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Ahmadi F, Lackner M. Recent findings in methanotrophs: genetics, molecular ecology, and biopotential. Appl Microbiol Biotechnol 2024; 108:60. [PMID: 38183483 DOI: 10.1007/s00253-023-12978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/08/2023] [Accepted: 10/01/2023] [Indexed: 01/08/2024]
Abstract
The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.
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Affiliation(s)
- Fatemeh Ahmadi
- School of Agriculture and Environment, University of Western Australia, Crawley, 6009, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, 7001, Australia
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Ding J, Liu F, Zeng J, Gu H, Zhang D, Yang X, Wu B, Shu L, He Z, Wang C. Homologous recombination and gene-specific selection co-shape the vertical nucleotide diversity of mangrove sediment microbial populations. Ecol Evol 2024; 14:e70040. [PMID: 39021733 PMCID: PMC11254452 DOI: 10.1002/ece3.70040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
Mangrove sediments host a diverse array of microbial populations and are characterized by high heterogeneity along their vertical depths. However, the genetic diversity within these populations is largely unknown, hindering our understanding of their adaptive evolution across the sediment depths. To elucidate their genetic diversity, we utilized metagenome sequencing to identify 16 high-frequency microbial populations comprised of two archaea and 14 bacteria from mangrove sediment cores (0-100 cm, with 10 depths) in Qi'ao Island, China. Our analysis of the genome-wide genetic variation revealed extensive nucleotide diversity in the microbial populations. The genes involved in the transport and the energy metabolism displayed a high nucleotide diversity (HND; 0.0045-0.0195; an indicator of shared minor alleles with the microbial populations). By tracking the processes of homologous recombination, we found that each microbial population was subjected to different purification selection levels at different depths (44.12% genes). This selection resulted in significant differences in synonymous/non-synonymous mutation ratio between 0-20 and 20-100 cm layers, indicating the adaptive evolutionary process of microbial populations. Furthermore, our assessment of differentiation in the allele frequencies between these two layers showed that the functional genes involved in the metabolic processes of amino acids or cofactors were highly differential in more than half of them. Together, we showed that the nucleotide diversity of microbial populations was shaped by homologous recombination and gene-specific selection, finally resulting in the stratified differentiation occurring between 0-20 and 20-100 cm. These results enhance our cognition of the microbial adaptation mechanisms to vertical environmental changes during the sedimentation process of coastal blue carbon ecosystems.
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Affiliation(s)
- Jijuan Ding
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Fei Liu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Jiaxiong Zeng
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Hang Gu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Dandan Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Xueqin Yang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Bo Wu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Cheng Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
- Key Laboratory of Watershed Earth Surface Processes and Ecological SecurityZhejiang Normal UniversityJinhuaChina
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Xu Y, Liu D, Yuan X, Yang Y, Li T, Deng Y, Wang Y. Deciphering the spatial heterogeneity of groundwater arsenic in Quaternary aquifers of the Central Yangtze River Basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172405. [PMID: 38626822 DOI: 10.1016/j.scitotenv.2024.172405] [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: 01/22/2024] [Revised: 03/29/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024]
Abstract
Significant spatial variability of groundwater arsenic (As) concentrations in South/Southeast Asia is closely associated with sedimentogenesis and biogeochemical cycling processes. However, the role of fine-scale differences in biogeochemical processes under similar sedimentological environments in controlling the spatial heterogeneity of groundwater As concentrations is poorly understood. Within the central Yangtze Basin, dissolved organic matter (DOM) and microbial functional communities in the groundwater and solid-phase As-Fe speciation in Jianghan Plain (JHP) and Jiangbei Plain (JBP) were compared to reveal mechanisms related to the spatial heterogeneity of groundwater As concentration. The optical signatures of DOM showed that low molecular terrestrial fulvic-like with highly humified was predominant in the groundwater of JHP, while terrestrial humic-like and microbial humic-like with high molecular weight were predominant in the groundwater of JBP. The inorganic carbon isotope, microbial functional communities, and solid-phase As-Fe speciation suggest that the primary process controlling As accumulation in JHP groundwater system is the degradation of highly humified OM by methanogens, which drive the reductive dissolution of amorphous iron oxides. While in JBP groundwater systems, anaerobic methane-oxidizing microorganisms (AOM) coupled with fermentative bacteria, iron reduction bacteria (IRB), and sulfate reduction bacteria (SRB) utilize low molecular weight DOM degradation to drive biotic/abiotic reduction of Fe oxides, further facilitating the formation of carbonate associated Fe and crystalline Fe oxides, resulting in As release into groundwater. Different biogeochemical cycling processes determine the evolution of As-enriched aquifer systems, and the coupling of multiple processes involving organic matter transformation‑iron cycling‑sulfur cycling-methane cycling leads to heterogeneity in the spatial distribution of As concentrations in groundwater. These findings provide new perspectives to decipher the spatial variability of As concentrations in groundwater.
