1
|
Lee J, Yun J, Yang Y, Jung JY, Lee YK, Yuan J, Ding W, Freeman C, Kang H. Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2647-2659. [PMID: 36719133 DOI: 10.1021/acs.est.2c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
CH4 emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH4 oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH4 produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH4 oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH4 oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH4 emissions via the reduction of CH4 oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO3- is responsible for the decrease in CH4 oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH4 oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH4 emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH4 dynamics in Arctic regions.
Collapse
Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Chris Freeman
- School of Natural Sciences, Bangor University, BangorLL57 2UW, U.K
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| |
Collapse
|
2
|
Kang H, Lee J, Zhou X, Kim J, Yang Y. The Effects of N Enrichment on Microbial Cycling of Non-CO 2 Greenhouse Gases in Soils-a Review and a Meta-analysis. MICROBIAL ECOLOGY 2022; 84:945-957. [PMID: 34725713 DOI: 10.1007/s00248-021-01911-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH4) and nitrous oxide (N2O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH4 at the global scale. We also address the effects of N enrichment on N2O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH4 oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH4+ enrichment, inhibits CH4 oxidation, resulting in higher CH4 emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N2O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.
Collapse
Affiliation(s)
- Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea.
| | - Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Xue Zhou
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
| | - Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| |
Collapse
|
3
|
Identification of Groundwater Pollution Characteristics and Health Risk Assessment of a Landfill in a Low Permeability Area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18147690. [PMID: 34300140 PMCID: PMC8307002 DOI: 10.3390/ijerph18147690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/26/2022]
Abstract
The shallow weathering fissure groundwater in the red-bed area of Southwest China is usually the only drinking water source for most rural residents. In this study, a typical landfill with surrounding residents drinking unpurified groundwater in red-bed area was selected and water quality detection, groundwater numerical simulation and human health risk assessment were used to identify and assess groundwater pollution in the region. The chemical type evolved from HCO3-SO4-Ca-Mg and HCO3-SO4-Ca to Na-Ca-Cl-HCO3 contaminated by the landfill. Na+ and Cl− were selected as factors for rapid identification of groundwater pollution. Subsequent analyses using these factors showed that the leachate pollution plume boundary was 190 m downstream of the landfill. Analysis of the redox conditions revealed that the area from the landfill to 5 m downstream was the reduction zone, while the area beyond 5 m was the oxidation zone. The migration and attenuation patterns of inorganic salts (such as SO42−) and heavy metals (such as Fe and Mn) in the oxidation and reduction zones differed obviously. Meanwhile, the organic pollutants in the leachate were reduced and decomposed into organic acids, which caused the groundwater 80 m downstream of the landfill to become weakly acidic (pH ranged from 6.51 to 6.83), and promoted re-entry of adsorbed heavy metals (such as Pb) into the groundwater. The groundwater risk assessment based on human health revealed that lead, manganese, chlorobenzene, dichloroethane and chloroform constituted a major health threat to the residents. The rank of non-carcinogenic risk was lead >manganese, and the maximum area of non-carcinogenic risk was 15,485 m2. The total carcinogenic risk caused by organic pollutants was 7.9 × 10−6, and the area of the carcinogenic risk zone was 11,414 m2. Overall, the results of this study provide a scientific basis for management of drinking water and groundwater remediation in the red-bed area with low permeability.
Collapse
|
4
|
Shi LD, Wang Z, Liu T, Wu M, Lai CY, Rittmann BE, Guo J, Zhao HP. Making good use of methane to remove oxidized contaminants from wastewater. WATER RESEARCH 2021; 197:117082. [PMID: 33819663 DOI: 10.1016/j.watres.2021.117082] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/13/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Being an energetic fuel, methane is able to support microbial growth and drive the reduction of various electron acceptors. These acceptors include a broad range of oxidized contaminants (e.g., nitrate, nitrite, perchlorate, bromate, selenate, chromate, antimonate and vanadate) that are ubiquitously detected in water environments and pose threats to human and ecological health. Using methane as electron donor to biologically reduce these contaminants into nontoxic forms is a promising solution to remediate polluted water, considering that methane is a widely available and inexpensive electron donor. The understanding of methane-based biological reduction processes and the responsible microorganisms has grown in the past decade. This review summarizes the fundamentals of metabolic pathways and microorganisms mediating microbial methane oxidation. Experimental demonstrations of methane as an electron donor to remove oxidized contaminants are summarized, compared, and evaluated. Finally, the review identifies opportunities and unsolved questions that deserve future explorations for broadening understanding of methane oxidation and promoting its practical applications.
