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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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Bai M, He J, Zheng F, Lv S, Wang Z, Hrynsphan D, Savitskaya T, Chen J. Gene cloning, expression and performance validation of nitric oxide dismutase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173455. [PMID: 38782282 DOI: 10.1016/j.scitotenv.2024.173455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Nitrous oxide (N2O) is a significant contributor to global warming and possesses an ozone-depleting impact nearly 298 times that of CO2. To reduce N2O emissions, the newly-discovered nod gene which can directly convert NO into N2 and O2 was successfully cloned from the anaerobic denitrification sludge. The recombinant plasmid containing the nod gene was built, and the expression of nod gene in Escherichia coli was determined, leading to the construction of recombinant engineering bacteria. Results showed that the recombinant engineering bacteria E. coli BL21 (DE3)-pET28a-nod could autonomously degrade NO, with a degradation rate of 72 % within 48 h, and could produce 2479.72 ppm of N2 and 75.12 mL of O2. The cumulative O2 production of the sludge sample and recombinant E. coli within 8 h was 1.75 mL and 8.45 mL, respectively. The cumulative O2 production of recombinant E. coli was at least 4.82 times higher than that of the sludge sample. The investigation proposed a new biodegradation pathway for nitrogen pollution.
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Affiliation(s)
- Mengwei Bai
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiamei He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fengzhen Zheng
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Sini Lv
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zeyu Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Dzmitry Hrynsphan
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk 220030, Belarus
| | - Tatsiana Savitskaya
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk 220030, Belarus
| | - Jun Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China.
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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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Takahashi K, Oshiki M, Ruan C, Morinaga K, Toyofuku M, Nomura N, Johnson DR. Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13221. [PMID: 38037543 PMCID: PMC10866065 DOI: 10.1111/1758-2229.13221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023]
Abstract
Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this phenomenon is well-established, its consequences on ecological and evolutionary processes remain poorly understood. We hypothesize here that denitrification in oxic environments can modify the accumulation profiles of nitrogen oxide intermediates with cascading effects on the evolutionary potentials of denitrifying microorganisms. To test this, we performed laboratory experiments with Paracoccus denitrificans and complemented them with individual-based computational modelling. We found that denitrification in low oxic environments significantly increases the accumulation of nitrite and nitric oxide. We further found that the increased accumulation of these intermediates has a negative effect on growth at low pH. Finally, we found that the increased negative effect at low pH increases the number of individuals that contribute to surface-associated growth. This increases the amount of genetic diversity that is preserved from the initial population, thus increasing the number of genetic targets for natural selection to act upon and resulting in higher evolutionary potentials. Together, our data highlight that denitrification in low oxic environments can affect the ecological processes and evolutionary potentials of denitrifying microorganisms by modifying the accumulation of nitrogen oxide intermediates.
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Affiliation(s)
- Kohei Takahashi
- Graduate School of Sciences and TechnologiesUniversity of TsukubaTsukubaIbarakiJapan
- Department of Environmental MicrobiologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Mamoru Oshiki
- Division of Environmental Engineering, Faculty of EngineeringHokkaido UniversitySapporoHokkaidoJapan
| | - Chujin Ruan
- Department of Environmental MicrobiologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Kana Morinaga
- Graduate School of Sciences and TechnologiesUniversity of TsukubaTsukubaIbarakiJapan
| | - Masanori Toyofuku
- Faculty of Life and Environmental SciencesUniversity of TsukubaTsukubaIbarakiJapan
- Microbiology Research Center for SustainabilityUniversity of TsukubaTsukubaIbarakiJapan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental SciencesUniversity of TsukubaTsukubaIbarakiJapan
- Microbiology Research Center for SustainabilityUniversity of TsukubaTsukubaIbarakiJapan
| | - David R. Johnson
- Department of Environmental MicrobiologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
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The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies. Microbiol Spectr 2022; 10:e0069522. [PMID: 36453888 PMCID: PMC9769761 DOI: 10.1128/spectrum.00695-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO3, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.
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Huang Q, Alengebawy A, Zhu X, Raza AF, Chen L, Chen W, Guo J, Ai P, Li D. Performance of Paracoccus pantotrophus MA3 in heterotrophic nitrification-anaerobic denitrification using formic acid as a carbon source. Bioprocess Biosyst Eng 2022; 45:1661-1672. [PMID: 35984504 DOI: 10.1007/s00449-022-02771-3] [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: 04/12/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022]
Abstract
Excess amount of nitrogen in wastewater has caused serious concerns, such as water eutrophication. Paracoccus pantotrophus MA3, a novel isolated strain of heterotrophic nitrification-anaerobic denitrification bacteria, was evaluated for nitrogen removal using formic acid as the sole carbon source. The results showed that the maximum ammonium removal efficiency was observed under the optimum conditions of 26.25 carbon to nitrogen ratio, 3.39% (v/v) inoculation amount, 34.64 °C temperature, and at 180 rpm shaking speed, respectively. In addition, quantitative real-time PCR technique analysis assured that the gene expression level of formate dehydrogenase, formate tetrahydrofolate ligase, 5,10-methylenetetrahydrofolate dehydrogenase, serine hydroxymethyltransferase, respiratory nitrate reductase beta subunit, L-glutamine synthetase, glutamate dehydrogenase, and glutamate synthase were up-regulated compared to the control group, and combined with nitrogen mass balance analysis to conclude that most of the ammonium was removed by assimilation. A small amount of nitrate and nearly no nitrite were accumulated during heterotrophic nitrification. MA3 exhibited significant denitrification potential under anaerobic conditions with a maximum nitrate removal rate of 4.39 mg/L/h, and the only gas produced was N2. Additionally, 11.50 ± 0.06 mg/L/h of NH4+-N removal rate from biogas slurry was achieved.
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Affiliation(s)
- Qun Huang
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, China
- Tianjin Key Laboratory for Industrial Biological, Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, West Seven Road, Airport Economic District, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Ahmed Alengebawy
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangyu Zhu
- Tianjin Key Laboratory for Industrial Biological, Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, West Seven Road, Airport Economic District, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Amin Farrukh Raza
- Tianjin Key Laboratory for Industrial Biological, Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, West Seven Road, Airport Economic District, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological, Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, West Seven Road, Airport Economic District, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological, Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, West Seven Road, Airport Economic District, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Jiahao Guo
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Ai
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological, Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, No. 32, West Seven Road, Airport Economic District, Tianjin, China.
- National Innovation Centre for Synthetic Biology, Tianjin, China.
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7
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Duan N, Li L, Liang X, Fine A, Zhuang J, Radosevich M, Schaeffer SM. Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production. Front Microbiol 2022; 13:847005. [PMID: 35444635 PMCID: PMC9015707 DOI: 10.3389/fmicb.2022.847005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.
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Affiliation(s)
- Ning Duan
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lidong Li
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Xiaolong Liang
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Aubrey Fine
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jie Zhuang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sean M. Schaeffer
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Genome Sequence and Description of Paracoccus denitrificans Strain R-1, Isolated from Activated Sludge. Microbiol Resour Announc 2022; 11:e0123621. [PMID: 35343764 PMCID: PMC9022511 DOI: 10.1128/mra.01236-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paracoccus denitrificans strain R-1 was isolated from an activated sludge sample from a sewage treatment plant in Taiwan. The complete genome, which was sequenced on the NovaSeq 6000 and PacBio Sequel platforms, consists of one chromosome with 4.05 Mb and one plasmid with 689 kb. Genome annotation predicts 4,167 protein-coding genes, 49 tRNAs, and 8 rRNAs.
