101
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Vertical distribution of nitrite-dependent anaerobic methane-oxidising bacteria in natural freshwater wetland soils. Appl Microbiol Biotechnol 2014; 99:349-57. [DOI: 10.1007/s00253-014-6031-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 12/13/2022]
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102
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He Z, Cai C, Shen L, Lou L, Zheng P, Xu X, Hu B. Effect of inoculum sources on the enrichment of nitrite-dependent anaerobic methane-oxidizing bacteria. Appl Microbiol Biotechnol 2014; 99:939-46. [DOI: 10.1007/s00253-014-6033-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 08/11/2014] [Accepted: 08/15/2014] [Indexed: 10/24/2022]
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103
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Chen X, Guo J, Shi Y, Hu S, Yuan Z, Ni BJ. Modeling of simultaneous anaerobic methane and ammonium oxidation in a membrane biofilm reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9540-9547. [PMID: 25055054 DOI: 10.1021/es502608s] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nitrogen removal by using the synergy of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) microorganisms in a membrane biofilm reactor (MBfR) has previously been demonstrated experimentally. In this work, a mathematical model is developed to describe the simultaneous anaerobic methane and ammonium oxidation by DAMO and Anammox microorganisms in an MBfR for the first time. In this model, DAMO archaea convert nitrate, both externally fed and/or produced by Anammox, to nitrite, with methane as the electron donor. Anammox and DAMO bacteria jointly remove the nitrite fed/produced, with ammonium and methane as the electron donor, respectively. The model is successfully calibrated and validated using the long-term (over 400 days) dynamic experimental data from the MBfR, as well as two independent batch tests at different operational stages of the MBfR. The model satisfactorily describes the methane oxidation and nitrogen conversion data from the system. Modeling results show the concentration gradients of methane and nitrogen would cause stratification of the biofilm, where Anammox bacteria mainly grow in the biofilm layer close to the bulk liquid and DAMO organisms attach close to the membrane surface. The low surface methane loadings result in a low fraction of DAMO microorganisms, but the high surface methane loadings would lead to overgrowth of DAMO bacteria, which would compete with Anammox for nitrite and decrease the fraction of Anammox bacteria. The results suggest an optimal methane supply under the given condition should be applied not only to benefit the nitrogen removal but also to avoid potential methane emissions.
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Affiliation(s)
- Xueming Chen
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane, QLD 4072, Australia
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104
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Ding ZW, Ding J, Fu L, Zhang F, Zeng RJ. Simultaneous enrichment of denitrifying methanotrophs and anammox bacteria. Appl Microbiol Biotechnol 2014; 98:10211-21. [DOI: 10.1007/s00253-014-5936-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
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105
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Hendrickx TLG, Kampman C, Zeeman G, Temmink H, Hu Z, Kartal B, Buisman CJN. High specific activity for anammox bacteria enriched from activated sludge at 10°C. BIORESOURCE TECHNOLOGY 2014; 163:214-221. [PMID: 24814247 DOI: 10.1016/j.biortech.2014.04.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
Anammox in the water line of a waste water treatment plant (WWTP) saves energy for aeration and allows for recovering biogas from organic material. Main challenges for applying the anammox process in the water line are related to the low temperature of <20°C, causing a significant drop in the specific anammox activity. The aim of this research was to enrich a cold-adapted anammox species, with a high specific activity. This was achieved in a 4.2L reactor operated at 10°C, fed with 61 mg (NH4+NO2)-N/L and inoculated with activated sludge from two selected municipal WWTPs. Candidatus Brocadia fulgida was the dominant species in the enriched biomass, with a specific activity was 30-44 mg N/(g VS d). This is two times higher than previously reported at 10°C, which is beneficial for full scale application. Biomass yield was 0.046 g biomass/g N converted, similar to that at higher temperatures.