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Affiliation(s)
- Yuxiao Xu
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China; School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Di Liu
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China; School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Xiaofang Yuan
- Geological Survey, China University of Geosciences, Wuhan 430074, China
| | - Yijun Yang
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China; School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Tian Li
- Geological Survey, China University of Geosciences, Wuhan 430074, China
| | - Yamin Deng
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China; School of Environmental Studies, China University of Geosciences, Wuhan 430078, China.
| | - Yanxin Wang
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China; School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
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Bromfield JI, Zaugg J, Straw RC, Cathie J, Krueger A, Sinha D, Chandra J, Hugenholtz P, Frazer IH. Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere 2024; 9:e0055523. [PMID: 38530017 PMCID: PMC11036808 DOI: 10.1128/msphere.00555-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/03/2024] [Indexed: 03/27/2024] Open
Abstract
Human cutaneous squamous cell carcinomas (SCCs) and actinic keratoses (AK) display microbial dysbiosis with an enrichment of staphylococcal species, which have been implicated in AK and SCC progression. SCCs are common in both felines and canines and are often diagnosed at late stages leading to high disease morbidity and mortality rates. Although recent studies support the involvement of the skin microbiome in AK and SCC progression in humans, there is no knowledge of this in companion animals. Here, we provide microbiome data for SCC in cats and dogs using culture-independent molecular profiling and show a significant decrease in microbial alpha diversity on SCC lesions compared to normal skin (P ≤ 0.05). Similar to human skin cancer, SCC samples had an elevated abundance of staphylococci relative to normal skin-50% (6/12) had >50% staphylococci, as did 16% (4/25) of perilesional samples. Analysis of Staphylococcus at the species level revealed an enrichment of the pathogenic species Staphylococcus felis in cat SCC samples, a higher prevalence of Staphylococcus pseudintermedius in dogs, and a higher abundance of Staphylococcus aureus compared to normal skin in both companion animals. Additionally, a comparison of previously published human SCC and perilesional samples against the present pet samples revealed that Staphylococcus was the most prevalent genera across human and companion animals for both sample types. Similarities between the microbial profile of human and cat/dog SCC lesions should facilitate future skin cancer research. IMPORTANCE The progression of precancerous actinic keratosis lesions (AK) to cutaneous squamous cell carcinoma (SCC) is poorly understood in humans and companion animals, despite causing a significant burden of disease. Recent studies have revealed that the microbiota may play a significant role in disease progression. Staphylococcus aureus has been found in high abundance on AK and SCC lesions, where it secretes DNA-damaging toxins, which could potentiate tumorigenesis. Currently, a suitable animal model to investigate this relationship is lacking. Thus, we examined the microbiome of cutaneous SCC in pets, revealing similarities to humans, with increased staphylococci and reduced commensals on SCC lesions and peri-lesional skin compared to normal skin. Two genera that were in abundance in SCC samples have also been found in human oral SCC lesions. These findings suggest the potential suitability of pets as a model for studying microbiome-related skin cancer progression.