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Li J, Sellner K, Place A, Cornwell J, Gao Y. Mitigation of CyanoHABs Using Phoslock ® to Reduce Water Column Phosphorus and Nutrient Release from Sediment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182413360. [PMID: 34948971 PMCID: PMC8705183 DOI: 10.3390/ijerph182413360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Abstract
Cyanobacterial blooms can be stimulated by excessive phosphorus (P) input, especially when diazotrophs are the dominant species. A series of mesocosm experiments were conducted in a lake dominated by a cyanobacteria bloom to study the effects of Phoslock®, a phosphorus adsorbent. The results showed that the addition of Phoslock® lowered the soluble reactive phosphate (SRP) concentrations in water due to efficient adsorption and mitigated the blooms. Once settled on the sediments, Phoslock® serves as a barrier to reduce P diffusion from sediments into the overlying waters. In short-term (1 day) incubation experiments, Phoslock® diminished or reversed SRP effluxes from bottom sediments. At the same time, the upward movement of the oxic-anoxic interface through the sediment column slightly enhanced NH4+ release and depressed N2 release, suggesting the inhibition of nitrification and denitrification. In a long-term (28 days) experiment, Phoslock® hindered the P release, reduced the cyanobacterial abundance, and alleviated the bloom-driven enhancements in the pH and oxygen. These results suggest that, through suppression of internal nutrient effluxes, Phoslock® can be used as an effective control technology to reduce cyanobacteria blooms common to many freshwater systems.
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Affiliation(s)
- Ji Li
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China;
| | - Kevin Sellner
- Center for Coastal & Watershed Studies, Hood College, Frederick, MD 21701, USA;
| | - Allen Place
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA;
| | - Jeffrey Cornwell
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA;
| | - Yonghui Gao
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China;
- Correspondence: ; Tel.: +86-15026761772
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Shan J, Sanford RA, Chee-Sanford J, Ooi SK, Löffler FE, Konstantinidis KT, Yang WH. Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions. GLOBAL CHANGE BIOLOGY 2021; 27:2669-2683. [PMID: 33547715 DOI: 10.1111/gcb.15545] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/11/2021] [Indexed: 05/02/2023]
Abstract
Many biotic and abiotic processes contribute to nitrous oxide (N2 O) production in the biosphere, but N2 O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N2 O reductase enzyme, NosZ, responsible for N2 O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N2 O reducers could play an important, previously unrecognized role in controlling N2 O emissions for several reasons, including: (1) the consumption of N2 O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N2 O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N2 O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N2 O reducers in regulating soil N2 O emissions.
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Affiliation(s)
- Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joanne Chee-Sanford
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture - Agricultural Research Station,, Urbana, IL, USA
| | - Sean K Ooi
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wendy H Yang
- Departments of Plant Biology and Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Miller C, Bates ST, Gielda LM, Creighton JC. The role of parental care in the establishment of the offspring digestive tract microbiome in Nicrophorus defodiens. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2020.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Niederdorfer R, Hausherr D, Palomo A, Wei J, Magyar P, Smets BF, Joss A, Bürgmann H. Temperature modulates stress response in mainstream anammox reactors. Commun Biol 2021; 4:23. [PMID: 33398049 PMCID: PMC7782526 DOI: 10.1038/s42003-020-01534-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/17/2020] [Indexed: 01/29/2023] Open
Abstract
Autotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen (DO) and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to DO shocks under 20 °C and 14 °C. While pulse disturbances of 0.3 mg L-1 DO prompted only moderate declines in the NH4+ removal rates, 1.0 mg L-1 DO led to complete but reversible inhibition of the NH4+ removal activity in all reactors. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of DO perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Community-wide gene expression differed significantly depending on the temperature regime in all reactors, and we found a noticeable impact of DO disturbances on genes involved in transcription, translation, replication and posttranslational modification at 20 °C but not 14 °C. Genome-centric analysis revealed that different anammox species and other key biofilm taxa differed in their transcriptional responses to distinct temperature regimes and DO disturbances.
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Affiliation(s)
- Robert Niederdorfer
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Surface Waters-Research and Management, 6047, Kastanienbaum, Switzerland.
| | - Damian Hausherr
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Process Engineering, 8600, Duebendorf, Switzerland
| | - Alejandro Palomo
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jing Wei
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Air Pollution & Environmental Technology, 8600, Duebendorf, Switzerland
| | - Paul Magyar
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Adriano Joss
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Process Engineering, 8600, Duebendorf, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Department of Surface Waters-Research and Management, 6047, Kastanienbaum, Switzerland
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13
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Nguyen J, Lara-Gutiérrez J, Stocker R. Environmental fluctuations and their effects on microbial communities, populations and individuals. FEMS Microbiol Rev 2020; 45:6041721. [PMID: 33338228 PMCID: PMC8371271 DOI: 10.1093/femsre/fuaa068] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/05/2020] [Indexed: 12/20/2022] Open
Abstract
From the homeostasis of human health to the cycling of Earth's elements, microbial activities underlie environmental, medical and industrial processes. These activities occur in chemical and physical landscapes that are highly dynamic and experienced by bacteria as fluctuations. In this review, we first discuss how bacteria can experience both spatial and temporal heterogeneity in their environments as temporal fluctuations of various timescales (seconds to seasons) and types (nutrient, sunlight, fluid flow, etc.). We then focus primarily on nutrient fluctuations to discuss how bacterial communities, populations and single cells respond to environmental fluctuations. Overall, we find that environmental fluctuations are ubiquitous and diverse, and strongly shape microbial behavior, ecology and evolution when compared with environments in which conditions remain constant over time. We hope this review may serve as a guide toward understanding the significance of environmental fluctuations in microbial life, such that their contributions and implications can be better assessed and exploited.
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Affiliation(s)
- Jen Nguyen
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juanita Lara-Gutiérrez
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
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14
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Wang L, Pang Q, Zhou Y, Peng F, He F, Li W, Xu B, Cui Y, Zhu X. Robust nitrate removal and bioenergy generation with elucidating functional microorganisms under carbon constraint in a novel multianode tidal constructed wetland coupled with microbial fuel cell. BIORESOURCE TECHNOLOGY 2020; 314:123744. [PMID: 32615443 DOI: 10.1016/j.biortech.2020.123744] [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: 04/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
This study investigated synthetic wastewater treatment under low inflow C/N ratio and characterized NO3--N-transforming and electricity-producing bacteria in a multi-anode tidal constructed wetland-microbial fuel cell (TFCW-MFC). The optimal concurrent average removal rates of NH4+-N and NO3--N were 73% and 78%, respectively, under a flood/rest/flood time of 4 h/2h/4h in "tide" mode accompanied by one recirculation. The lowest NO3--N concentration among all anodes was observed when the electrode gap was 45 cm. Similarly, the 45 cm anode exhibited selective enrichment of Variovorax and Azoarcus. Correction analysis showed that the high relative abundance of Azoarcus was crucial in enhancing NO3--N removal, and the internal resistance significantly decreased as the relative abundance of Acidovorax increased. These results suggest that NO3--N removal and bioelectricity generation can be promoted in a TFCW-MFC with limited carbon by improving the culture conditions for specific genera.
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Affiliation(s)
- Longmian Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China.
| | - Qingqing Pang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China
| | - Ying Zhou
- College of Environment, Hohai University, Nanjing 210098, PR China
| | - Fuquan Peng
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China
| | - Fei He
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China
| | - Weixin Li
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China; Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing University of Information Science & Technology, Nanjing 210044, PR China
| | - Bin Xu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China
| | - Yibin Cui
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China
| | - Xiang Zhu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, PR China
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15
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Pascual MB, Sánchez-Monedero MÁ, Cayuela ML, Li S, Haderlein SB, Ruser R, Kappler A. Biochar as electron donor for reduction of N2O by Paracoccus denitrificans. FEMS Microbiol Ecol 2020; 96:fiaa133. [PMID: 32602887 PMCID: PMC7360485 DOI: 10.1093/femsec/fiaa133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Biochar (BC) has been shown to influence microbial denitrification and mitigate soil N2O emissions. However, it is unclear if BC is able to directly stimulate the microbial reduction of N2O to N2. We hypothesized that the ability of BC to lower N2O emissions could be related not only to its ability to store electrons, but to donate them to bacteria that enzymatically reduce N2O. Therefore, we carried out anoxic incubations with Paracoccus denitrificans, known amounts of N2O, and nine contrasting BCs, in the absence of any other electron donor or acceptor. We found a strong and direct correlation between the extent and rates of N2O reduction with BC's EDC/EEC (electron donating capacity/electron exchange capacity). Apart from the redox capacity, other BC properties were found to regulate the BC's ability to increase N2O reduction by P. denitrificans. For this specific BC series, we found that a high H/C and ash content, low surface area and poor lignin feedstocks favored N2O reduction. This provides valuable information for producing tailored BCs with the potential to assist and promote the reduction of N2O in the pursuit of reducing this greenhouse gas emissions.