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Affiliation(s)
- Tim L G Hendrickx
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
| | - Christel Kampman
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Grietje Zeeman
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Hardy Temmink
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Ziye Hu
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Cees J N Buisman
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
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106
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Kampman C, Temmink H, Hendrickx TLG, Zeeman G, Buisman CJN. Enrichment of denitrifying methanotrophic bacteria from municipal wastewater sludge in a membrane bioreactor at 20°C. JOURNAL OF HAZARDOUS MATERIALS 2014; 274:428-435. [PMID: 24809733 DOI: 10.1016/j.jhazmat.2014.04.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 04/13/2014] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
Simultaneous nitrogen and methane removal by the slow growing denitrifying methanotrophic bacterium 'Candidatus Methylomirabilis oxyfera' offers opportunities for a new approach to wastewater treatment. However, volumetric nitrite consumption rates should be increased by an order of magnitude before application in wastewater treatment becomes possible. A maximum volumetric nitrite consumption rate of 36 mg NO2(-)-N/L d was achieved in a membrane bioreactor inoculated with wastewater sludge and operated at 20°C. This rate is similar to maximum rates reported in literature, though it was thought that by strict biomass retention using membranes, higher rates would be achieved. In experiments lasting several years, growth was not stable: every experiment showed a decrease in activity after 1-2 years. The cause remains unknown. Rates increased after addition of copper and operating a membrane bioreactor at shorter hydraulic retention times. Further research should focus on long-term effects of copper addition and operation at hydraulic retention times in the order of hours using membrane bioreactors.
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Affiliation(s)
- Christel Kampman
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.
| | - Hardy Temmink
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Tim L G Hendrickx
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Grietje Zeeman
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Cees J N Buisman
- Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
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107
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Hu B, He Z, Geng S, Cai C, Lou L, Zheng P, Xu X. Cultivation of nitrite-dependent anaerobic methane-oxidizing bacteria: impact of reactor configuration. Appl Microbiol Biotechnol 2014; 98:7983-91. [DOI: 10.1007/s00253-014-5835-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
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108
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Chen J, Zhou ZC, Gu JD. Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes. Appl Microbiol Biotechnol 2014; 98:5685-96. [PMID: 24769903 DOI: 10.1007/s00253-014-5733-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 01/19/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo) process is unique in linking the microbial carbon and nitrogen cycles, but the presence of n-damo bacteria in marine ecosystem and the associated environmental factors are still poorly understood. In the present study, detection of n-damo bacteria using 16S rRNA and pmoA gene-based PCR primers was successfully employed to reveal their diversity and distribution in the surface and subsurface sediments of the South China Sea (SCS). The widespread occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity has been confirmed in this study. The pmoA gene-amplified sequences clustered within three newly erected subclusters, namely SCS-1, SCS-2, and SCS-3, suggesting the unique niche specificity of n-damo bacteria in the marine ecosystem. Results indicated the presence of n-damo bacteria in the west Pacific Ocean with a wide distribution from the continental shelf (E201S) to the deep abyss (E407S and E407B). Community structures of n-damo bacteria in SCS are clearly different from those of nonmarine ones known. It is also found that NO x (-) and NH4 (+) affected the community structures and distribution of n-damo bacteria in the SCS sediments differently. Salinity is another important factor identified, shaping the n-damo communities in marine environments. The community based on pmoA gene-amplified sequences, and community richness and diversity based on 16S rRNA gene-amplified sequences correlated with temperature.
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Affiliation(s)
- Jing Chen
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
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109
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Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands. Proc Natl Acad Sci U S A 2014; 111:4495-500. [PMID: 24616523 DOI: 10.1073/pnas.1318393111] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The process of nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and shown to be mediated by "Candidatus Methylomirabilis oxyfera" (M. oxyfera). Here, evidence for n-damo in three different freshwater wetlands located in southeastern China was obtained using stable isotope measurements, quantitative PCR assays, and 16S rRNA and particulate methane monooxygenase gene clone library analyses. Stable isotope experiments confirmed the occurrence of n-damo in the examined wetlands, and the potential n-damo rates ranged from 0.31 to 5.43 nmol CO2 per gram of dry soil per day at different depths of soil cores. A combined analysis of 16S rRNA and particulate methane monooxygenase genes demonstrated that M. oxyfera-like bacteria were mainly present in the deep soil with a maximum abundance of 3.2 × 10(7) gene copies per gram of dry soil. It is estimated that ∼0.51 g of CH4 m(-2) per year could be linked to the n-damo process in the examined wetlands based on the measured potential n-damo rates. This study presents previously unidentified confirmation that the n-damo process is a previously overlooked microbial methane sink in wetlands, and n-damo has the potential to be a globally important methane sink due to increasing nitrogen pollution.