Collapse
Affiliation(s)
- Ling-Dong Shi
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Lab Water Pollution Control & Environment, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Wang
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Lab Water Pollution Control & Environment, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Liu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Mengxiong Wu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Chun-Yu Lai
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, Arizona 85287-5701, U.S.A
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Lab Water Pollution Control & Environment, Zhejiang University, Hangzhou, Zhejiang, China.
| |
Collapse
|
5
|
Bajar S, Singh A, Kaushik CP, Kaushik A. Suitability assessment of dumpsite soil biocover to reduce methane emission from landfills under interactive influence of nutrients. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:1519-1532. [PMID: 32840750 DOI: 10.1007/s11356-020-10441-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
Biocovers are known for their role as key facilitator to reduce landfill methane (CH4) emission on improving microbial methane bio-oxidation. Methanotrophs existing in the aerobic zone of dumped wastes are the only known biological sinks for CH4 being emitted from the lower anaerobic section of landfill sites and even from the atmosphere. However, their efficacy remains under the influence of landfill environment and biocover characteristics. Therefore, the present study was executed to explore the suitability and efficacy of dumpsite soil as biocover to achieve enhanced methane bio-oxidation under the interactive influence of nutrients, carbon source, and environmental factors using statistical-mathematical models. The Placket-Burman design (PBD) was employed to identify the significant factors out of 07 tested factors having considerable impact on CH4 bio-oxidation. The normal plot and Student's t test of PBD indicated that ammonical nitrogen (NH4+-N), nitrate nitrogen (NO3--N), methane (CH4), and copper (Cu) concentration were found significant. A three-level Box-Behnken design (BBD) was further applied to optimize the significant factors identified from PBD. The BBD results revealed that interactive interaction of CH4 with NH4+-N and NO3--N affected the CH4 bio-oxidation significantly. The sequential statistical approach predicted that maximum CH4 bio-oxidation of 27.32 μg CH4 h-1 could be achieved with CH4 (35%), NO3--N (250 μg g-1), NH4+-N (25 μg g-1), and Cu (50 mg g-1) concentration. Conclusively, waste dumpsite soil could be a good alternative over conventional soil cover to improve CH4 bio-oxidation and lessen the emission of greenhouse gas from waste sector.
Collapse
Affiliation(s)
- Somvir Bajar
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India.
- Department of Environmental Sciences, YMCA, J.C. Bose University of Science and Technology, Faridabad, Haryana, 121006, India.
| | - Anita Singh
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
- Department of Environmental Sciences, Central University of Jammu, Jammu & Kashmir, 180011, India
| | - C P Kaushik
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
| | - Anubha Kaushik
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
- University School of Environment Management, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, 110075, India
| |
Collapse
|
6
|
Liew FJ, Schilling JS. High-efficiency methane capture by living fungi and dried fungal hyphae (necromass). JOURNAL OF ENVIRONMENTAL QUALITY 2020; 49:1467-1476. [PMID: 33118202 DOI: 10.1002/jeq2.20136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/19/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Fungi can hasten microbial degradation of hydrophobic compounds by enhancing capture and dissolution into biofilms. For methane (CH4 ) released from natural soils and agricultural systems, prokaryotes are ultimately responsible for oxidation and degradation; however, in many cases Henry's law of gas dissolution, not oxidation, is rate-limiting. Given that fungi can improve capture and bioremediation of other hydrophobic compounds (e.g., toluene), we tested fungi for CH4 capture. We used a batch system of CH4 -flooded vials to screen candidate fungi. We found 79% removal efficiency by Ganoderma lucidum relative to activated carbon. In a follow-up, we found comparable efficiency in other Ganoderma species (G. applanatum, G. meredithae). However, these efficiency gains by Ganoderma species could not be sustained when inoculated wood substrates were placed in "live" soils. Substrates colonized naturally, without preinoculations, performed similarly to those deployed with (native) test strains, likely because inoculated fungi were outcompeted and displaced by native colonizers. Instead of rescreening using more combative fungi, we tested an alternative way to present fungi with high single-strain efficiencies for filtration: in dried form as dead biomass (necromass). In dried biomass trials, dried G. lucidum biomass performed better than when testing living biomass, again with the highest strain-specific removal efficiencies (84% of activated carbon). These results demonstrate the potential for G. lucidum, commonly used in biomaterial production, in a variety of indoor and outdoor biofiltration scenarios. It also implies an overlooked, potentially large role for fungi and their soil necromass in capturing and reducing CH4 emissions from soils in nature.
Collapse
Affiliation(s)
- Feng Jin Liew
- Dep. of Bioproducts and Biosystems Engineering, Univ. of Minnesota, 2004 Folwell Ave, Saint Paul, MN, 55108, USA
| | - Jonathan S Schilling
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, 1500 Gortner Ave., Saint Paul, MN, 55108, USA
| |
Collapse
|
7
|
Versantvoort W, Pol A, Jetten MSM, van Niftrik L, Reimann J, Kartal B, Op den Camp HJM. Multiheme hydroxylamine oxidoreductases produce NO during ammonia oxidation in methanotrophs. Proc Natl Acad Sci U S A 2020; 117:24459-24463. [PMID: 32913059 PMCID: PMC7533708 DOI: 10.1073/pnas.2011299117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aerobic and nitrite-dependent methanotrophs make a living from oxidizing methane via methanol to carbon dioxide. In addition, these microorganisms cometabolize ammonia due to its structural similarities to methane. The first step in both of these processes is catalyzed by methane monooxygenase, which converts methane or ammonia into methanol or hydroxylamine, respectively. Methanotrophs use methanol for energy conservation, whereas toxic hydroxylamine is a potent inhibitor that needs to be rapidly removed. It is suggested that many methanotrophs encode a hydroxylamine oxidoreductase (mHAO) in their genome to remove hydroxylamine, although biochemical evidence for this is lacking. HAOs also play a crucial role in the metabolism of aerobic and anaerobic ammonia oxidizers by converting hydroxylamine to nitric oxide (NO). Here, we purified an HAO from the thermophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV and characterized its kinetic properties. This mHAO possesses the characteristic P460 chromophore and is active up to at least 80 °C. It catalyzes the rapid oxidation of hydroxylamine to NO. In methanotrophs, mHAO efficiently removes hydroxylamine, which severely inhibits calcium-dependent, and as we show here, lanthanide-dependent methanol dehydrogenases, which are more prevalent in the environment. Our results indicate that mHAO allows methanotrophs to thrive under high ammonia concentrations in natural and engineered ecosystems, such as those observed in rice paddy fields, landfills, or volcanic mud pots, by preventing the accumulation of inhibitory hydroxylamine. Under oxic conditions, methanotrophs mainly oxidize ammonia to nitrite, whereas in hypoxic and anoxic environments reduction of both ammonia-derived nitrite and NO could lead to nitrous oxide (N2O) production.