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Affiliation(s)
- Mª Blanca Pascual
- Department of Soil and Water Conservation and Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo 30100 Murcia, Spain
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
| | - Miguel Ángel Sánchez-Monedero
- Department of Soil and Water Conservation and Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo 30100 Murcia, Spain
| | - María L Cayuela
- Department of Soil and Water Conservation and Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo 30100 Murcia, Spain
| | - Shun Li
- Environmental Mineralogy and Chemistry, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
| | - Stefan B Haderlein
- Environmental Mineralogy and Chemistry, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
| | - Reiner Ruser
- Institute of Crop Science, Department of Fertilization and Soil Matter Dynamics, University of Hohenheim, Fruwirthstraβe 20, 70599 Stuttgart, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Sigwartstrasse 10, 72074 Tübingen, Germany
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16
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Rahimi S, Modin O, Mijakovic I. Technologies for biological removal and recovery of nitrogen from wastewater. Biotechnol Adv 2020; 43:107570. [PMID: 32531318 DOI: 10.1016/j.biotechadv.2020.107570] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022]
Abstract
Water contamination is a growing environmental issue. Several harmful effects on human health and the environment are attributed to nitrogen contamination of water sources. Consequently, many countries have strict regulations on nitrogen compound concentrations in wastewater effluents. Wastewater treatment is carried out using energy- and cost-intensive biological processes, which convert nitrogen compounds into innocuous dinitrogen gas. On the other hand, nitrogen is also an essential nutrient. Artificial fertilizers are produced by fixing dinitrogen gas from the atmosphere, in an energy-intensive chemical process. Ideally, we should be able to spend less energy and chemicals to remove nitrogen from wastewater and instead recover a fraction of it for use in fertilizers and similar applications. In this review, we present an overview of various technologies of biological nitrogen removal including nitrification, denitrification, anaerobic ammonium oxidation (anammox), as well as bioelectrochemical systems and microalgal growth for nitrogen recovery. We highlighted the nitrogen removal efficiency of these systems at different temperatures and operating conditions. The advantages, practical challenges, and potential for nitrogen recovery of different treatment methods are discussed.
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Affiliation(s)
- Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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17
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Wang X, Duo Y, He J, Yao J, Qian H, Hrynsphan D, Tatsiana S, Chen J. A newly isolated and rapid denitrifier Pseudomonas citronellolis WXP-4: difference in N2O emissions under aerobic and anaerobic conditions. Bioprocess Biosyst Eng 2020; 43:811-820. [DOI: 10.1007/s00449-019-02276-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022]
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18
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Mukherjee C, Chowdhury R, Begam MM, Ganguli S, Basak R, Chaudhuri B, Ray K. Effect of Varying Nitrate Concentrations on Denitrifying Phosphorus Uptake by DPAOs With a Molecular Insight Into Pho Regulon Gene Expression. Front Microbiol 2019; 10:2586. [PMID: 31787959 PMCID: PMC6856094 DOI: 10.3389/fmicb.2019.02586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/25/2019] [Indexed: 11/16/2022] Open
Abstract
Bacterial Pho regulon is a key regulator component in biological phosphorus-uptake. Poly-phosphate accumulating bacteria used in enhanced biological phosphorus removal (EBPR) system encounter negative regulation of the Pho regulon, resulting in reduced phosphorus-uptake from phosphorus-replete waste effluents. This study demonstrates possible trends of overcoming the PhoU negative regulation, resulting in excessive PO4 3--P uptake at varying concentrations of NO3 --N through denitrifying phosphorus removal process. We investigated the Pho regulon gene expression pattern and kinetic studies of P-removal by denitrifying phosphate accumulating organisms (DPAOs) which are able to remove both PO4 3--P and NO3 --N in single anoxic stage with the utilization of external carbon sources, without the use of stored polyhydroxyalkanoate (PHA) and without any anaerobic-aerobic or anaerobic-anoxic switches. Our study establishes that a minimum addition of 100 ppm NO3 --N leads to the withdrawal of the negative regulation of Pho regulon and results in ∼100% P-removal with concomitant escalated poly-phosphate accumulation by our established DPAO isolates and their artificially made consortium, isolated from sludge sample of PO4 3- -rich parboiled rice mill effluent, in a settling tank within 12 h of treatment. The same results were obtained when a phosphate rich effluent (stillage from distillery) mixed with a nitrate rich effluent (from explosive industry) was treated together in a single phase anoxic batch reactor, eliminating the need for alternating anaerobic/aerobic or anaerobic/anoxic switches for removing both the pollutants simultaneously. The highest poly-phosphate accumulation was observed to be more than 17% of cell dry weight. Our studies unequivocally establish that nitrate induction of Pho regulon is parallely associated with the repression of PhoU gene transcription, which is the negative regulator of Pho regulon. Based on earlier observations where similar nitrate mediated transcriptional repression was cited, we hypothesize the possible involvement of NarL/NarP transcriptional regulator proteins in PhoU repression. At present, we propose this denitrifying phosphorus removal endeavor as an innovative methodology to overcome the negative regulation of Pho regulon for accelerated unhindered phosphorus remediation from phosphate rich wastewater in India and the developing world where the stringency of EBPR and other reactors prevent their use due to financial reasons.
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Affiliation(s)
- Chandan Mukherjee
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Rajojit Chowdhury
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Mst. Momtaj Begam
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Sayak Ganguli
- Theoretical and Computational Biology Division, AIIST and The Biome, Kolkata, India
| | - Ritabrata Basak
- Department of Biochemistry, Ballygunge Science College, University of Calcutta, Kolkata, India
| | | | - Krishna Ray
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
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19
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INDISIM-Denitrification, an individual-based model for study the denitrification process. J Ind Microbiol Biotechnol 2019; 47:1-20. [PMID: 31691030 DOI: 10.1007/s10295-019-02245-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022]
Abstract
Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than 100 years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria. INDISIM-Denitrification simulates a bioreactor that contains a culture medium with succinate as a carbon source, ammonium as nitrogen source and various electron acceptors. To implement INDISIM-Denitrification, the individual-based model INDISIM was used to give sub-models for nutrient uptake, stirring and reproduction cycle. Using a thermodynamic approach, the denitrification pathway, cellular maintenance and individual mass degradation were modeled using microbial metabolic reactions. These equations are the basis of the sub-models for metabolic maintenance, individual mass synthesis and reducing internal cytotoxic products. The model was implemented in the open-access platform NetLogo. INDISIM-Denitrification is validated using a set of experimental data of two denitrifying bacteria in two different experimental conditions. This provides an interactive tool to study the denitrification process carried out by any denitrifying bacterium since INDISIM-Denitrification allows changes in the microbial empirical formula and in the energy-transfer-efficiency used to represent the metabolic pathways involved in the denitrification process. The simulator can be obtained from the authors on request.
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20
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Guo H, Chen Z, Guo J, Lu C, Song Y, Han Y, Li H, Hou Y. Enhanced denitrification performance and biocatalysis mechanisms of polyoxometalates as environmentally-friendly inorganic redox mediators. BIORESOURCE TECHNOLOGY 2019; 291:121816. [PMID: 31344631 DOI: 10.1016/j.biortech.2019.121816] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
Polyoxometalates (POMs) used in chemical catalysis field were first explored their effect on the denitrification process. Experiments demonstrated that NO3--N reduction rate with 0.05 mM phosphomolybdic acid (PMo12) was approximately 3.93-fold higher than the PMo12-free system. Simultaneously, PMo12 also had positive effect on NO2--N reduction. Compared with the PMo12-free system, the solution resistance and oxidation-reduction potential were decreased, and the activation energy (Ea) was reduced by 51.84 kJ/mol. Besides, electron conductive substances in extracellular polymeric substances were stimulated by PMo12. NADH and riboflavin were enhanced to increase denitrification electron transport system activity. Higher microbial diversity and enrichment of Salmonella were observed in the PMo12-supplemented system. Based on the above analysis, the catalyzing mechanisms of PMo12 are proposed that PMo12 made it easier for electron transferring from electron donor to electron acceptor and shifted bacterial community structure. These findings may provide a promising strategy for nitrogen wastewater treatment.
