respiration in a chemostat culture to explore (i) the extent to which simultaneous respiration of N2O and O2 can occur, (ii) the mechanism governing the competition for N2O and O2, and (iii) how the N2O-reducing capacity of a community is affected by dynamic oxic/anoxic shifts such as those that may occur during nitrogen removal in wastewater treatment systems. Despite its prolonged growth and enrichment with N2O as the sole electron acceptor, the culture readily switched to aerobic respiration upon exposure to O2. When supplied simultaneously, N2O reduction to N2 was only detected when the O2 concentration was limiting the respiration rate. The biomass yields per electron accepted during growth on N2O are in agreement with our current knowledge of electron transport chain biochemistry in model denitrifiers like Paracoccus denitrificans. The culture’s affinity constant (KS) for O2 was found to be two orders of magnitude lower than the value for N2O, explaining the preferential use of O2 over N2O under most environmentally relevant conditions.
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37
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Zhang H, Zhao Z, Chen S, Kang P, Wang Y, Feng J, Jia J, Yan M, Wang Y, Xu L. Paracoccus versutus KS293 adaptation to aerobic and anaerobic denitrification: Insights from nitrogen removal, functional gene abundance, and proteomic profiling analysis. BIORESOURCE TECHNOLOGY 2018; 260:321-328. [PMID: 29631182 DOI: 10.1016/j.biortech.2018.03.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
A novel strain KS293 exhibiting excellent aerobic and anaerobic denitrification performance was isolated and identified as Paracoccus versutus KS293. Nitrate nitrogen and total organic carbon could be effectively removed by P. versutus KS293 without nitrite accumulation, whilst 82% and 85% of total nitrogen was converted into gaseous products under aerobic and anaerobic conditions (P > .05), respectively. Based on the ratio of anaerobic to aerobic, relative abundance values were increased 1.41, 1.45, and 2.31 folds for nirS, nosZ, and narG, respectively. A comparison of the two-dimensional gel electrophoresis and principal component analysis showed significant differences in proteomic profiles between aerobic and anaerobic conditions. In total, 78 proteins that displayed fluctuations in relative expression were observed. 10 proteins including nitrate reductase, maintenance of cell membrane (TolA), and RNA polymerase-binding transcription factor (DksA) were differentially expressed. These findings demonstrated that P. versutus KS293 was effective for nitrogen removal under aerobic or anaerobic conditions.
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Affiliation(s)
- Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China.
| | - Zhenfang Zhao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Shengnan Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Pengliang Kang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Ji Feng
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Jingyu Jia
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Miaomiao Yan
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Yan Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Lei Xu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
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38
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Gonzalez-Martinez A, Margareto A, Rodriguez-Sanchez A, Pesciaroli C, Diaz-Cruz S, Barcelo D, Vahala R. Linking the Effect of Antibiotics on Partial-Nitritation Biofilters: Performance, Microbial Communities and Microbial Activities. Front Microbiol 2018. [PMID: 29535704 PMCID: PMC5834488 DOI: 10.3389/fmicb.2018.00354] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The emergence and spread of antibiotics resistance in wastewater treatment systems have been pointed as a major environmental health problem. Nevertheless, research about adaptation and antibiotics resistance gain in wastewater treatment systems subjected to antibiotics has not been successfully developed considering bioreactor performance, microbial community dynamics and microbial activity dynamics at the same time. To observe this in autotrophic nitrogen removal systems, a partial-nitritation biofilter was subjected to a continuous loading of antibiotics mix of azithromycin, norfloxacin, trimethoprim, and sulfamethoxazole. The effect of the antibiotics mix over the performance, bacterial communities and bacterial activity in the system was evaluated. The addition of antibiotics caused a drop of ammonium oxidation efficiency (from 50 to 5%) and of biomass concentration in the bioreactor, which was coupled to the loss of ammonium oxidizing bacteria Nitrosomonas in the bacterial community from 40 to 3%. Biomass in the partial nitritation biofilter experienced a sharp decrease of about 80% due to antibiotics loading, but the biomass adapted and experienced a growth by stabilization under antibiotics feeding. During the experiment several bacterial genera appeared, such as Alcaligenes, Paracoccus, and Acidovorax, clearly dominating the bacterial community with >20% relative abundance. The system reached around 30% ammonium oxidation efficiency after adaptation to antibiotics, but no effluent nitrite was found, suggesting that dominant antibiotics-resistant phylotypes could be involved in nitrification–denitrification metabolisms. The activity of ammonium oxidation measured as amoA and hao gene expression dropped a 98.25% and 99.21%, respectively, comparing the system before and after the addition of antibiotics. On the other hand, denitrifying activity increased as observed by higher expression of nir and nos genes (83.14% and 252.54%, respectively). In addition, heterotrophic nitrification cyt c-551 was active only after the antibiotics addition. Resistance to the antibiotics was presumably given by ermF, carA and msrA for azithromycin, mutations of the gyrA and grlB for norfloxacin, and by sul123 genes for sulfamethoxazole. Joined physicochemical and microbiological characterization of the system were used to investigate the effect of the antibiotics over the bioprocess. Despite the antibiotics resistance, activity of Bacteria decreased while the activity of Archaea and Fungi increased.