Collapse
Affiliation(s)
- Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
8
|
Semrau JD, DiSpirito AA, Obulisamy PK, Kang-Yun CS. Methanobactin from methanotrophs: genetics, structure, function and potential applications. FEMS Microbiol Lett 2020; 367:5804726. [PMID: 32166327 DOI: 10.1093/femsle/fnaa045] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.
Collapse
Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | | | - Christina S Kang-Yun
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
| |
Collapse
|
9
|
Show PL, Pal P, Leong HY, Juan JC, Ling TC. A review on the advanced leachate treatment technologies and their performance comparison: an opportunity to keep the environment safe. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:227. [PMID: 30887225 DOI: 10.1007/s10661-019-7380-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Landfill application is the most common approach for biowaste treatment via leachate treatment system. When municipal solid waste deposited in the landfills, microbial decomposition breaks down the wastes generating the end products, such as carbon dioxide, methane, volatile organic compounds, and liquid leachate. However, due to the landfill age, the fluctuation in the characteristics of landfill leachate is foreseen in the leachate treatment plant. The focuses of the researchers are keeping leachate from contaminating groundwater besides keeping potent methane emissions from reaching the atmosphere. To address the above issues, scientists are required to adopt green biological methods to keep the environment safe. This review focuses on the assorting of research papers on organic content and nitrogen removal from the leachate via recent effective biological technologies instead of conventional nitrification and denitrification process. The published researches on the characteristics of various Malaysian landfill sites were also discussed. The understanding of the mechanism behind the nitrification and denitrification process will help to select an optimized and effective biological treatment option in treating the leachate waste. Recently, widely studied technologies for the biological treatment process are aerobic methane oxidation coupled to denitrification (AME-D) and partial nitritation-anammox (PN/A) process, and both were discussed in this review article. This paper gives the idea of the modification of the conventional treatment technologies, such as combining the present processes to make the treatment process more effective. With the integration of biological process in the leachate treatment, the effluent discharge could be treated in shortcut and novel pathways, and it can lead to achieving "3Rs" of reduce, reuse, and recycle approach.
Collapse
Affiliation(s)
- Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
- Bioseparation Research Group, Faculty of Science and Engineering, Centre for Food and Bioproduct Processing, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Preeti Pal
- School of Environmental Science and Engineering, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
| | - Hui Yi Leong
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Joon Ching Juan
- Nanotechnology and Catalysis Research Centre (NANOCAT), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tau Chuan Ling
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| |
Collapse
|
10
|
Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
Collapse
|
11
|
A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase. J Microbiol 2017; 55:775-782. [DOI: 10.1007/s12275-017-7317-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
|
12
|
Mohammadi SS, Pol A, van Alen T, Jetten MSM, Op den Camp HJM. Ammonia Oxidation and Nitrite Reduction in the Verrucomicrobial Methanotroph Methylacidiphilum fumariolicum SolV. Front Microbiol 2017; 8:1901. [PMID: 29021790 PMCID: PMC5623727 DOI: 10.3389/fmicb.2017.01901] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/15/2017] [Indexed: 01/12/2023] Open
Abstract
The Solfatara volcano near Naples (Italy), the origin of the recently discovered verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV was shown to contain ammonium ([Formula: see text]) at concentrations ranging from 1 to 28 mM. Ammonia (NH3) can be converted to toxic hydroxylamine (NH2OH) by the particulate methane monooxygenase (pMMO), the first enzyme of the methane (CH4) oxidation pathway. Methanotrophs rapidly detoxify the intermediate NH2OH. Here, we show that strain SolV performs ammonium oxidation to nitrite at a rate of 48.2 nmol [Formula: see text].h-1.mg DW-1 under O2 limitation in a continuous culture grown on hydrogen (H2) as an electron donor. In addition, strain SolV carries out nitrite reduction at a rate of 74.4 nmol [Formula: see text].h-1.mg DW-1 under anoxic condition at pH 5-6. This range of pH was selected to minimize the chemical conversion of nitrite ([Formula: see text]) potentially occurring at more acidic pH values. Furthermore, at pH 6, we showed that the affinity constants (K s ) of the cells for NH3 vary from 5 to 270 μM in the batch incubations with 0.5-8% (v/v) CH4, respectively. Detailed kinetic analysis showed competitive substrate inhibition between CH4 and NH3. Using transcriptome analysis, we showed up-regulation of the gene encoding hydroxylamine dehydrogenase (haoA) cells grown on H2/[Formula: see text] compared to the cells grown on CH4/[Formula: see text] which do not have to cope with reactive N-compounds. The denitrifying genes nirk and norC showed high expression in H2/[Formula: see text] and CH4/[Formula: see text] grown cells compared to cells growing at μmax (with no limitation) while the norB gene showed downregulation in CH4/[Formula: see text] grown cells. These cells showed a strong upregulation of the genes in nitrate/nitrite assimilation. Our results demonstrate that strain SolV can perform ammonium oxidation producing nitrite. At high concentrations of ammonium this may results in toxic effects. However, at low oxygen concentrations strain SolV is able to reduce nitrite to N2O to cope with this toxicity.