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Affiliation(s)
- Haixiao Guo
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Zhi Chen
- Department of Building, Civil, and Environmental Engineering, Concordia University, 1455 de Maisonneuve Blvd. W, Montreal, Quebec, Canada
| | - Jianbo Guo
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China.
| | - Caicai Lu
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China.
| | - Yuanyuan Song
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Yi Han
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Haibo Li
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Yanan Hou
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
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21
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Li D, Liang X, Li Z, Jin Y, Zhou R, Wu C. Effect of chemical oxygen demand load on the nitrification and microbial communities in activated sludge from an aerobic nitrifying reactor. Can J Microbiol 2019; 66:59-70. [PMID: 31644885 DOI: 10.1139/cjm-2018-0599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we explored the effect of chemical oxygen demand (COD) load on the nitrification and microbial communities in activated sludge isolated from an aerobic nitrifying tank. The activated sludge was cultured in three different COD groups: L-COD, 200 mg/L; M-COD, 1200 mg/L; H-COD, 4200 mg/L. The results indicated that the COD exerts a negligible effect on the nitrogen removal ability within the first 24 h. However, the nitrification rate decreased with culture time; the ammonium degradation rates were found to be 80.26%, 57.56%, and 43.43% at 72 h in the three COD groups, respectively. These values correspond to decreases of 19.40%, 41.83%, and 51.48%, respectively, in relation to those observed at 24 h. The activated sludge in the different COD groups exhibited similar community compositions after 24 h, as assessed by Illumina high-throughput sequencing, while a significant difference in the relative abundances of some organisms occurred after 48 and 72 h. Proteobacteria was the main phylum, with a relative abundance of >51.45%. The genera Aridibacter, Paracoccus, Nitrospira, and Nitrosomonas were suppressed by COD load over time. This study may contribute to our knowledge about the nitrification ability and microbial communities in activated sludge at different COD load levels.
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Affiliation(s)
- Dan Li
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Xihong Liang
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Zhengwei Li
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Yao Jin
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Rongqing Zhou
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Chongde Wu
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
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22
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Si YY, Xu KH, Yu XY, Wang MF, Chen XH. Complete genome sequence of Paracoccus denitrificans ATCC 19367 and its denitrification characteristics. Can J Microbiol 2019; 65:486-495. [PMID: 30897350 DOI: 10.1139/cjm-2019-0037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Studies show that Paracoccus denitrificans can denitrify nitrogen sources under aerobic conditions. However, the lack of data on its genome sequence has restricted molecular studies and practical applications. In this study, the complete genome of P. denitrificans ATCC 19367 was sequenced and its nitrogen metabolism properties were characterized. The size of the whole genome is 5 242 327 bp, with two chromosomes and one plasmid. The average G + C content is 66.8%, and it contains 5308 protein-coding genes, 54 tRNA genes, and nine rRNA operons. Among the protein-coding genes, 71.35% could be assigned to the Gene Ontology (GO) pathway, 86.66% to the Clusters of Orthologous Groups (COG) pathway, and 50.57% to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Comparative genome analysis between P. denitrificans ATCC 19367 and P. denitrificans PD1222 revealed that there are 428 genes specific to ATCC 19367 and 4738 core genes. Furthermore, the expression of genes related to denitrification, biofilm formation, and nitrogen metabolism (nar, nir, and nor) by P. denitrificans ATCC 19367 under aerobic conditions was affected by incubation time and shaking speed. This study elucidates the genomic background of P. denitrificans ATCC 19367 and suggests the possibility of controlling nitrogen pollution in the environment by using this bacterium.
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Affiliation(s)
- Yuan-Yuan Si
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China.,b Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, 529566, People's Republic of China
| | - Kai-Hang Xu
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China
| | - Xiang-Yong Yu
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China
| | - Mei-Fang Wang
- a College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China
| | - Xing-Han Chen
- b Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, 529566, People's Republic of China
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23
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Hamza RA, Zaghloul MS, Iorhemen OT, Sheng Z, Tay JH. Optimization of organics to nutrients (COD:N:P) ratio for aerobic granular sludge treating high-strength organic wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:3168-3179. [PMID: 30373093 DOI: 10.1016/j.scitotenv.2018.10.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
The present study attempted to optimize the nutrients required for biological growth and biomass synthesis in the treatment of high-strength organics wastewater using aerobic granular sludge (AGS). Three identical sequencing batch reactors (SBRs) were used to cultivate aerobic granules at COD concentration of ~5000 mg/L at COD:N:P ratios of 100:2.8:0.4, 100:4.4:0.5, and 100:5:0.7. Results indicated that the amount of nutrients needed for biomass growth does not follow the conventional organics to nutrients ratio (COD:N:P) of 100:5:1 when dealing with high-strength organics wastewater. The highest removal efficiency was achieved at COD:N:P ratio of 100:2.8:0.4, where COD, TN, and P removal was 98.8 ± 0.3%, 100.0 ± 0.0%, and 99.3 ± 1.0%, respectively. Moreover, the presence of high amounts of organics led to the dominance of the fast-growing heterotrophs in all SBRs, with the genus Thauera identified as the most abundant genera (23-40%), while autotrophic nitrifiers disappeared. The observed biomass yield at COD:N ratio of 100:2.8 suggested that heterotrophic nitrification may have occurred, while at COD:N ratios of 100:4.4 and 100:5, all the nitrogen was used for biomass synthesis. Moreover, at COD:N ratio of 100:5, almost 1/5 of the organics were utilized by the biomass cells to produce EPS as defensive action against the effects of free ammonia. Batch optimization experiments showed that the fastest rate of removal occurred at COD:N:P ratio of 100:1.1:0.4. After 4 h, the COD, TN, and P removal efficiencies were 95%, 99%, and 96%, achieving overall removal efficiencies of 98%, 100%, and 97% respectively, at HRT of 8 h. The bacterial behavior in consuming the organics was altered under nutrient-deficient conditions, where faster degradation rates were observed as the amounts of nutrients decreased, with higher relative abundance of heterotrophs and diazotrophic bacterial populations.
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Affiliation(s)
- Rania Ahmed Hamza
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Mohamed Sherif Zaghloul
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Oliver Terna Iorhemen
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Zhiya Sheng
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Joo Hwa Tay
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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Hamza RA, Sheng Z, Iorhemen OT, Zaghloul MS, Tay JH. Impact of food-to-microorganisms ratio on the stability of aerobic granular sludge treating high-strength organic wastewater. WATER RESEARCH 2018; 147:287-298. [PMID: 30317038 DOI: 10.1016/j.watres.2018.09.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/30/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
This work investigated the long-term stability of aerobic granular sludge treating high-strength organic wastewater in a semi-pilot scale sequential batch reactor (SBR). The reactor was operated for 316 days under different operational conditions. It was found that the F/M ratio is an important parameter affecting granules formation and stability. Three selection mechanisms were investigated: (1) cultivation and maturation at moderately high influent COD concentration (2500 mg/L) followed by increase in influent COD concentration to 7500 mg/L; (2) stressed cultivation and operation at high influent COD concentration of 4500 mg/L; and (3) alternate feed loading strategy (variable influent COD concentration across the daily schedule of cycles at 50%, 75%, and 100% of the peak concentration of 5000 mg/L). It was found that adopting high OLR at the reactor start-up accelerated the formation of granules. However, the overgrowth of biomass under high organics concentration negatively affected the stability of granules and led to disintegration due to the presence of methanogens in the granule core. Cultivation at high organics concentration resulted in a rapid loss of microbial diversity and reactor failure. Under alternate feed loading, adequate selection of microbial community was maintained and resulted in stable reactor performance. Moreover, a strong correlation between F/M ratio and the granules settling ability was observed. When F/M ratio exceeded 1.5 gCOD/gSS.d, granules showed poor settleability and under very high sludge loading rates (above 2.5), sludge bulking occurred and led to washout of sludge due to the strong selection pressure of short settling time. Operating the reactor at F/M ratio of 0.5-1.4 gCOD/gSS.d appears to favor stable long-term granule stability.