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Affiliation(s)
- Jacoba I. Bromfield
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, Australia
| | - Rodney C. Straw
- Brisbane Veterinary Specialist Centre and the Australian Animal Cancer Foundation, Albany Creek, Queensland, Australia
| | - Julia Cathie
- Brisbane Veterinary Specialist Centre and the Australian Animal Cancer Foundation, Albany Creek, Queensland, Australia
| | - Annika Krueger
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Debottam Sinha
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Janin Chandra
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, Australia
| | - Ian H. Frazer
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
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Fan SQ, Wen WR, Xie GJ, Lu Y, Nie WB, Liu BF, Xing DF, Ma J, Ren NQ. Revisiting the Engineering Roadmap of Nitrate/Nitrite-Dependent Anaerobic Methane Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:20975-20991. [PMID: 37931214 DOI: 10.1021/acs.est.3c02806] [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: 11/08/2023]
Abstract
Nitrate/nitrite-dependent anaerobic oxidation of methane (n-DAMO) is a recently discovered process, which provides a sustainable perspective for simultaneous nitrogen removal and greenhouse gas emission (GHG) mitigation by using methane as an electron donor for denitrification. However, the engineering roadmap of the n-DAMO process is still unclear. This work constitutes a state-of-the-art review on the classical and most recently discovered metabolic mechanisms of the n-DAMO process. The versatile combinations of the n-DAMO process with nitrification, nitritation, and partial nitritation for nitrogen removal are also clearly presented and discussed. Additionally, the recent advances in bioreactor development are systematically reviewed and evaluated comprehensively in terms of methane supply, biomass retention, membrane requirement, startup time, reactor performance, and limitations. The key issues including enrichment and operation strategy for the scaling up of n-DAMO-based processes are also critically addressed. Moreover, the challenges inherent to implementing the n-DAMO process in practical applications, including application scenario recognition, GHG emission mitigation, and operation under realistic conditions, are highlighted. Finally, prospects as well as opportunities for future research are proposed. Overall, this review provides a roadmap for potential applications and further development of the n-DAMO process in the field of wastewater treatment.
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Affiliation(s)
- Sheng-Qiang Fan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wan-Ru Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Wen-Bo Nie
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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Frank J, Zhang X, Marcellin E, Yuan Z, Hu S. Salinity effect on an anaerobic methane- and ammonium-oxidising consortium: Shifts in activity, morphology, osmoregulation and syntrophic relationship. WATER RESEARCH 2023; 242:120090. [PMID: 37331229 DOI: 10.1016/j.watres.2023.120090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
Nitrate-dependent anaerobic methane oxidation (AOM) is a microbial process of both ecological significance for global methane mitigation and application potential for wastewater treatment. It is mediated by organisms belonging to the archaeal family 'Candidatus Methanoperedenaceae', which have so far mainly been found in freshwater environments. Their potential distribution in saline environments and their physiological responses to salinity variation were still poorly understood. In this study, the responses of the freshwater 'Candidatus Methanoperedens nitroreducens'-dominated consortium to different salinities were investigated using short- and long-term setups. Short-term exposure to salt stress significantly affected nitrate reduction and methane oxidation activities over the tested concentration range of 15-200‰ NaCl, and 'Ca. M. nitroreducens' showed the higher tolerance to high salinity stress than its partner of anammox bacteria. At high salinity concentration, near marine conditions of 37‰, the target organism 'Ca. M. nitroreducens' showed stabilized nitrate reduction activity of 208.5 µmol day-1 gCDW-1 in long-term bioreactors over 300 days, in comparison to 362.9 and 334.3 µmol day-1 gCDW-1 under low-salinity conditions (1.7‰ NaCl) and control conditions (∼15‰ NaCl). Different partners of 'Ca. M. nitroreducens' evolved in the consortia with three different salinity conditions, suggesting the different syntrophic mechanisms shaped by changes in salinity. A new syntrophic relationship between 'Ca. M. nitroreducens' and Fimicutes and/or Chloroflexi denitrifying populations was identified under the marine salinity condition. Metaproteomic analysis shows that the salinity changes lead to higher expression of response regulators and selective ion (Na+/H+) channeling proteins that can regulate the osmotic pressure between the cell and its environment. The reverse methanogenesis pathway was, however, not impacted. The finding of this study has important implications for the ecological distribution of the nitrate-dependent AOM process in marine environments and the potential of this biotechnological process for the treatment of high-salinity industrial wastewater.
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Affiliation(s)
- Joshua Frank
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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Peres FV, Paula FS, Bendia AG, Gontijo JB, de Mahiques MM, Pellizari VH. Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales. Sci Rep 2023; 13:12782. [PMID: 37550336 PMCID: PMC10406867 DOI: 10.1038/s41598-023-39415-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
Continental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0-2 cm) and subsurface (18-20 or 22-24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1-5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1-5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1-5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.