Collapse
Affiliation(s)
| | | | | | | | - Huub J. M. Op den Camp
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| |
Collapse
|
13
|
Zhang T, Zhou J, Wang X, Zhang Y. Coupled effects of methane monooxygenase and nitrogen source on growth and poly-β-hydroxybutyrate (PHB) production of Methylosinus trichosporium OB3b. J Environ Sci (China) 2017; 52:49-57. [PMID: 28254057 DOI: 10.1016/j.jes.2016.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 06/06/2023]
Abstract
The coupled effects of nitrogen source and methane monooxygenase (MMO) on the growth and poly-β-hydroxybutyrate (PHB) accumulation capacity of methanotrophs were explored. The ammonia-supplied methanotrophs expressing soluble MMO (sMMO) grew at the highest rate, while N2-fixing bacteria expressing particulate MMO (pMMO) grew at the lowest rate. Further study showed that more hydroxylamine and nitrite was formed by ammonia-supplied bacteria containing pMMO, which might cause their slightly lower growth rate. The highest PHB content (51.0%) was obtained under nitrogen-limiting conditions with the inoculation of nitrate-supplied bacteria containing pMMO. Ammonia-supplied bacteria also accumulated a higher content of PHB (45.2%) with the expression of pMMO, while N2-fixing bacteria containing pMMO only showed low PHB production capacity (32.1%). The maximal PHB contents of bacteria expressing sMMO were low, with no significant change under different nitrogen source conditions. The low MMO activity, low cell growth rate and low PHB production capacity of methanotrophs continuously cultivated with N2 with the expression of pMMO were greatly improved in the cyclic NO3-N2 cultivation regime, indicating that long-term deficiency of nitrogen sources was detrimental to the activity of methanotrophs expressing pMMO.
Collapse
Affiliation(s)
- Tingting Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Xiaowei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yu Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| |
Collapse
|
14
|
Nagamori M, Mowjood MIM, Watanabe Y, Isobe Y, Ishigaki T, Kawamoto K. Characterization of temporal variations in landfill gas components inside an open solid waste dump site in Sri Lanka. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2016; 66:1257-1267. [PMID: 27575846 DOI: 10.1080/10962247.2016.1212746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
UNLABELLED A long-term monitoring of composition of landfill gases in the region with high rainfall was conducted using an argon assay in order to discuss air intrusion into the dump site. Gas samples were taken from vertical gas monitoring pipes installed along transects at two sections (called new and old) of an abandoned waste dump site in Sri Lanka. N2O concentrations varied especially widely, by more than three orders of magnitude (0.046-140 ppmv). The nitrogen/argon ratio of landfill gas was normally higher than that of fresh air, implying that denitrification occurred in the dump site. Argon assays indicate that both N2 and N2O production occurred inside waste and more significantly in the old section. The Ar assay would help for evaluations of N2O emission in developing countries. IMPLICATIONS A long-term monitoring of composition of landfill gases in the region with high rainfall was conducted using an argon assay in order to discuss air intrusion into the dump site. Argon assays indicate that both N2 and N2O production occurred inside waste and more significantly in the old section.
Collapse
Affiliation(s)
- Masanao Nagamori
- a Center for Environmental Science in Saitama , Kazo , Saitama , Japan
| | - M I M Mowjood
- b Department of Agricultural Engineering, Faculty of Agriculture , University of Peradeniya , Peradeniya , Sri Lanka
| | - Youichi Watanabe
- a Center for Environmental Science in Saitama , Kazo , Saitama , Japan
| | - Yugo Isobe
- a Center for Environmental Science in Saitama , Kazo , Saitama , Japan
| | - Tomonori Ishigaki
- c Center for Material Cycles and Waste Management, National Institute for Environmental Studies , Tsukuba , Ibaraki , Japan
| | - Ken Kawamoto
- d Graduate School of Science and Engineering, Saitama University , Sakura-ku, Saitama , Saitama , Japan
| |
Collapse
|
15
|
Zhu J, Wang Q, Yuan M, Tan GYA, Sun F, Wang C, Wu W, Lee PH. Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review. WATER RESEARCH 2016; 90:203-215. [PMID: 26734780 DOI: 10.1016/j.watres.2015.12.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/10/2015] [Accepted: 12/12/2015] [Indexed: 06/05/2023]
Abstract
Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking water and groundwater, bottlenecks and potential issues are also discussed.