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Affiliation(s)
- Rania Ahmed Hamza
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
| | - Zhiya Sheng
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Oliver Terna Iorhemen
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Mohamed Sherif Zaghloul
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Joo Hwa Tay
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
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Amberkar U, Khandeparker R, Parab P. Nitrate Reductase Gene Expression in Idiomarina Strain cos21 Obtained from Oxygen Minimum Zone of Arabian Sea. Curr Microbiol 2018; 76:63-69. [DOI: 10.1007/s00284-018-1585-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2018] [Indexed: 10/28/2022]
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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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Wan R, Chen Y, Zheng X, Su Y, Huang H. Effect of CO 2 on NADH production of denitrifying microbes via inhibiting carbon source transport and its metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:896-904. [PMID: 29426214 DOI: 10.1016/j.scitotenv.2018.01.315] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/19/2018] [Accepted: 01/30/2018] [Indexed: 05/24/2023]
Abstract
The potential effect of CO2 on environmental microbes has drawn much attention recently. As an important section of the nitrogen cycle, biological denitrification requires electron donor to reduce nitrogen oxide. Nicotinamide adenine dinucleotide (NADH), which is formed during carbon source metabolism, is a widely reported electron donor for denitrification. Here we studied the effect of CO2 on NADH production and carbon source utilization in the denitrifying microbe Paracoccus denitrificans. We observed that NADH level was decreased by 45.5% with the increase of CO2 concentration from 0 to 30,000ppm, which was attributed to the significantly decreased utilization of carbon source (i.e., acetate). Further study showed that CO2 inhibited carbon source utilization because of multiple negative influences: (1) suppressing the growth and viability of denitrifier cells, (2) weakening the driving force for carbon source transport by decreasing bacterial membrane potential, and (3) downregulating the expression of genes encoding key enzymes involved in intracellular carbon metabolism, such as citrate synthase, aconitate hydratase, isocitrate dehydrogenase, succinate dehydrogenase, and fumarate reductase. This study suggests that the inhibitory effect of CO2 on NADH production in denitrifiers might deteriorate the denitrification performance in an elevated CO2 climate scenario.
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Affiliation(s)
- Rui Wan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, College of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui 241002, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Zeng J, Chen M, Zheng M, Qiu Y, He W, He Y, Liu X. Effects of particles on potential denitrification in the coastal waters of the Beibu Gulf in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:1274-1286. [PMID: 29929240 DOI: 10.1016/j.scitotenv.2017.12.192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/16/2017] [Accepted: 12/17/2017] [Indexed: 06/08/2023]
Abstract
Although the influence of suspended particulate matter (SPM) on denitrifying activity has been identified in river waters recently through metabolic incubations and community gene analysis, the regulations of SPM to denitrification in marine systems are still poorly understood. In the present study, the effects of suspended particle properties (including concentration, composition and size) on potential denitrification were explored in the coastal Beibu Gulf water columns based on a series of 15N-labeled incubations under artificial anaerobic condition. A gradient of oxygen (O2) concentrations was also manipulated in the incubated seawaters to test the sensitivity of denitrification to O2 exposure. According to our experiments, potential denitrification was the dominant pathway for N2 production with major contribution (>60%) recovered from the particle-associated (PA) fraction. The Highest rate occurred in the benthic nepheloid layer, where high particle content induced by sediment resuspension were observed, suggesting that resuspended particles may act as a hot spot for marine nitrogen (N) loss. Both content and lability of particulate organic carbon (POC) were tightly related to the denitrification rates, with denitrification enhanced by autochthonous POC fractions more significantly. The PA denitrification was higher on small particles (1.2-10μm) compared to the large ones (>10μm), probably due to larger specific surface area and higher specific POC content in small particles. O2 suppressed denitrifying activity for both bulk water samples and PA fractions. Although in situ denitrifying activity should be minor or neglected because of high-O2 inhibition, the novel findings of particle effects on anaerobic denitrification can still be applied to hypoxic marine environments. Our research also implies that resuspended particles from sediment may act as a hot spot for N loss, and therefore to be a first step toward future studies in high particle loaded marine regimes.
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Affiliation(s)
- Jian Zeng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Min Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China.
| | - Minfang Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Yusheng Qiu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Wentao He
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Yingxue He
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xiao Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
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Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater. GENOME ANNOUNCEMENTS 2018; 6:6/15/e00210-18. [PMID: 29650568 PMCID: PMC5897812 DOI: 10.1128/genomea.00210-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses.
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Suenaga T, Riya S, Hosomi M, Terada A. Biokinetic Characterization and Activities of N 2O-Reducing Bacteria in Response to Various Oxygen Levels. Front Microbiol 2018; 9:697. [PMID: 29692767 PMCID: PMC5902568 DOI: 10.3389/fmicb.2018.00697] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/26/2018] [Indexed: 11/13/2022] Open
Abstract
Nitrous oxide (N2O)-reducing bacteria, which reduce N2O to nitrogen in the absence of oxygen, are phylogenetically spread throughout various taxa and have a potential role as N2O sinks in the environment. However, research on their physiological traits has been limited. In particular, their activities under microaerophilic and aerobic conditions, which severely inhibit N2O reduction, remain poorly understood. We used an O2 and N2O micro-respirometric system to compare the N2O reduction kinetics of four strains, i.e., two strains of an Azospira sp., harboring clade II type nosZ, and Pseudomonas stutzeri and Paracoccus denitrificans, harboring clade I type nosZ, in the presence and absence of oxygen. In the absence of oxygen, the highest N2O-reducing activity, Vm,N2O, was 5.80 ± 1.78 × 10-3 pmol/h/cell of Azospira sp. I13, and the highest and lowest half-saturation constants were 34.8 ± 10.2 μM for Pa. denitirificans and 0.866 ± 0.29 μM for Azospira sp. I09. Only Azospira sp. I09 showed N2O-reducing activity under microaerophilic conditions at oxygen concentrations below 110 μM, although the activity was low (10% of Vm,N2O). This trait is represented by the higher O2 inhibition coefficient than those of the other strains. The activation rates of N2O reductase, which describe the resilience of the N2O reduction activity after O2 exposure, differ for the two strains of Azospira sp. (0.319 ± 0.028 h-1 for strain I09 and 0.397 ± 0.064 h-1 for strain I13) and Ps. stutzeri (0.200 ± 0.013 h-1), suggesting that Azospira sp. has a potential for rapid recovery of N2O reduction and tolerance against O2 inhibition. These physiological characteristics of Azospira sp. can be of promise for mitigation of N2O emission in industrial applications.
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Affiliation(s)
- Toshikazu Suenaga
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan
| | - Shohei Riya
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan
| | - Masaaki Hosomi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan
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31
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Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. Sci Rep 2018; 8:5550. [PMID: 29615803 PMCID: PMC5882942 DOI: 10.1038/s41598-018-23858-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Integrative and conjugative elements (ICEs) comprise ubiquitous large mobile regions in prokaryotic chromosomes that transmit vertically to daughter cells and transfer horizontally to distantly related lineages. Their evolutionary success originates in maximized combined ICE-host fitness trade-offs, but how the ICE impacts on the host metabolism and physiology is poorly understood. Here we investigate global changes in the host genetic network and physiology of Pseudomonas putida with or without an integrated ICEclc, a model ICE widely distributed in proteobacterial genomes. Genome-wide gene expression differences were analyzed by RNA-seq using exponentially growing or stationary phase-restimulated cultures on 3-chlorobenzoate, an aromatic compound metabolizable thanks to specific ICEclc-located genes. We found that the presence of ICEclc imposes a variety of changes in global pathways such as cell cycle and amino acid metabolism, which were more numerous in stationary-restimulated than exponential phase cells. Unexpectedly, ICEclc stimulates cellular motility and leads to more rapid growth on 3-chlorobenzoate than cells carrying only the integrated clc genes. ICEclc also concomitantly activates the P. putida Pspu28-prophage, but this in itself did not provoke measurable fitness effects. ICEclc thus interferes in a number of cellular pathways, inducing both direct benefits as well as indirect costs in P. putida.