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Affiliation(s)
- Francielli V Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil.
| | - Amanda G Bendia
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Centre for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Michel M de Mahiques
- Department of Physical, Chemical and Geological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Vivian H Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
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Yun H, Liang B, He Z, Li M, Zong S, Wang Z, Ge B, Zhang P, Li X, Wang A. Insights into methanogenesis of mesophilic-psychrophilic varied anaerobic digestion of municipal sludge with antibiotic stress. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 331:117278. [PMID: 36634423 DOI: 10.1016/j.jenvman.2023.117278] [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: 10/13/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 06/17/2023]
Abstract
Methane production through anaerobic digestion (AD) of municipal sludge is economic and eco-friendly, which is commonly affected by temperature and pollutants residues. However, little is known about methanogenesis in psychrophilic AD (PAD) with temperature variations that simulating seasonal variations and with antibiotic stress. Here, two groups of AD systems with oxytetracycline (OTC) were operated with temperature maintained at 35 °C and 15 °C or variation to explore the influence to methanogenesis. The acetic acid was noticeably accumulated in OTC groups initially (P < 0.001). Methane production was noticeably inhibited initially in PAD with OTC, but had been stimulated later at 35 °C. The dominant acetoclastic methanogens Methanosaeta gradually decreased to 15.48% and was replaced by methylotrophic Methanomethylovorans (73.43%) in PAD with OTC. Correspondingly, the abundances of functional genes related to methylotrophic methanogenesis were also higher in these groups. Besides, genes involving in methane oxidation had over 50 times higher abundances in PAD with OTC groups in the second phase. Further investigation is essential to understand the main dynamics of methanogenesis in PAD and to clear the related molecular mechanism for future methane production regulation in sludge systems.
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Affiliation(s)
- Hui Yun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Lanzhou, 730020, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Zhangwei He
- Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Minghan Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150001, China
| | - Simin Zong
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhenfei Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Lanzhou, 730020, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Bin Ge
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Lanzhou, 730020, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Peng Zhang
- Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Lanzhou, 730020, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Lanzhou, 730020, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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9
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Chen J, Zhou Z, Gu JD. Distribution pattern of N-damo bacteria along an anthropogenic nitrogen input gradient from the coastal mangrove wetland to the South China sea sediments. MARINE ENVIRONMENTAL RESEARCH 2022; 181:105739. [PMID: 36084374 DOI: 10.1016/j.marenvres.2022.105739] [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: 07/23/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Microbial nitrite-dependent anaerobic methane oxidation (n-damo) process is important for mitigating methane emission and anthropogenic nitrogen inputs in the marine environment. However, the distribution pattern of n-damo bacteria along an anthropogenic N-input gradient from the coastal wetland to the pristine South China Sea is poorly understood. This study investigated the diversity and abundance of n-damo bacteria in samples collected along a N-input gradient from Mai Po (MP) mangrove wetland sediments of the Pearl River Estuary (PRE) to the deep ocean sediments of the South China Sea (SCS). Retrieved 16S rDNA sequences showed a shift of n-damo community composition of complex structures with both freshwater and marine n-damo lineages in MP intertidal sediments to marine dominated characteristic in SCS sediments. The observed variation of Shannon and Chao1 indexes of n-damo bacteria shared a similar trend of a decrease at first followed by an increase along the targeting gradient with previously investigated methanogens, anaerobic methanotrophic archaea, ammonia-oxidizing archaea and ammonia-oxidizing bacteria, but had a reverse pattern with anammox bacteria. The community structure of pmoA gene sequences contained freshwater lineages only in SCS continental shelf sediments closer to the PRE, and turned to group with other marine samples in deeper and pristine sediments. Results suggested that n-damo bacteria might be a major contributor to anaerobic denitrification in the SCS sediments because their abundances were much higher than previously studied anammox bacteria in the same sample set. The distribution pattern of n-damo bacterial diversity, richness and abundance along the anthropogenic N-input gradient implies that they could be used as a bio-indicator for monitoring the anthropogenic/terrestrial inputs in marine environments.