Collapse
Affiliation(s)
- Jing Zhu
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qian Wang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Mengdong Yuan
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Giin-Yu Amy Tan
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Faqian Sun
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Cheng Wang
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| |
Collapse
|
16
|
Maanoja ST, Rintala JA. Methane oxidation potential of boreal landfill cover materials: The governing factors and enhancement by nutrient manipulation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 46:399-407. [PMID: 26298483 DOI: 10.1016/j.wasman.2015.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 06/04/2023]
Abstract
Methanotrophs inhabiting landfill covers are in a crucial role in mitigating CH4 emissions, but the characteristics of the cover material or ambient temperature do not always enable the maximal CH4 oxidation potential (MOP). This study aimed at identifying the factors governing MOPs of different materials used for constructing biocovers and other cover structures. We also tested whether the activity of methanotrophs could be enhanced at cold temperature (4 and 12°C) by improving the nutrient content (NO3(-), PO4(3-), trace elements) of the cover material. Compost samples from biocovers designed to support CH4 oxidation were exhibiting the highest MOPs (4.16 μmol CH4 g dw(-1) h(-1)), but also the soil samples collected from other cover structures were oxidising CH4 (0.41 μmol CH4 g dw(-1) h(-1)). The best predictors for the MOPs were the NO3(-) content and activity of heterotrophic bacteria at 72.8%, which were higher in the compost samples than in the soil samples. The depletion of NO3(-) from the landfill cover material limiting the activity of methanotrophs could not be confirmed by the nutrient manipulation assay at 4°C as the addition of nitrogen decreased the MOPs from 0.090 μmol CH4 g dw(-1) h(-1) to <0.085 μmol CH4 g dw(-1) h(-1). At 12°C, all nutrient additions reduced the MOPs. The inhibition was believed to result from high ionic concentration caused by nutrient addition. At 4°C, the addition of trace elements increased the MOPs (>0.096 μmol CH4 g dw(-1)h(-1)) suggesting that this was attributable to stimulation of the enzymatic activity of the psychrotolerant methanotrophs.
Collapse
Affiliation(s)
- Susanna T Maanoja
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland.
| | - Jukka A Rintala
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland.
| |
Collapse
|
17
|
He Z, Geng S, Pan Y, Cai C, Wang J, Wang L, Liu S, Zheng P, Xu X, Hu B. Improvement of the trace metal composition of medium for nitrite-dependent anaerobic methane oxidation bacteria: Iron (II) and copper (II) make a difference. WATER RESEARCH 2015; 85:235-243. [PMID: 26340061 DOI: 10.1016/j.watres.2015.08.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/18/2015] [Accepted: 08/22/2015] [Indexed: 06/05/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo) is a potential bioprocess for treating nitrogen-containing wastewater. This process uses methane, an inexpensive and nontoxic end-product of anaerobic digestion, as an external electron donor. However, the low turnover rate and slow growth rate of n-damo functional bacteria limit the practical application of this process. In the present study, the short- and long-term effects of variations in trace metal concentrations on n-damo bacteria were investigated, and the concentrations of trace metal elements of medium were improved. The results were subsequently verified by a group of long-term inoculations (90 days) and were applied in a sequencing batch reactor (SBR) (84 days). The results indicated that iron (Fe(II)) and copper (Cu(II)) (20 and 10 μmol L(-1), respectively) significantly stimulated the activity and the growth of n-damo bacteria, whereas other trace metal elements, including zinc (Zn), molybdenum (Mo), cobalt (Co), manganese (Mn), and nickel (Ni), had no significant effect on n-damo bacteria in the tested concentration ranges. Interestingly, fluorescence in situ hybridization (FISH) showed that a large number of dense, large aggregates (10-50 μm) of n-damo bacteria were formed by cell adhesion in the SBR reactor after using the improved medium, and to our knowledge this is the first discovery of large aggregates of n-damo bacteria.
Collapse
Affiliation(s)
- Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Sha Geng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yawei Pan
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Chaoyang Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Liqiao Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xinhua Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
18
|
Myung J, Wang Z, Yuan T, Zhang P, Van Nostrand JD, Zhou J, Criddle CS. Production of Nitrous Oxide from Nitrite in Stable Type II Methanotrophic Enrichments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:10969-10975. [PMID: 26301949 DOI: 10.1021/acs.est.5b03385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The coupled aerobic-anoxic nitrous decomposition operation is a new process for wastewater treatment that removes nitrogen from wastewater and recovers energy from the nitrogen in three steps: (1) NH4(+) oxidation to NO2(-), (2) NO2(-) reduction to N2O, and (3) N2O conversion to N2 with energy production. Here, we demonstrate that type II methanotrophic enrichments can mediate step two by coupling oxidation of poly(3-hydroxybutyrate) (P3HB) to NO2(-) reduction. Enrichments grown with NH4(+) and NO2(-) were subject to alternating 48-h aerobic and anoxic periods, in which CH4 and NO2(-) were added together in a "coupled" mode of operation or separately in a "decoupled mode". Community structure was stable in both modes and dominated by Methylocystis. In the coupled mode, production of P3HB and N2O was low. In the decoupled mode, significant P3HB was produced, and oxidation of P3HB drove reduction of NO2(-) to N2O with ∼ 70% conversion for >30 cycles (120 d). In batch tests of wasted cells from the decoupled mode, N2O production rates increased at low O2 or high NO2(-) levels. The results are significant for the development of engineered processes that remove nitrogen from wastewater and for understanding of conditions that favor environmental production of N2O.