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110
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Molecular evidence for nitrite-dependent anaerobic methane-oxidising bacteria in the Jiaojiang Estuary of the East Sea (China). Appl Microbiol Biotechnol 2014; 98:5029-38. [DOI: 10.1007/s00253-014-5556-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/10/2014] [Accepted: 01/18/2014] [Indexed: 10/25/2022]
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111
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Langone M, Yan J, Haaijer SCM, Op den Camp HJM, Jetten MSM, Andreottola G. Coexistence of nitrifying, anammox and denitrifying bacteria in a sequencing batch reactor. Front Microbiol 2014; 5:28. [PMID: 24550899 PMCID: PMC3912432 DOI: 10.3389/fmicb.2014.00028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 01/17/2014] [Indexed: 11/13/2022] Open
Abstract
Elevated nitrogen removal efficiencies from ammonium-rich wastewaters have been demonstrated by several applications, that combine nitritation and anammox processes. Denitrification will occur simultaneously when organic carbon is also present. In this study, the activity of aerobic ammonia oxidizing, anammox and denitrifying bacteria in a full scale sequencing batch reactor, treating digester supernatants, was studied by means of batch-assays. AOB and anammox activities were maximum at pH of 8.0 and 7.8–8.0, respectively. Short term effect of nitrite on anammox activity was studied, showing nitrite up to 42 mg/L did not result in inhibition. Both denitrification via nitrate and nitrite were measured. To reduce nitrite-oxidizing activity, high NH3-N (1.9–10 mg NH3-N/L) and low nitrite (3–8 mg TNN/L) are required conditions during the whole SBR cycle. Molecular analysis showed the nitritation-anammox sludge harbored a high microbial diversity, where each microorganism has a specific role. Using ammonia monooxygenase α–subunit (amoA) gene as a marker, our analyses suggested different macro- and micro-environments in the reactor strongly affect the AOB community, allowing the development of different AOB species, such as N. europaea/eutropha and N. oligotropha groups, which improve the stability of nitritation process. A specific PCR primer set, used to target the 16S rRNA gene of anammox bacteria, confirmed the presence of the “Ca. Brocadia fulgida” type, able to grow in presence of organic matter and to tolerate high nitrite concentrations. The diversity of denitrifiers was assessed by using dissimilatory nitrite reductase (nirS) gene-based analyses, who showed denitifiers were related to different betaproteobacterial genera, such as Thauera, Pseudomonas, Dechloromonas and Aromatoleum, able to assist in forming microbial aggregates. Concerning possible secondary processes, no n-damo bacteria were found while NOB from the genus Nitrobacter was detected.
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Affiliation(s)
- Michela Langone
- Department of Civil, Environmental and Mechanical Engineering, University of Trento Trento, Italy
| | - Jia Yan
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands ; Department of Environmental Engineering, College of Environment and Energy, South China University of Technology Guangzhou, China
| | - Suzanne C M Haaijer
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
| | - Gianni Andreottola
- Department of Civil, Environmental and Mechanical Engineering, University of Trento Trento, Italy
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112
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Shen LD, Liu S, Zhu Q, Li XY, Cai C, Cheng DQ, Lou LP, Xu XY, Zheng P, Hu BL. Distribution and diversity of nitrite-dependent anaerobic methane-oxidising bacteria in the sediments of the Qiantang River. MICROBIAL ECOLOGY 2014; 67:341-349. [PMID: 24272281 DOI: 10.1007/s00248-013-0330-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 11/12/2013] [Indexed: 06/02/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo) process was reported to be mediated by "Candidatus Methylomirabilis oxyfera", which belongs to the candidate phylum NC10. M. oxyfera-like bacteria have been detected in lake ecosystems, while their distribution, diversity and abundance in river ecosystems have not been well studied. In this study, both the 16S rRNA and the pmoA molecular biomarkers confirmed the presence of diverse NC10 phylum bacteria related to M. oxyfera in a river ecosystem-the Qiantang River, Zhejiang Province (China). Phylogenetic analysis of 16S rRNA genes demonstrated that the recovered M. oxyfera-like sequences could be grouped into several distinct clusters that exhibited 89.8% to 98.9% identity to the M. oxyfera 16S rRNA gene. Similarly, several different clusters of pmoA gene sequences were observed, and these clusters displayed 85.1-95.4% sequence identity to the pmoA gene of M. oxyfera. Quantitative PCR showed that the abundance of M. oxyfera-like bacteria varied from 1.32 ± 0.16 × 10(6) to 1.03 ± 0.12 × 10(7) copies g (dry weight)(-1). Correlation analysis demonstrated that the total inorganic nitrogen content, the ammonium content and the organic content of the sediment were important factors affecting the distribution of M. oxyfera-like bacterial groups in the examined sediments. This study demonstrated the distribution of diverse M. oxyfera-like bacteria and their correlation with environmental factors in Qiantang River sediments.