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Affiliation(s)
| | - Alejandro Margareto
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research, Barcelona, Spain.,Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, Girona, Spain
| | | | | | - Silvia Diaz-Cruz
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research, Barcelona, Spain.,Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Damia Barcelo
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research, Barcelona, Spain.,Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Riku Vahala
- Department of Built Environment, School of Engineering, Aalto University, Espoo, Finland
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Conthe M, Wittorf L, Kuenen JG, Kleerebezem R, van Loosdrecht MCM, Hallin S. Life on N 2O: deciphering the ecophysiology of N 2O respiring bacterial communities in a continuous culture. ISME JOURNAL 2018; 12:1142-1153. [PMID: 29416125 PMCID: PMC5864245 DOI: 10.1038/s41396-018-0063-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/19/2017] [Accepted: 12/29/2017] [Indexed: 01/04/2023]
Abstract
Reduction of the greenhouse gas N2O to N2 is a trait among denitrifying and non-denitrifying microorganisms having an N2O reductase, encoded by nosZ. The nosZ phylogeny has two major clades, I and II, and physiological differences among organisms within the clades may affect N2O emissions from ecosystems. To increase our understanding of the ecophysiology of N2O reducers, we determined the thermodynamic growth efficiency of N2O reduction and the selection of N2O reducers under N2O- or acetate-limiting conditions in a continuous culture enriched from a natural community with N2O as electron acceptor and acetate as electron donor. The biomass yields were higher during N2O limitation, irrespective of dilution rate and community composition. The former was corroborated in a continuous culture of Pseudomonas stutzeri and was potentially due to cytotoxic effects of surplus N2O. Denitrifiers were favored over non-denitrifying N2O reducers under all conditions and Proteobacteria harboring clade I nosZ dominated. The abundance of nosZ clade II increased when allowing for lower growth rates, but bacteria with nosZ clade I had a higher affinity for N2O, as defined by μmax/Ks. Thus, the specific growth rate is likely a key factor determining the composition of communities living on N2O respiration under growth-limited conditions.
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Affiliation(s)
- Monica Conthe
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J Gijs Kuenen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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40
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Zheng X, Su Y, Chen Y, Huang H, Shen Q. Global transcriptional responses of denitrifying bacteria to functionalized single-walled carbon nanotubes revealed by weighted gene-coexpression network analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:1240-1249. [PMID: 28958131 DOI: 10.1016/j.scitotenv.2017.09.193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/18/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
Functionalized single-walled carbon nanotubes (f-SWNTs) are widely used in many fields due to the unique structure and the excellent properties. Although these nanomaterials have been reported to enable to cause negative effects on denitrifying bacteria once they enter the environment, the toxic behaviors and regulatory mechanisms of f-SWNTs to denitrification remain unclear. In this study, the denitrification performance of a model denitrifier exposed to pristine and functionalized SWNTs was investigated, and the global transcriptional responses were comprehensively explored by RNA-seq and weighted gene-coexpression network analysis (WGCNA). Although both hydroxyl SWNTs (SWNTs-OH) and carboxyl SWNTs (SWNTs-COOH) showed inhibitory effects on bacterial denitrification, the former more severely inhibited denitrification than the latter. Transcriptional profiles showed that compared with SWNTs-COOH, SWNTs-OH much more strongly influenced the expressions of the key genes related to signal transduction, substance transport, electron transfer and transcriptional regulation. Functional analysis further indicated that the genes associated with substrate transport, carbon source metabolism and electron transfer underwent dramatic down-regulation. Using WGCNA, 12 gene modules were established corresponding to various types of carbon nanotubes, and eigengene adjacency analysis revealed the key gene modules related to denitrification performance under different conditions. Hub gene network analysis revealed the key regulatory factors of bacterial denitrification induced by f-SWNTs. The results suggested that f-SWNTs modulated the key genes responsible for the glycerolipid/free fatty acid (GL/FFA) cycle, and thus disturb processes associated with denitrification, including signaling process, energy homeostasis, intracellular redox balance and transportation.