Collapse
Affiliation(s)
- Jaewook Myung
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Zhiyue Wang
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ping Zhang
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
- Woods Institute for the Environment, Stanford, California 94305, United States
- William and Cloy Codiga Resource Recovery Center, Stanford, California 94305, United States
| |
Collapse
|
19
|
Soil-borne microbial functional structure across different land uses. ScientificWorldJournal 2014; 2014:216071. [PMID: 25177716 PMCID: PMC4142738 DOI: 10.1155/2014/216071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/26/2014] [Accepted: 07/16/2014] [Indexed: 12/03/2022] Open
Abstract
Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.
Collapse
|
20
|
Hoefman S, van der Ha D, Boon N, Vandamme P, De Vos P, Heylen K. Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit. BMC Microbiol 2014; 14:83. [PMID: 24708438 PMCID: PMC3997834 DOI: 10.1186/1471-2180-14-83] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. RESULTS We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. CONCLUSIONS Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.
Collapse
Affiliation(s)
- Sven Hoefman
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - David van der Ha
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
21
|
Hoefman S, van der Ha D, Boon N, Vandamme P, De Vos P, Heylen K. Customized media based on miniaturized screening improve growth rate and cell yield of methane-oxidizing bacteria of the genus Methylomonas. Antonie van Leeuwenhoek 2013; 105:353-66. [DOI: 10.1007/s10482-013-0083-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/17/2013] [Indexed: 11/29/2022]
|
22
|
Gao J, Zhang H, Cao X, Ding J, Yu G, Xu H. Characteristics and kinetics of ammonia and N2O emissions of aged refuse irrigated from landfill leachate. WASTE MANAGEMENT (NEW YORK, N.Y.) 2013; 33:1229-1236. [PMID: 23474206 DOI: 10.1016/j.wasman.2013.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 01/19/2013] [Accepted: 02/08/2013] [Indexed: 06/01/2023]
Abstract
This is the first attempt to report the gaseous nitrogen emissions from landfill leachate filtration methods by irrigating the aged refuse. A first-order reaction model was a good fit for the increase in ammonia emissions from aged refuse, clay and sandy soil incubated for 120 h after adding the leachate-N solution. The emissions of ammonia and N2O by the three experimental materials fit well to first-order and zero-order models, respectively. The maximum ammonia emission from aged refuse was approximately 1.17 mg NH4(+)-Nkg(-1) d.w. and the calculated emission factor was 1.95‰, which was 3.76 and 2.67 times lower than that of sandy and clay soils, respectively. The tendencies of NH4(+)-N nitrification and NO3(-)-N generations fit well to the zero-order reaction model and the net nitrification rate by the aged refuse was 1.30 (p<0.05) and 1.71 (p<0.05) times that of clay soil and sandy soil, respectively. At the same time, the net NO4(-)-N generation rate by the aged refuse was 1.56 (p<0.05) and 2.33 (p<0.05) times that of clay soil and sandy soil, respectively. The quantity of nitrogen emitted by aged refuse as N2O was 2.46 times greater than that emitted as ammonia. The emission factor for N2O from aged refuse was 8.28 (p<0.05) and 16.11 (p<0.05) times greater than that of clay and sandy soils, respectively. For the leachate irrigation, N2O emissions should be of greater concern than ammonia emissions.
Collapse
Affiliation(s)
- Jixi Gao
- Nanjing Institute of Environmental Sciences of the Ministry of Environmental Protection of PR China, Nanjing, Jiangsu 210042, PR China
| | | | | | | | | | | |
Collapse
|
23
|
Lizik W, Im J, Semrau JD, Barcelona MJ. A field trial of nutrient stimulation of methanotrophs to reduce greenhouse gas emissions from landfill cover soils. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2013; 63:300-309. [PMID: 23556240 DOI: 10.1080/10962247.2012.755137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
UNLABELLED Landfills are among the major sources of anthropogenic methane (CH4) estimated to reach 40 x 10(9) kg per year worldwide by 2015 (IPCC, 2007). A 2 1/2-year field experiment was conducted at a closed landfill in western Michigan where methanotrophs, methane-consuming bacteria, were stimulated by nutrient addition to the soil without significantly increasing biogenic nitrous oxide (N2O) production. The effects of the nitrogen amendments (KNO3 and NH4Cl), phenylacetylene (a selective inhibitor of nitrifying bacteria that contribute to N2O production), and a canopy (to reduce direct water infiltration) on the vertical soil gas profiles of CH4, CO2, and O2 were measured in the top meter of the soil. Methane and nitrous oxide fluxes were calculated from the corresponding soil gas concentration gradients with respect to depth and a Millington-Quirk diffusivity coefficient in soil derived empirically from soil porosity, water content, and diffusivity coefficients in air from the literature. Methane flux estimates were as high as 218.4 g m(-2) day(-1) in the fall and 12.8 g/m(-2) day(-1) in the summer. During the spring and summer CH4 fluxes were reduced by more than half by adding KNO3 and NH4Cl into the soil as compared to control plots, while N2O fluxes increased substantially. The concurrent addition of phenylacetylene to the amendment decreased peak N2O production by half and the rate of peak methane oxidation by about one-third. The seasonal average methane and N2O flux data were extrapolated to estimate the reduction of CH4 and N2O fluxes into the atmosphere by nitrogen and inhibitor addition to the cover soils. The results suggest that such additions coupled with soil moisture management may provide a potential strategy to significantly reduce greenhouse gas emissions from landfills. IMPLICATIONS The results of a 2 1/2-year study of effects of nutrient stimulation on methane oxidation in landfill cover soils demonstrates that nutrient addition does decrease methane emissions. The work further underscores the control which soil moisture exerts on methane oxidation. Water management is critical to the success of methane oxidation strategies.