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Affiliation(s)
- Li-dong Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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113
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A newly designed degenerate PCR primer based on pmoA gene for detection of nitrite-dependent anaerobic methane-oxidizing bacteria from different ecological niches. Appl Microbiol Biotechnol 2013; 97:10155-62. [PMID: 24201910 DOI: 10.1007/s00253-013-5260-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
Abstract
A new pmoA gene-based PCR primer set was designed for detection of nitrite-dependent anaerobic oxidation of methane (n-damo) bacteria from four different ecosystems, namely rice paddy soil, freshwater reservoir, reed bed, and sludge from wastewater treatment plant. This primer set showed high specificity and efficiency in recovering n-damo bacteria from these diverse samples. The obtained sequences showed 88-94 and 90-96% similarity to nucleotide and amino acid sequences, respectively, with the known NC10 phylum bacterium. According to the UniFrac principal coordinates analysis (PCoA), DNA sequences retrieved by the new PCR primer set in this study formed a separate group from the reported sequences, indicating higher diversity of n-damo in the environment. This newly designed PCR primer is capable of amplifying not only the currently known n-damo bacteria but also those that have not been reported, providing new information on the ecological diversity and distribution of this group of microorganisms in the ecosystem.
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114
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Shi Y, Hu S, Lou J, Lu P, Keller J, Yuan Z. Nitrogen removal from wastewater by coupling anammox and methane-dependent denitrification in a membrane biofilm reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:11577-11583. [PMID: 24033254 DOI: 10.1021/es402775z] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This work demonstrates, for the first time, the feasibility of nitrogen removal by using the synergy of anammox and denitrifying anaerobic methane oxidation (DAMO) microorganisms in a membrane biofilm reactor (MBfR). The reactor was fed with synthetic wastewater containing nitrate and ammonium. Methane was delivered from the interior of hollow fibres in the MBfR to the biofilm that grew on the fiber's outer wall. After 24 months of operation, the system achieved a nitrate and an ammonium removal rate of about 190 mgN L(-1) d(-1) (or 86 mgN m(-2) d(-1), with m(2) referring to biofilm surface area) and 60 mgN L(-1) d(-1) (27 mgN m(-2) d(-1)), respectively. No nitrite accumulation was observed. Fluorescence in situ hybridization (FISH) analysis indicated that DAMO bacteria (20-30%), DAMO archaea (20-30%) and anammox bacteria (20-30%) jointly dominated the microbial community. Based on the known metabolism of these microorganisms, mass balance, and isotope studies, we hypothesize that DAMO archaea converted nitrate, both externally fed and produced by anammox, to nitrite, with methane as the electron donor. Anammox and DAMO bacteria jointly removed the nitrite produced, with ammonium and methane as the electron donor, respectively. The process could potentially be used for anaerobic nitrogen removal from wastewater streams containing ammonium and nitrate/nitrite.