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Affiliation(s)
- Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Key Laboratory for Urban and Ecological Restoration of Shanghai, School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Qiuting Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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41
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Torregrosa-Crespo J, Bergaust L, Pire C, Martínez-Espinosa RM. Denitrifying haloarchaea: sources and sinks of nitrogenous gases. FEMS Microbiol Lett 2017; 365:4718458. [DOI: 10.1093/femsle/fnx270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/08/2017] [Indexed: 11/14/2022] Open
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42
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Yoon H, Song MJ, Yoon S. Design and Feasibility Analysis of a Self-Sustaining Biofiltration System for Removal of Low Concentration N 2O Emitted from Wastewater Treatment Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10736-10745. [PMID: 28849922 DOI: 10.1021/acs.est.7b02750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
N2O is a potent greenhouse gas and ozone-depletion agent. In this study, a biofiltration system was designed for removal of N2O emitted at low concentrations (<200 ppmv) from wastewater treatment plants. The proposed biofiltration system utilizes untreated wastewater from the primary sedimentation basin as the source of electron donor and nutrients and energy requirement is minimized by utilizing gravitational force and pressure differential to direct liquid medium and gas through the biofilter. The experiments performed with laboratory-scale biofilter in two different configurations confirmed the feasibility of the biofiltration system. The biofilter operated with cycling of raw wastewater exhibited up to 94% and 53% removal efficiency with 100 ppmv N2O in N2 and air, respectively, as the feed gas, corroborating that untreated wastewater can serve as a robust source of electron donor and nutrients. The laboratory-scale biofilter operated with a continuous flow-through of synthetic wastewater attained >99.9% removal of N2O from N2 background at the gas flow rate up to 2,000 mL·min-1 and >50% N2O removal from air background at the gas flow rate of 200 mL·min-1. nosZ-containing bacterial genera including Flavobacterium (5.92%), Pseudomonas (4.26%) and Bosea (2.39%) were identified in the biofilm samples collected from the oxic biofilter, indicating these organisms were responsible for N2O removal.
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Affiliation(s)
- Hyun Yoon
- Department of Civil and Environmental Engineering, KAIST , Daejeon, 34141, Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, KAIST , Daejeon, 34141, Korea
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, KAIST , Daejeon, 34141, Korea
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Torres MJ, Bueno E, Jiménez-Leiva A, Cabrera JJ, Bedmar EJ, Mesa S, Delgado MJ. FixK 2 Is the Main Transcriptional Activator of Bradyrhizobium diazoefficiens nosRZDYFLX Genes in Response to Low Oxygen. Front Microbiol 2017; 8:1621. [PMID: 28912756 PMCID: PMC5582078 DOI: 10.3389/fmicb.2017.01621] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/09/2017] [Indexed: 11/29/2022] Open
Abstract
The powerful greenhouse gas, nitrous oxide (N2O) has a strong potential to drive climate change. Soils are the major source of N2O and microbial nitrification and denitrification the main processes involved. The soybean endosymbiont Bradyrhizobium diazoefficiens is considered a model to study rhizobial denitrification, which depends on the napEDABC, nirK, norCBQD, and nosRZDYFLX genes. In this bacterium, the role of the regulatory cascade FixLJ-FixK2-NnrR in the expression of napEDABC, nirK, and norCBQD genes involved in N2O synthesis has been previously unraveled. However, much remains to be discovered regarding the regulation of the respiratory N2O reductase (N2OR), the key enzyme that mitigates N2O emissions. In this work, we have demonstrated that nosRZDYFLX genes constitute an operon which is transcribed from a major promoter located upstream of the nosR gene. Low oxygen was shown to be the main inducer of expression of nosRZDYFLX genes and N2OR activity, FixK2 being the regulatory protein involved in such control. Further, by using an in vitro transcription assay with purified FixK2 protein and B. diazoefficiens RNA polymerase we were able to show that the nosRZDYFLX genes are direct targets of FixK2.