Collapse
Affiliation(s)
- William Lizik
- US. Defense Logistics Agency, Richmond, Virginia, USA
| | | | | | | |
Collapse
|
24
|
Microorganisms in landfill bioreactors for accelerated stabilization of solid wastes. J Biosci Bioeng 2012; 114:243-50. [DOI: 10.1016/j.jbiosc.2012.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 03/24/2012] [Accepted: 04/06/2012] [Indexed: 11/22/2022]
|
25
|
Abstract
Nitrous oxide, a potent greenhouse gas and ozone-depleting molecule, continues to accumulate in the atmosphere as a product of anthropogenic activities and land-use change. Nitrogen oxides are intermediates of nitrification and denitrification and are released as terminal products under conditions such as high nitrogen load and low oxygen tension among other factors. The rapid completion and public availability of microbial genome sequences has revealed a high level of enzymatic redundancy in pathways terminating in nitrogen oxide metabolites, with few enzymes involved in returning nitrogen oxides to dinitrogen. The aerobic methanotrophic bacteria are particularly useful for discovering and analysing diverse mechanisms for nitrogen oxide production, as these microbes both nitrify (oxidize ammonia to nitrite) and denitrify (reduce nitrate/nitrite to nitrous oxide via nitric oxide), and yet do not rely on these pathways for growth. The fact that methanotrophs have a rich inventory for nitrogen oxide metabolism is, in part, a consequence of their evolutionary relatedness to ammonia-oxidizing bacteria. Furthermore, the ability of individual methanotrophic taxa to resist toxic intermediates of nitrogen metabolism affects the relative abundance of nitrogen oxides released into the environment, the composition of their community, and the balance between nitrogen and methane cycling.
Collapse
|
26
|
Fagerstone KD, Quinn JC, Bradley TH, De Long SK, Marchese AJ. Quantitative measurement of direct nitrous oxide emissions from microalgae cultivation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:9449-9456. [PMID: 21939252 DOI: 10.1021/es202573f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Although numerous lifecycle assessments (LCA) of microalgae-based biofuels have suggested net reductions of greenhouse gas emissions, limited experimental data exist on direct emissions from microalgae cultivation systems. For example, nitrous oxide (N(2)O) is a potent greenhouse gas that has been detected from microalgae cultivation. However, little quantitative experimental data exist on direct N(2)O emissions from microalgae cultivation, which has inhibited LCA performed to date. In this study, microalgae species Nannochloropsis salina was cultivated with diurnal light-dark cycling using a nitrate nitrogen source. Gaseous N(2)O emissions were quantitatively measured using Fourier transform infrared spectrometry. Under a nitrogen headspace (photobioreactor simulation), the reactors exhibited elevated N(2)O emissions during dark periods, and reduced N(2)O emissions during light periods. Under air headspace conditions (open pond simulation), N(2)O emissions were negligible during both light and dark periods. Results show that N(2)O production was induced by anoxic conditions when nitrate was present, suggesting that N(2)O was produced by denitrifying bacteria within the culture. The presence of denitrifying bacteria was verified through PCR-based detection of norB genes and antibiotic treatments, the latter of which substantially reduced N(2)O emissions. Application of these results to LCA and strategies for growth management to reduce N(2)O emissions are discussed.