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Affiliation(s)
- Ying Shi
- Advanced Water Management Centre (AWMC), The University of Queensland , St Lucia, Brisbane, Queensland, 4072, Australia
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115
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Abstract
The methanotrophic potential in sewage treatment sludge was investigated. We detected a diverse aerobic methanotrophic community that potentially plays a significant role in mitigating methane emission in this environment. The results suggest that community structure was determined by conditions specific to the processes in a sewage treatment plant.
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116
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Rare branched fatty acids characterize the lipid composition of the intra-aerobic methane oxidizer "Candidatus Methylomirabilis oxyfera". Appl Environ Microbiol 2012; 78:8650-6. [PMID: 23042164 DOI: 10.1128/aem.02099-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recently described bacterium "Candidatus Methylomirabilis oxyfera" couples the oxidation of the important greenhouse gas methane to the reduction of nitrite. The ecological significance of "Ca. Methylomirabilis oxyfera" is still underexplored, as our ability to identify the presence of this bacterium is thus far limited to DNA-based techniques. Here, we investigated the lipid composition of "Ca. Methylomirabilis oxyfera" to identify new, gene-independent biomarkers for the environmental detection of this bacterium. Multiple "Ca. Methylomirabilis oxyfera" enrichment cultures were investigated. In all cultures, the lipid profile was dominated up to 46% by the fatty acid (FA) 10-methylhexadecanoic acid (10MeC(16:0)). Furthermore, a unique FA was identified that has not been reported elsewhere: the monounsaturated 10-methylhexadecenoic acid with a double bond at the Δ7 position (10MeC(16:1Δ7)), which comprised up to 10% of the total FA profile. We propose that the typical branched fatty acids 10MeC(16:0) and 10MeC(16:1Δ7) are key and characteristic components of the lipid profile of "Ca. Methylomirabilis oxyfera." The successful detection of these fatty acids in a peatland from which one of the enrichment cultures originated supports the potential of these unique lipids as biomarkers for the process of nitrite-dependent methane oxidation in the environment.
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117
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Anaerobic oxidization of methane in a minerotrophic peatland: enrichment of nitrite-dependent methane-oxidizing bacteria. Appl Environ Microbiol 2012; 78:8657-65. [PMID: 23042166 DOI: 10.1128/aem.02102-12] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The importance of anaerobic oxidation of methane (AOM) as a methane sink in freshwater systems is largely unexplored, particularly in peat ecosystems. Nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and reported to be catalyzed by the bacterium "Candidatus Methylomirabilis oxyfera," which is affiliated with the NC10 phylum. So far, several "Ca. Methylomirabilis oxyfera" enrichment cultures have been obtained using a limited number of freshwater sediments or wastewater treatment sludge as the inoculum. In this study, using stable isotope measurements and porewater profiles, we investigated the potential of n-damo in a minerotrophic peatland in the south of the Netherlands that is infiltrated by nitrate-rich ground water. Methane and nitrate profiles suggested that all methane produced was oxidized before reaching the oxic layer, and NC10 bacteria could be active in the transition zone where countergradients of methane and nitrate occur. Quantitative PCR showed high NC10 bacterial cell numbers at this methane-nitrate transition zone. This soil section was used to enrich the prevalent NC10 bacteria in a continuous culture supplied with methane and nitrite at an in situ pH of 6.2. An enrichment of nitrite-reducing methanotrophic NC10 bacteria was successfully obtained. Phylogenetic analysis of retrieved 16S rRNA and pmoA genes showed that the enriched bacteria were very similar to the ones found in situ and constituted a new branch of NC10 bacteria with an identity of less than 96 and 90% to the 16S rRNA and pmoA genes of "Ca. Methylomirabilis oxyfera," respectively. The results of this study expand our knowledge of the diversity and distribution of NC10 bacteria in the environment and highlight their potential contribution to nitrogen and methane cycles.