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Affiliation(s)
- Jing Chen
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, PR China; Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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10
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Li C, Ding A, Guo J, Song F, Lu P. Response of denitrifying anaerobic methane oxidation enrichment to salinity stress: Process and microbiology. ENVIRONMENTAL RESEARCH 2022; 214:114069. [PMID: 35964668 DOI: 10.1016/j.envres.2022.114069] [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: 06/19/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) is a novel biological process which could decrease nitrogen pollution and methane emission simultaneously in wastewater treatment. Salinity as a key environmental factor has important effects on microbial community and activity, however, it remains unclear for DAMO microorganisms. In this study, response of the enrichment of DAMO archaea and bacteria to different salinity was investigated from the aspect of process and microbiology. The results showed that the increasing salinity from 0.14% to 25% evidently deteriorated DAMO process, with the average removal rate of nitrate and methane decreased from 1.91 mg N/(L·d) to 0.07 mg N/(L·d) and 3.22 μmol/d to 0.59 μmol/d, respectively. The observed IC50 value of salinity on the DAMO culture was 1.73%. Further microbial analyses at the gene level suggested that the relative abundance of DAMO archaea in the enrichment decreased to 46%, 39%, 38% and 33% of the initial value. However, DAMO bacteria suffered less impact with the relative abundance maintaining over 75% of the initial value (except 1% salinity). In functional genes of DAMO bacteria, pmoA, decreased gradually from 100% to 86%, 43%, 15% and 2%, while mcrA (DAMO archaea) maintained at 67%-97%. This difference probably indicated DAMO bacteria appeared functional inhibition prior to community inhibition, which was opposite for the DAMO archaea. Results above-mentioned concluded that, though the process of nitrate-dependent anaerobic methane oxidation was driven by the couple of DAMO archaea and bacteria, they individually featured different response to high salinity stress. These findings could be helpful for the application of DAMO-based process in high salinity wastewater treatment, and also the understanding to DAMO microorganisms.
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Affiliation(s)
- Chaoyang Li
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Aqiang Ding
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
| | - Junliang Guo
- Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Fuzhong Song
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
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11
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Contreras JA, Valenzuela EI, Quijano G. Nitrate/nitrite-dependent anaerobic oxidation of methane (N-AOM) as a technology platform for greenhouse gas abatement in wastewater treatment plants: State-of-the-art and challenges. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115671. [PMID: 35816965 DOI: 10.1016/j.jenvman.2022.115671] [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: 04/15/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Nitrate/nitrite-dependent anaerobic oxidation of methane (N-AOM) is a metabolic process recently discovered and partially characterized in terms of the microorganisms and pathways involved. The N-AOM process can be a powerful tool for mitigating the impacts of greenhouse gas emissions from wastewater treatment plants by coupling the reduction of nitrate or nitrite with the oxidation of residual dissolved methane. Besides specific anaerobic methanotrophs such as bacteria members of the phylum NC10 and archaea belonging to the lineage ANME-2d, recent reports suggested that other methane-oxidizing bacteria in syntrophy with denitrifiers can also perform the N-AOM process, which facilitates the application of this metabolic process for the oxidation of residual methane under realistic scenarios. This work constitutes a state-of-art review that includes the fundamentals of the N-AOM process, new information on process microbiology, bioreactor configurations, and operating conditions for process implementation in WWTP. Potential advantages of the N-AOM process over aerobic methanotrophic biotechnologies are presented, including the potential interrelation of the N-AOM with other nitrogen removal processes within the WWTP, such as the anaerobic ammonium oxidation. This work also addressed the challenges of this biotechnology towards its application at full scale, identifying and discussing critical research niches.
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Affiliation(s)
- José A Contreras
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro, 76230, Mexico
| | - Edgardo I Valenzuela
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro, 76230, Mexico
| | - Guillermo Quijano
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro, 76230, Mexico.
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12
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Zhu B, Karwautz C, Andrei S, Klingl A, Pernthaler J, Lueders T. A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction. MLIFE 2022; 1:323-328. [PMID: 38818217 PMCID: PMC10989891 DOI: 10.1002/mlf2.12033] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/01/2022] [Accepted: 06/12/2022] [Indexed: 06/01/2024]
Abstract
Methane oxidizing microbes play a key role in reducing the emission of this potent greenhouse gas to the atmosphere. The known versatility of the recently discovered anaerobic Methylomirabilota methanotrophs is limited. Here, we report a novel uncultured Methylomirabilis species, Candidatus Methylomirabilis iodofontis, with the genetic potential of iodate respiration from biofilm in iodine-rich cavern spring water. Star-like cells resembling Methylomirabilis oxyfera were directly observed from the biofilm and a high-quality metagenome-assembled genome (MAG) of Ca. M. iodofontis was assembled. In addition to oxygenic denitrification and aerobic methane oxidation pathways, the M. iodofontis MAG also indicated its iodate-reducing potential, a capability that would enable the bacterium to use iodate other than nitrite as an electron acceptor, a hitherto unrecognized metabolic potential of Methylomirabilota methanotrophs. The results advance the current understanding of the ecophysiology of anaerobic Methylomirabilota methanotrophs and may suggest an additional methane sink, especially in iodate-rich ecosystems.