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Affiliation(s)
- María J Torres
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Emilio Bueno
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
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Marchant HK, Ahmerkamp S, Lavik G, Tegetmeyer HE, Graf J, Klatt JM, Holtappels M, Walpersdorf E, Kuypers MMM. Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously. THE ISME JOURNAL 2017; 11:1799-1812. [PMID: 28463234 PMCID: PMC5520038 DOI: 10.1038/ismej.2017.51] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 02/08/2017] [Accepted: 03/03/2017] [Indexed: 01/20/2023]
Abstract
Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales. The response of denitrifiers to these fluctuations are largely unknown, although previous observations suggest they may denitrify under aerobic conditions. We examined the response of benthic denitrification to fluctuating oxygen concentrations, finding that denitrification not only occurred at high O2 concentrations but was stimulated by frequent switches between oxic and anoxic conditions. Throughout a tidal cycle, in situtranscription of genes for aerobic respiration and denitrification were positively correlated within diverse bacterial classes, regardless of O2 concentrations, indicating that denitrification gene transcription is not strongly regulated by O2 in sandy sediments. This allows microbes to respond rapidly to changing environmental conditions, but also means that denitrification is utilized as an auxiliary respiration under aerobic conditions when imbalances occur in electron donor and acceptor supply. Aerobic denitrification therefore contributes significantly to N-loss in permeable sediments making the process an important sink for anthropogenic N-inputs.
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Affiliation(s)
| | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Jon Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Judith M Klatt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Geomicrobiology Laboratory, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor MI, USA
| | - Moritz Holtappels
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- Marum—Centre for Marine Environmental Science, Bremen, Germany
| | - Eva Walpersdorf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Nitrous Oxide Reduction by an Obligate Aerobic Bacterium, Gemmatimonas aurantiaca Strain T-27. Appl Environ Microbiol 2017; 83:AEM.00502-17. [PMID: 28389533 DOI: 10.1128/aem.00502-17] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/30/2017] [Indexed: 11/20/2022] Open
Abstract
N2O-reducing organisms with nitrous oxide reductases (NosZ) are known as the only biological sink of N2O in the environment. Among the most abundant nosZ genes found in the environment are nosZ genes affiliated with the understudied Gemmatimonadetes phylum. In this study, a unique regulatory mechanism of N2O reduction in Gemmatimonas aurantiaca strain T-27, an isolate affiliated with the Gemmatimonadetes phylum, was examined. Strain T-27 was incubated with N2O and/or O2 as the electron acceptor. Significant N2O reduction was observed only when O2 was initially present. When batch cultures of strain T-27 were amended with O2 and N2O, N2O reduction commenced after O2 was depleted. In a long-term incubation with the addition of N2O upon depletion, the N2O reduction rate decreased over time and came to an eventual stop. Spiking of the culture with O2 resulted in the resuscitation of N2O reduction activity, supporting the hypothesis that N2O reduction by strain T-27 required the transient presence of O2 The highest level of nosZ transcription (8.97 nosZ transcripts/recA transcript) was observed immediately after O2 depletion, and transcription decreased ∼25-fold within 85 h, supporting the observed phenotype. The observed difference between responses of strain T-27 cultures amended with and without N2O to O2 starvation suggested that N2O helped sustain the viability of strain T-27 during temporary anoxia, although N2O reduction was not coupled to growth. The findings in this study suggest that obligate aerobic microorganisms with nosZ genes may utilize N2O as a temporary surrogate for O2 to survive periodic anoxia.IMPORTANCE Emission of N2O, a potent greenhouse gas and ozone depletion agent, from the soil environment is largely determined by microbial sources and sinks. N2O reduction by organisms with N2O reductases (NosZ) is the only known biological sink of N2O at environmentally relevant concentrations (up to ∼1,000 parts per million by volume [ppmv]). Although a large fraction of nosZ genes recovered from soil is affiliated with nosZ found in the genomes of the obligate aerobic phylum Gemmatimonadetes, N2O reduction has not yet been confirmed in any of these organisms. This study demonstrates that N2O is reduced by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27, and suggests a novel regulation mechanism for N2O reduction in this organism, which may also be applicable to other obligate aerobic organisms possessing nosZ genes. We expect that these findings will significantly advance the understanding of N2O dynamics in environments with frequent transitions between oxic and anoxic conditions.
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Phylogenetic and functional potential links pH and N 2O emissions in pasture soils. Sci Rep 2016; 6:35990. [PMID: 27782174 PMCID: PMC5080606 DOI: 10.1038/srep35990] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/10/2016] [Indexed: 01/18/2023] Open
Abstract
Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.
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Torres M, Simon J, Rowley G, Bedmar E, Richardson D, Gates A, Delgado M. Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria: Physiology and Regulatory Mechanisms. Adv Microb Physiol 2016; 68:353-432. [PMID: 27134026 DOI: 10.1016/bs.ampbs.2016.02.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.
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