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118
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Wang Y, Zhu G, Harhangi HR, Zhu B, Jetten MS, Yin C, Op den Camp HJ. Co-occurrence and distribution of nitrite-dependent anaerobic ammonium and methane-oxidizing bacteria in a paddy soil. FEMS Microbiol Lett 2012; 336:79-88. [DOI: 10.1111/j.1574-6968.2012.02654.x] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/31/2012] [Accepted: 08/07/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yu Wang
- State Key Laboratory of Environmental Aquatic Quality; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing; China
| | - Guibing Zhu
- State Key Laboratory of Environmental Aquatic Quality; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing; China
| | - Harry R. Harhangi
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen; The Netherlands
| | - Baoli Zhu
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen; The Netherlands
| | - Mike S.M. Jetten
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen; The Netherlands
| | - Chengqing Yin
- State Key Laboratory of Environmental Aquatic Quality; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing; China
| | - Huub J.M. Op den Camp
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen; The Netherlands
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119
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Shen LD, He ZF, Zhu Q, Chen DQ, Lou LP, Xu XY, Zheng P, Hu BL. Microbiology, ecology, and application of the nitrite-dependent anaerobic methane oxidation process. Front Microbiol 2012; 3:269. [PMID: 22905032 PMCID: PMC3408237 DOI: 10.3389/fmicb.2012.00269] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 07/10/2012] [Indexed: 01/11/2023] Open
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo), which couples the anaerobic oxidation of methane to denitrification, is a recently discovered process mediated by "Candidatus Methylomirabilis oxyfera." M. oxyfera is affiliated with the "NC10" phylum, a phylum having no members in pure culture. Based on the isotopic labeling experiments, it is hypothesized that M. oxyfera has an unusual intra-aerobic pathway for the production of oxygen via the dismutation of nitric oxide into dinitrogen gas and oxygen. In addition, the bacterial species has a unique ultrastructure that is distinct from that of other previously described microorganisms. M. oxyfera-like sequences have been recovered from different natural habitats, suggesting that the n-damo process potentially contributes to global carbon and nitrogen cycles. The n-damo process is a process that can reduce the greenhouse effect, as methane is more effective in heat-trapping than carbon dioxide. The n-damo process, which uses methane instead of organic matter to drive denitrification, is also an economical nitrogen removal process because methane is a relatively inexpensive electron donor. This mini-review summarizes the peculiar microbiology of M. oxyfera and discusses the potential ecological importance and engineering application of the n-damo process.
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Affiliation(s)
- Li-Dong Shen
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
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Kojima H, Tsutsumi M, Ishikawa K, Iwata T, Mußmann M, Fukui M. Distribution of putative denitrifying methane oxidizing bacteria in sediment of a freshwater lake, Lake Biwa. Syst Appl Microbiol 2012; 35:233-8. [DOI: 10.1016/j.syapm.2012.03.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/07/2012] [Accepted: 03/08/2012] [Indexed: 10/28/2022]
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Luesken FA, Wu ML, Op den Camp HJM, Keltjens JT, Stunnenberg H, Francoijs KJ, Strous M, Jetten MSM. Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis. Environ Microbiol 2012; 14:1024-34. [PMID: 22221911 DOI: 10.1111/j.1462-2920.2011.02682.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
'Candidatus Methylomirabilis oxyfera' is a denitrifying methanotroph that performs nitrite-dependent anaerobic methane oxidation through a newly discovered intra-aerobic pathway. In this study, we investigated the response of a M. oxyfera enrichment culture to oxygen. Addition of either 2% or 8% oxygen resulted in an instant decrease of methane and nitrite conversion rates. Oxygen exposure also led to a deviation in the nitrite to methane oxidation stoichiometry. Oxygen-uptake and inhibition studies with cell-free extracts displayed a change from cytochrome c to quinol as electron donor after exposure to oxygen. The change in global gene expression was monitored by deep sequencing of cDNA using Illumina technology. After 24 h of oxygen exposure, transcription levels of 1109 (out of 2303) genes changed significantly when compared with the anoxic period. Most of the genes encoding enzymes of the methane oxidation pathway were constitutively expressed. Genes from the denitrification pathway, with exception of one of the putative nitric oxide reductases, norZ2, were severely downregulated. The majority of known genes involved in the vital cellular functions, such as nucleic acid and protein biosynthesis and cell division processes, were downregulated. The alkyl hydroperoxide reductase, ahpC, and genes involved in the synthesis/repair of the iron-sulfur clusters were among the few upregulated genes. Further, transcription of the pmoCAB genes of aerobic methanotrophs present in the non-M. oxyfera community were triggered by the presence of oxygen. Our results show that oxygen-exposed cells of M. oxyfera were under oxidative stress and that in spite of its oxygenic capacity, exposure to microoxic conditions has an overall detrimental effect.