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32
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Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances. SCIENCE CHINA-LIFE SCIENCES 2018; 61:753-761. [DOI: 10.1007/s11427-017-9228-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
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33
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Xu Q, Li S, Wan Y, Wang S, Ma B, She Z, Guo L, Gao M, Zhao Y, Jin C, Dong J, Li Z. Impacts of silver nanoparticles on performance and microbial community and enzymatic activity of a sequencing batch reactor. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 204:667-673. [PMID: 28950236 DOI: 10.1016/j.jenvman.2017.09.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
The performance, microbial community and enzymatic activity of a sequencing batch reactor (SBR) were evaluated under silver nanoparticles (Ag NPs) stress. Over 5 mg/L Ag NPs inhibited the COD and phosphorus removals, whereas the NH4+ removal kept stable during the whole operational period. The organic matter, nitrogen and phosphorus removal rates were obviously inhibited under Ag NPs stress, which showed similar varying trends with the corresponding microbial enzymatic activities. The change of Ag content in the activated sludge indicated that some Ag NPs were absorbed by the sludge. The presence of Ag NPs promoted the increase of reactive oxygen species (ROS) and lactate dehydrogenase (LDH) of microorganism due to the microbial response to the Ag NPs toxicity, which could impact on the microbial morphology and physiological functions. The presence of Ag NPs could produce some evident changes in the microbial community.
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Affiliation(s)
- Qiaoyan Xu
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao, 266100, China
| | - Shanshan Li
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Yiping Wan
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Sen Wang
- School of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Bingrui Ma
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Zonglian She
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Liang Guo
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Mengchun Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
| | - Yangguo Zhao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Chunji Jin
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; School of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Junwei Dong
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Zhiwei Li
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
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Li M, Qian WJ, Gao Y, Shi L, Liu C. Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11848-11857. [PMID: 28891285 DOI: 10.1021/acs.est.7b03158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The kinetics of biogeochemical processes in natural and engineered environmental systems is typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial communities that catalyze biogeochemical reactions. A major challenge of applying such models is the difficulty of quantitatively measuring functional biomass for the constraining and validation of the models. However, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here, we propose an enzyme-based model that can incorporate omics data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes as time-variable catalysts for biogeochemical reactions and applies a biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are required in the model. The application of the model was demonstrated using denitrification, as an example, by comparing model simulations with measured functional enzymes, genes, denitrification substrates, and intermediates.
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Affiliation(s)
- Minjing Li
- School of Environmental Studies, China University of Geosciences , Wuhan 430074, China
| | - Wei-Jun Qian
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Yuqian Gao
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences , Wuhan 430074, China
| | - Chongxuan Liu
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
- School of Environmental Science and Engineering, Southern University of Science and Technology , Shenzhen 518055, China
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35
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Li M, Gao Y, Qian WJ, Shi L, Liu Y, Nelson WC, Nicora CD, Resch CT, Thompson C, Yan S, Fredrickson JK, Zachara JM, Liu C. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:512-521. [PMID: 28618201 DOI: 10.1111/1758-2229.12558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data. Quantification of the signature peptides then allows estimation of the targeted enzyme abundance. To achieve analyses of the requisite sensitivity for complex environmental samples with low available biomass, we adapted a recently developed ultrasensitive targeted quantification technology, termed high-pressure high-resolution separations with intelligent selection and multiplexing (PRISM) by improving peptide separation efficiency and method detection sensitivity. Nitrate reduction dynamics catalyzed by dissimilatory and assimilatory enzymes in a hyporheic zone sediment was used as an example to demonstrate the application of the enzyme quantification approach. Together with the measurements of biogeochemical species, the approach enables investigating the dynamic linkage between functional enzymes and biogeochemical processes.
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Affiliation(s)
- Minjing Li
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wei-Jun Qian
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Liang Shi
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yuanyuan Liu
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Carrie D Nicora
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Charles T Resch
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Sen Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, People's Republic of China
| | | | - John M Zachara
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chongxuan Liu
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
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Zeng J, Chen M, Zheng M, Hu W, Qiu Y. A potential nitrogen sink discovered in the oxygenated Chukchi Shelf waters of the Arctic. GEOCHEMICAL TRANSACTIONS 2017; 18:5. [PMID: 29086802 PMCID: PMC5607156 DOI: 10.1186/s12932-017-0043-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
The western Arctic Shelf has long been considered as an important sink of nitrogen because high primary productivity of the shelf water fuels active denitrification within the sediments, which has been recognized to account for all the nitrogen (N) removal of the Pacific water inflow. However, potentially high denitrifying activity was discovered within the oxygenated Chukchi Shelf water during our summer expedition. Based on 15N-isotope pairing incubations, we estimated denitrification rates ranging from 1.8 ± 0.4 to 75.9 ± 8.7 nmol N2 L-1 h-1. We find that the spatial pattern of denitrifying activity follows well with primary productivity, which supplies plentiful fresh organic matter, and there was a strong correlation between integrated denitrification and integrated primary productivity. Considering the active hydrodynamics over the Chukchi Shelf during summer, resuspension of benthic sediment coupled with particle-associated bacteria induces an active denitrification process in the oxic water column. We further extrapolate to the whole Chukchi Shelf and estimate an N removal flux from this cold Arctic shelf water to be 12.2 Tg-N year-1, which compensates for the difference between sediment cores incubation (~ 3 Tg-N year-1) and geochemical estimation based on N deficit relative to phosphorous (~ 16 Tg-N year-1). We infer that dynamic sediment resuspension combined with high biological productivity stimulates intensive denitrification in the water column, potentially creating a nitrogen sink over the shallow Arctic shelves that have previously been unrecognized.
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Affiliation(s)
- Jian Zeng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Min Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Minfang Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Wangjiang Hu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
| | - Yusheng Qiu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
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Rohe L, Well R, Lewicka-Szczebak D. Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1297-1312. [PMID: 28556299 DOI: 10.1002/rcm.7909] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Fungal denitrifiers can contribute substantially to N2 O emissions from arable soil and show a distinct site preference for N2 O (SP(N2 O)). This study sought to identify another process-specific isotopic tool to improve precise identification of N2 O of fungal origin by mass spectrometric analysis of the N2 O produced. METHODS Three pure bacterial and three fungal species were incubated under denitrifying conditions in treatments with natural abundance and stable isotope labelling to analyse the N2 O produced. Combining different applications of isotope ratio mass spectrometry enabled us to estimate the oxygen (O) exchange accelerated by denitrifying enzymes and the ongoing microbial pathway in parallel. This experimental set-up allowed the determination of δ18 O(N2 O) values and isotopic fractionation of O, as well as SP(N2 O) values, as a perspective to differentiate between microbial denitrifiers. RESULTS Oxygen exchange during N2 O production was lower for bacteria than for fungi, differed between species, and depended also on incubation time. Apparent O isotopic fractionation during denitrification was in a similar range for bacteria and fungi, but application of the fractionation model indicated that different enzymes in bacteria and fungi were responsible for O exchange. This difference was associated with different isotopic fractionation for bacteria and fungi. CONCLUSIONS δ18 O(N2 O) values depend on isotopic fractionation and isotopic fractionation may differ between processes and organism groups. By comparing SP(N2 O) values, O exchange and the isotopic signature of precursors, we propose here a novel tool for differentiating between different sources of N2 O.