Collapse
Affiliation(s)
- Kelly D Fagerstone
- Department of Mechanical Engineering, Colorado State University, Fort Collins, Colorado, 80523-1374 United States
| | | | | | | | | |
Collapse
|
27
|
Effect of compost, nitrogen salts, and NPK fertilizers on methane oxidation potential at different temperatures. Appl Microbiol Biotechnol 2011; 93:2633-43. [DOI: 10.1007/s00253-011-3560-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 08/09/2011] [Accepted: 08/18/2011] [Indexed: 11/26/2022]
|
28
|
Yang N, Lü F, He P, Shao L. Response of methanotrophs and methane oxidation on ammonium application in landfill soils. Appl Microbiol Biotechnol 2011; 92:1073-82. [DOI: 10.1007/s00253-011-3389-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 05/15/2011] [Accepted: 05/15/2011] [Indexed: 10/18/2022]
|
29
|
Proteomic and targeted qPCR analyses of subsurface microbial communities for presence of methane monooxygenase. Biodegradation 2011; 22:1045-59. [DOI: 10.1007/s10532-011-9462-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 02/17/2011] [Indexed: 01/21/2023]
|
30
|
Current knowledge of microbial community structures in landfills and its cover soils. Appl Microbiol Biotechnol 2010; 89:961-9. [DOI: 10.1007/s00253-010-3024-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 11/17/2010] [Accepted: 11/17/2010] [Indexed: 10/18/2022]
|
31
|
Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b. J Bacteriol 2010; 192:6497-8. [PMID: 20952571 DOI: 10.1128/jb.01144-10] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methylosinus trichosporium OB3b (for "oddball" strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This strain has since been used extensively to elucidate the structure and function of several key enzymes of methane oxidation, including both particulate and soluble methane monooxygenase (sMMO) and the extracellular copper chelator methanobactin. In particular, the catalytic properties of soluble methane monooxygenase from M. trichosporium OB3b have been well characterized in context with biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of the M. trichosporium OB3b genome is the first reported from a member of the Methylocystaceae family in the order Rhizobiales.
Collapse
|
32
|
Upadhyaya G, Jackson J, Clancy TM, Hyun SP, Brown J, Hayes KF, Raskin L. Simultaneous removal of nitrate and arsenic from drinking water sources utilizing a fixed-bed bioreactor system. WATER RESEARCH 2010; 44:4958-4969. [PMID: 20732708 DOI: 10.1016/j.watres.2010.07.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 07/06/2010] [Accepted: 07/13/2010] [Indexed: 05/29/2023]
Abstract
A novel bioreactor system, consisting of two biologically active carbon (BAC) reactors in series, was developed for the simultaneous removal of nitrate and arsenic from a synthetic groundwater supplemented with acetic acid. A mixed biofilm microbial community that developed on the BAC was capable of utilizing dissolved oxygen, nitrate, arsenate, and sulfate as the electron acceptors. Nitrate was removed from a concentration of approximately 50 mg/L in the influent to below the detection limit of 0.2 mg/L. Biologically generated sulfides resulted in the precipitation of the iron sulfides mackinawite and greigite, which concomitantly removed arsenic from an influent concentration of approximately 200 ug/L to below 20 ug/L through arsenic sulfide precipitation and surface precipitation on iron sulfides. This study showed for the first time that arsenic and nitrate can be simultaneously removed from drinking water sources utilizing a bioreactor system.
Collapse
Affiliation(s)
- Giridhar Upadhyaya
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | | | | | | |
Collapse
|
33
|
Field application of nitrogen and phenylacetylene to mitigate greenhouse gas emissions from landfill cover soils: effects on microbial community structure. Appl Microbiol Biotechnol 2010; 89:189-200. [PMID: 20809077 DOI: 10.1007/s00253-010-2811-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 07/17/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
Abstract
Landfills are large sources of CH(4), but a considerable amount of CH(4) can be removed in situ by methanotrophs if their activity can be stimulated through the addition of nitrogen. Nitrogen can, however, lead to increased N(2)O production. To examine the effects of nitrogen and a selective inhibitor on CH(4) oxidation and N(2)O production in situ, 0.5 M of NH(4)Cl and 0.25 M of KNO(3), with and without 0.01% (w/v) phenylacetylene, were applied to test plots at a landfill in Kalamazoo, MI from 2007 November to 2009 July. Nitrogen amendments stimulated N(2)O production but had no effect on CH(4) oxidation. The addition of phenylacetylene stimulated CH(4) oxidation while reducing N(2)O production. Methanotrophs possessing particulate methane monooxygenase and archaeal ammonia-oxidizers (AOAs) were abundant. The addition of nitrogen reduced methanotrophic diversity, particularly for type I methanotrophs. The simultaneous addition of phenylacetylene increased methanotrophic diversity and the presence of type I methanotrophs. Clone libraries of the archaeal amoA gene showed that the addition of nitrogen increased AOAs affiliated with Crenarchaeal group 1.1b, while they decreased with the simultaneous addition of phenylacetylene. These results suggest that the addition of phenylacetylene with nitrogen reduces N(2)O production by selectively inhibiting AOAs and/or type II methanotrophs.
Collapse
|
34
|
Effects of ammonium and nitrite on growth and competitive fitness of cultivated methanotrophic bacteria. Appl Environ Microbiol 2010; 76:5648-51. [PMID: 20601518 DOI: 10.1128/aem.00747-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of nitrite and ammonium on cultivated methanotrophic bacteria were investigated. Methylomicrobium album ATCC 33003 outcompeted Methylocystis sp. strain ATCC 49242 in cultures with high nitrite levels, whereas cultures with high ammonium levels allowed Methylocystis sp. to compete more easily. M. album pure cultures and cocultures consumed nitrite and produced nitrous oxide, suggesting a connection between denitrification and nitrite tolerance.
Collapse
|
35
|
Abstract
Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.
Collapse
Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, The University of Michigan, Ann Arbor, MI, USA.
| | | | | |
Collapse
|