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Affiliation(s)
- Francisca A Luesken
- Department of Microbiology, Radboud University Nijmegen, Institute for Water and Wetland Research, Nijmegen, The Netherlands
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Combined anaerobic ammonium and methane oxidation for nitrogen and methane removal. Biochem Soc Trans 2011; 39:1822-5. [DOI: 10.1042/bst20110704] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Anammox (anaerobic ammonium oxidation) is an environment-friendly and cost-efficient nitrogen-removal process currently applied to high-ammonium-loaded wastewaters such as anaerobic digester effluents. In these wastewaters, dissolved methane is also present and should be removed to prevent greenhouse gas emissions into the environment. Potentially, another recently discovered microbial pathway, n-damo (nitrite-dependent anaerobic methane oxidation) could be used for this purpose. In the present paper, we explore the feasibility of simultaneously removing methane and ammonium anaerobically, starting with granules from a full-scale anammox bioreactor. We describe the development of a co-culture of anammox and n-damo bacteria using a medium containing methane, ammonium and nitrite. The results are discussed in the context of other recent studies on the application of anaerobic methane- and ammonia-oxidizing bacteria for wastewater treatment.
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Ultrastructure of the denitrifying methanotroph "Candidatus Methylomirabilis oxyfera," a novel polygon-shaped bacterium. J Bacteriol 2011; 194:284-91. [PMID: 22020652 DOI: 10.1128/jb.05816-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
"Candidatus Methylomirabilis oxyfera" is a newly discovered denitrifying methanotroph that is unrelated to previously known methanotrophs. This bacterium is a member of the NC10 phylum and couples methane oxidation to denitrification through a newly discovered intra-aerobic pathway. In the present study, we report the first ultrastructural study of "Ca. Methylomirabilis oxyfera" using scanning electron microscopy, transmission electron microscopy, and electron tomography in combination with different sample preparation methods. We observed that "Ca. Methylomirabilis oxyfera" cells possess an atypical polygonal shape that is distinct from other bacterial shapes described so far. Also, an additional layer was observed as the outermost sheath, which might represent a (glyco)protein surface layer. Further, intracytoplasmic membranes, which are a common feature among proteobacterial methanotrophs, were never observed under the current growth conditions. Our results indicate that "Ca. Methylomirabilis oxyfera" is ultrastructurally distinct from other bacteria by its atypical cell shape and from the classical proteobacterial methanotrophs by its apparent lack of intracytoplasmic membranes.
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Simultaneous nitrite-dependent anaerobic methane and ammonium oxidation processes. Appl Environ Microbiol 2011; 77:6802-7. [PMID: 21841030 DOI: 10.1128/aem.05539-11] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrite-dependent anaerobic oxidation of methane (n-damo) and ammonium (anammox) are two recently discovered processes in the nitrogen cycle that are catalyzed by n-damo bacteria, including "Candidatus Methylomirabilis oxyfera," and anammox bacteria, respectively. The feasibility of coculturing anammox and n-damo bacteria is important for implementation in wastewater treatment systems that contain substantial amounts of both methane and ammonium. Here we tested this possible coexistence experimentally. To obtain such a coculture, ammonium was fed to a stable enrichment culture of n-damo bacteria that still contained some residual anammox bacteria. The ammonium supplied to the reactor was consumed rapidly and could be gradually increased from 1 to 20 mM/day. The enriched coculture was monitored by fluorescence in situ hybridization and 16S rRNA and pmoA gene clone libraries and activity measurements. After 161 days, a coculture with about equal amounts of n-damo and anammox bacteria was established that converted nitrite at a rate of 0.1 kg-N/m(3)/day (17.2 mmol day(-1)). This indicated that the application of such a coculture for nitrogen removal may be feasible in the near future.
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