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Affiliation(s)
- Lena Rohe
- Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Reinhard Well
- Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany
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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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Li Z, Wang X, Ma B, Wang S, Zheng D, She Z, Guo L, Zhao Y, Xu Q, Jin C, Li S, Gao M. Long-term impacts of titanium dioxide nanoparticles (TiO 2 NPs) on performance and microbial community of activated sludge. BIORESOURCE TECHNOLOGY 2017; 238:361-368. [PMID: 28456044 DOI: 10.1016/j.biortech.2017.04.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
The long-term impacts of titanium dioxide nanoparticles (TiO2 NPs) on the performance and microbial community of activated sludge were evaluated in a sequencing batch reactor (SBR). TiO2 NPs impacted the COD and phosphorus removals of activated sludge, whereas the NH4+-N removal efficiency had no distinct change at 0-60mg/L TiO2 NPs. The presence of TiO2 NPs obviously inhibited the organic matter and nitrogen removal rates of activated sludge. The phosphorus removal rate gradually reduced at 0-5mg/L TiO2 NPs and then increased at 10-60mg/L TiO2 NPs. The removal rates of organic matter, nitrogen and phosphorus had the similar varying trends to the corresponding microbial enzymatic activities. High TiO2 NPs concentration promoted more reactive oxygen species (ROS) production and lactate dehydrogenase (LDH) release of activated sludge. The microbial richness and diversity of activated sludge were obviously affected at the phyla, class and genus levels.
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Affiliation(s)
- Zhiwei Li
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Qingdao 266100, China
| | - Xuejiao Wang
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Bingrui Ma
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Sen Wang
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Dong Zheng
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Zonglian She
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Liang Guo
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Qingdao 266100, China
| | - Yangguo Zhao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Qingdao 266100, China
| | - Qiaoyan Xu
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Chunji Jin
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Shanshan Li
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Mengchun Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China.
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Genome Sequence of Paracoccus contaminans LMG 29738 T, Isolated from a Water Microcosm. GENOME ANNOUNCEMENTS 2017; 5:5/23/e00487-17. [PMID: 28596405 PMCID: PMC5465624 DOI: 10.1128/genomea.00487-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We announce here the complete genome sequence of Paracoccus contaminans LMG 29738T, which we recently isolated from a contaminated water microcosm. The genome consists of a 2.94-Mb chromosome and a 94-kb plasmid. To our knowledge, we provide the first DNA methylation analysis of a Paracoccus species.
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Ma B, Wang S, Li Z, Gao M, Li S, Guo L, She Z, Zhao Y, Zheng D, Jin C, Wang X, Gao F. Magnetic Fe 3O 4 nanoparticles induced effects on performance and microbial community of activated sludge from a sequencing batch reactor under long-term exposure. BIORESOURCE TECHNOLOGY 2017; 225:377-385. [PMID: 27956330 DOI: 10.1016/j.biortech.2016.11.130] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
The performance and microbial community of activated sludge from a sequencing batch reactor (SBR) were investigated under long-term exposure of magnetic Fe3O4 nanoparticles (Fe3O4 NPs). The COD removal showed a slight decrease at 5-60mg/L Fe3O4 NPs compared to 0mg/L Fe3O4 NPs, whereas the NH4+-N removal had no obvious variation at 0-60mg/L Fe3O4 NPs. It was found that 10-60mg/L Fe3O4 NPs improved the denitrification process and phosphorus removal of activated sludge. The microbial enzymatic activities of activated sludge could be affected by Fe3O4 NPs, which had similar variation trends to the nitrogen and phosphorus removal rates of activated sludge. The reactive oxygen species (ROS) production and lactate dehydrogenase (LDH) release demonstrated that Fe3O4 NPs led to the toxicity to activated sludge and destroyed the integrity of microbial cytomembrane. High throughput sequencing indicated that Fe3O4 NPs could obviously affect the microbial richness and diversity of activated sludge.
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Affiliation(s)
- Bingrui Ma
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao 266100, China
| | - Sen Wang
- Shcool of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Zhiwei Li
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Mengchun Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao 266100, China.
| | - Shanshan Li
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Liang Guo
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Zonglian She
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao 266100, China
| | - Yangguo Zhao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Dong Zheng
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Chunji Jin
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Xuejiao Wang
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Feng Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
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Carlos C, Pereira LB, Ottoboni LMM. Comparative genomics of Paracoccus sp. SM22M-07 isolated from coral mucus: insights into bacteria-host interactions. Curr Genet 2016; 63:509-518. [PMID: 27796486 DOI: 10.1007/s00294-016-0658-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
One of the main goals of coral microbiology is to understand the ways in which coral-bacteria associations are established and maintained. This work describes the sequencing of the genome of Paracoccus sp. SM22M-07 isolated from the mucus of the endemic Brazilian coral species Mussismilia hispida. Comparative analysis was used to identify unique genomic features of SM22M-07 that might be involved in its adaptation to the marine ecosystem and the nutrient-rich environment provided by coral mucus, as well as in the establishment and strengthening of the interaction with the host. These features included genes related to the type IV protein secretion system, erythritol catabolism, and succinoglycan biosynthesis. We experimentally confirmed the production of succinoglycan by Paracoccus sp. SM22M-07 and we hypothesize that it may be involved in the association of the bacterium with coral surfaces.
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Affiliation(s)
- Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53703, USA.
| | - Letícia Bianca Pereira
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), C. P. 6010, Campinas, SP, 13083-875, Brazil
| | - Laura Maria Mariscal Ottoboni
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), C. P. 6010, Campinas, SP, 13083-875, Brazil
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Wan R, Chen Y, Zheng X, Su Y, Li M. Effect of CO2 on Microbial Denitrification via Inhibiting Electron Transport and Consumption. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:9915-22. [PMID: 27562440 DOI: 10.1021/acs.est.5b05850] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Increasing anthropogenic CO2 emissions have been reported to influence global biogeochemical processes; however, in the literature the effects of CO2 on denitrification have mainly been attributed to the changes it causes in environmental factors, while the direct effects of CO2 on denitrification remain unknown. In this study, increasing CO2 from 0 to 30 000 ppm under constant environmental conditions decreased total nitrogen removal efficiency from 97% to 54%, but increased N2O generation by 240 fold. A subsequent mechanistic study revealed that CO2 damaged the bacterial membrane and directly inhibited the transport and consumption of intracellular electrons by causing intracellular reactive nitrogen species (RNS) accumulation, suppressing the expression of key electron transfer proteins (flavoprotein, succinate dehydrogenase, and cytochrome c) and the synthesis and activity of key denitrifying enzymes. Further study indicated that the inhibitory effects of CO2 on the transport and consumption of electrons were caused by the decrease of intracellular iron due to key iron transporters (AfuA, FhuC, and FhuD) being down-regulated. Overall, this study suggests that the direct effect of CO2 on denitrifying microbes via inhibition of intracellular electron transport and consumption is an important reason for its negative influence on denitrification.
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Affiliation(s)
- Rui Wan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Mu Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
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Li H, Pan M, Zhou S, Huang S, Zhang Y. Characterization of nitrous oxide emissions from a thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1 in an aerated sequencing batch reactor. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Direct Nitrous Oxide Emission from the Aquacultured Pacific White Shrimp (Litopenaeus vannamei). Appl Environ Microbiol 2016; 82:4028-4034. [PMID: 27129966 DOI: 10.1128/aem.00396-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/21/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Pacific white shrimp (Litopenaeus vannamei) is widely used in aquaculture, where it is reared at high stocking densities, temperatures, and nutrient concentrations. Here we report that adult L. vannamei shrimp emit the greenhouse gas nitrous oxide (N2O) at an average rate of 4.3 nmol N2O/individual × h, which is 1 to 2 orders of magnitude higher than previously measured N2O emission rates for free-living aquatic invertebrates. Dissection, incubation, and inhibitor experiments with specimens from a shrimp farm in Germany indicated that N2O is mainly produced in the animal's gut by microbial denitrification. Microsensor measurements demonstrated that the gut interior is anoxic and nearly neutral and thus is favorable for denitrification by ingested bacteria. Dinitrogen (N2) and N2O accounted for 64% and 36%, respectively, of the nitrogen gas flux from the gut, suggesting that the gut passage is too fast for complete denitrification to be fully established. Indeed, shifting the rearing water bacterial community, a diet component of shrimp, from oxic to anoxic conditions induced N2O accumulation that outlasted the gut passage time. Shrimp-associated N2O production was estimated to account for 6.5% of total N2O production in the shrimp farm studied here and to contribute to the very high N2O supersaturation measured in the rearing tanks (2,099%). Microbial N2O production directly associated with aquacultured animals should be implemented into life cycle assessments of seafood production. IMPORTANCE The most widely used shrimp species in global aquaculture, Litopenaeus vannamei, is shown to emit the potent greenhouse gas nitrous oxide (N2O) at a particularly high rate. Detailed experiments reveal that N2O is produced in the oxygen-depleted gut of the animal by bacteria that are part of the shrimp diet. Upon ingestion, these bacteria experience a shift from oxic to anoxic conditions and therefore switch their metabolism to the anaerobic denitrification process, which produces N2O as an intermediate and dinitrogen (N2) gas as an end product. The N2O/N2 production ratio is unusually high in the shrimp gut, because denitrification cannot be fully established during the short gut passage time of food-associated bacteria. Nitrous oxide emission directly mediated by L. vannamei contributes significantly to the overall N2O emission from aquaculture facilities.
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Palmer K, Köpp J, Gebauer G, Horn MA. Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen. Front Microbiol 2016; 7:727. [PMID: 27313566 PMCID: PMC4887476 DOI: 10.3389/fmicb.2016.00727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/02/2016] [Indexed: 02/04/2023] Open
Abstract
Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities vmax were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting mitigation of N2O emissions by increased N2O-reduction rates after flooding. N2O was consumed to subatmospheric levels in all microcosms after flooding. The collective data indicate that water table manipulations had only minor effects on in situ N2O fluxes, denitrifier abundance, and denitrifier community composition of the acidic fen, while active subpopulations of denitrifiers changed in response to water table manipulations, suggesting functionally redundant subpopulations occupying distinct ecological niches in the fen.
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Affiliation(s)
- Katharina Palmer
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany; Water Resources and Environmental Engineering Research Group, University of OuluOulu, Finland
| | - Julia Köpp
- BayCEER-Laboratory of Isotope Biogeochemistry, University of Bayreuth Bayreuth, Germany
| | - Gerhard Gebauer
- BayCEER-Laboratory of Isotope Biogeochemistry, University of Bayreuth Bayreuth, Germany
| | - Marcus A Horn
- Department of Ecological Microbiology, University of Bayreuth Bayreuth, Germany
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Chao Y, Mao Y, Yu K, Zhang T. Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach. Appl Microbiol Biotechnol 2016; 100:8225-37. [PMID: 27287850 DOI: 10.1007/s00253-016-7655-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 10/21/2022]
Abstract
Biofilms are widely used in wastewater treatment for their particular enhancement of nitrogen removal and other significant advantages. In this study, the diversity and potential functions of nitrogen removal bacteria in suspended activated sludge (AS) and biofilm of a full-scale hybrid reactor were uncovered by metagenomes (∼34 Gb), coupled with PCR-based 454 reads (>33 K reads). The results indicated that the diversity and abundance of nitrifiers and denitrifiers in biofilm did not surpass that in AS, while more nitrification and denitrification genes were indeed found in biofilm than AS, suggesting that the increased nitrogen removal ability by applying biofilm might be attributed to the enhancement of removal efficiency, rather than the biomass accumulation of nitrogen removal bacteria. The gene annotation and phylogenetic analysis results revealed that AS and biofilm samples consisted of 6.0 % and 9.4 % of novel functional genes for nitrogen removal and 18 % and 30 % of new Nitrospira species for nitrite-oxidizing bacteria, respectively. Moreover, the identification of Nitrospira-like amoA genes provided metagenomic evidence for the presence of complete ammonia oxidizer (comammox) with the functional potential to perform the complete oxidation of ammonia to nitrate. These findings have significant implications in expanding our knowledge of the biological nitrogen transformations in wastewater treatment.
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Affiliation(s)
- Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong.,College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510275, China
| | - Ke Yu
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong.
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Araujo Granda P, Gras A, Ginovart M, Moulton V. INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium. J Theor Biol 2016; 403:45-58. [PMID: 27179457 DOI: 10.1016/j.jtbi.2016.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 05/05/2016] [Accepted: 05/07/2016] [Indexed: 11/30/2022]
Abstract
We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans. The individuals in the model represent microbes and the individual-based model INDISIM gives the behavior-rules that they use for their nutrient uptake and reproduction cycle. Three previously described metabolic pathways for P. denitrificans were selected and translated into balanced chemical equations using a thermodynamic model. These stoichiometric reactions are an intracellular model for the individual behavior-rules for metabolic maintenance and biomass synthesis and result in the release of different nitrogen oxides to the medium. The model was implemented using the NetLogo platform and it provides an interactive tool to investigate the different steps of denitrification carried out by a denitrifying bacterium. The simulator can be obtained from the authors on request.
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Affiliation(s)
- Pablo Araujo Granda
- Chemical Engineering Faculty, Central University of Ecuador, Ciudad Universitaria - Ritter s/n y Bolivia, P.O. Box. 17-01-3972, Quito - Ecuador; Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona - Spain.
| | - Anna Gras
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona - Spain.
| | - Marta Ginovart
- Department of Mathematics, Universitat Politència de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona - Spain.
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ - United Kingdom.
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Qu Z, Bakken LR, Molstad L, Frostegård Å, Bergaust LL. Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions. Environ Microbiol 2016; 18:2951-63. [PMID: 26568281 DOI: 10.1111/1462-2920.13128] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 11/27/2022]
Abstract
Oxygen is known to repress denitrification at the transcriptional and metabolic levels. It has been a common notion that nitrous oxide reductase (N2 OR) is the most sensitive enzyme among the four N-oxide reductases involved in denitrification, potentially leading to increased N2 O production under suboxic or fluctuating oxygen conditions. We present detailed gas kinetics and transcription patterns from batch culture experiments with Paracoccus denitrificans, allowing in vivo estimation of e(-) -flow to O2 and N2 O under various O2 regimes. Transcription of nosZ took place concomitantly with that of narG under suboxic conditions, whereas transcription of nirS and norB was inhibited until O2 levels approached 0 μM in the liquid. Catalytically functional N2 OR was synthesized and active in aerobically raised cells transferred to vials with 7 vol% O2 in headspace, but N2 O reduction rates were 10 times higher when anaerobic pre-cultures were subjected to the same conditions. Upon oxygen exposure, there was an incomplete and transient inactivation of N2 OR that could be ascribed to its lower ability to compete for electrons compared with terminal oxidases. The demonstrated reduction of N2 O at high O2 partial pressure and low N2 O concentrations by a bacterium not known as a typical aerobic denitrifier may provide one clue to the understanding of why some soils appear to act as sinks rather than sources for atmospheric N2 O.
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Affiliation(s)
- Zhi Qu
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars R Bakken
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars Molstad
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Linda L Bergaust
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway.
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Zhou S, Huang T, Zhang C, Fang K, Xia C, Bai S, Zeng M, Qiu X. Illumina MiSeq sequencing reveals the community composition of NirS-Type and NirK-Type denitrifiers in Zhoucun reservoir – a large shallow eutrophic reservoir in northern China. RSC Adv 2016. [DOI: 10.1039/c6ra18017e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Denitrification is a major biological process that reduces nitrate to nitrogen gas (N2or N2O).
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Affiliation(s)
- Shilei Zhou
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
| | - Tinglin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
| | - Chunhua Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
| | - Kaikai Fang
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
| | - Chao Xia
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
| | - Shiyuan Bai
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
| | - Mingzheng Zeng
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
| | - Xiaopeng Qiu
- Key Laboratory of Northwest Water Resource, Environment and Ecology
- MOE
- Xi'an University of Architecture and Technology
- Xi'an
- PR China
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