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Affiliation(s)
- Baoli Zhu
- Key Laboratory of Agro‐Ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
- Department of Plant and Microbial Biology, Limnological StationUniversity of ZurichZurichSwitzerland
| | - Clemens Karwautz
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
- Department of Limnology and Bio‐OceanographyUniversity of ViennaViennaAustria
| | - Stefan Andrei
- Department of Plant and Microbial Biology, Limnological StationUniversity of ZurichZurichSwitzerland
| | - Andreas Klingl
- Biocenter of the LMU MunichPlant Development & Electron MicroscopyPlanegg‐MartinsriedGermany
| | - Jakob Pernthaler
- Department of Plant and Microbial Biology, Limnological StationUniversity of ZurichZurichSwitzerland
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
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13
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Zhou Z, Meng H, Gu W, Li J, Deng M, Gu JD. High-throughput sequencing reveals the main drivers of niche-differentiation of bacterial community in the surface sediments of the northern South China sea. MARINE ENVIRONMENTAL RESEARCH 2022; 178:105641. [PMID: 35594805 DOI: 10.1016/j.marenvres.2022.105641] [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: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 05/16/2023]
Abstract
Studies on marine bacterial communities have revealed endemism in local communities, yet the underlying mechanisms remained elusive. Environmental gradient settings can benefit the straightaway study of community composition changes and the mechanisms explaining them. Here, MiSeq-based 16S rRNA gene sequencing was performed on 12 surface sediment samples from the northern South China Sea (nSCS) revealing that shallow-sea samples had a higher alpha diversity than deep-sea samples, and were differentiated from them significantly based on beta diversity. Temperature, seawater depth, and salinity were the top three influential factors. Bacterial 16S rRNA gene abundance was positively correlated with temperature, and negatively correlated with salinity. Sulfate-reducing bacteria including Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteraceae were enriched in shallow-sea sediments, co-abundant with nitrite-oxidizing Nitrospira and potential sulfur-oxidizing shallow-sea specific Woeseiaceae/JTB255 clade. Meanwhile, the co-existing and co-abundant of marine anammox and n-damo bacteria were enriched in deep-sea sediments, which was firstly evidenced in this study. The global deep-sea cosmopolitans, OM1 clade, and deep-sea specific Woeseiaceae/JTB255 clade were also found enriched in deep-sea sediments of nSCS. The discovery of novel taxa which were differentially enriched in shallow-/deep-sea sediments not only shed light on enigmatic physiological properties and the natural selection mechanism, but also provided the potential ecological-functional links which invoked further genomics-based metabolic characteristics.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Meng
- School of Environment, Nanjing Normal University, 122 Ninghai Road, Nanjing, Jiangsu, 210023, China
| | - Wenjie Gu
- Insitute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences/Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, 66 Jinying Road, Guangzhou, Guangdong, 510640, China
| | - Jing Li
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Maocheng Deng
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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14
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Díaz-Torres O, Lugo-Melchor OY, de Anda J, Pacheco A, Yebra-Montes C, Gradilla-Hernández MS, Senés-Guerrero C. Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season. Front Microbiol 2022; 13:832477. [PMID: 35479621 PMCID: PMC9037096 DOI: 10.3389/fmicb.2022.832477] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake’s water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH4+, and NO3–. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.
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Affiliation(s)
- Osiris Díaz-Torres
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - Ofelia Yadira Lugo-Melchor
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - José de Anda
- Departamento de Tecnologia Ambiental, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Mexico
| | - Adriana Pacheco
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Monterrey, Mexico
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15
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Roldán DM, Carrizo D, Sánchez-García L, Menes RJ. Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica. Front Microbiol 2022; 13:822552. [PMID: 35369426 PMCID: PMC8969513 DOI: 10.3389/fmicb.2022.822552] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH4) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH4 oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH4 gdw–1 day–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH4 oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH4 emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH4 oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.
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Affiliation(s)
- Diego M. Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Daniel Carrizo
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Laura Sánchez-García
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- *Correspondence: Rodolfo Javier Menes,
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16
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Variable Inhibition of Nitrous Oxide Reduction in Denitrifying Bacteria by Different Forms of Methanobactin. Appl Environ Microbiol 2022; 88:e0234621. [PMID: 35285718 DOI: 10.1128/aem.02346-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic methanotrophic activity is highly dependent on copper availability, and methanotrophs have developed multiple strategies to collect copper. Specifically, when copper is limiting (ambient concentrations less than 1 μM), some methanotrophs produce and secret a small modified peptide (less than 1,300 Da) termed methanobactin (MB) that binds copper with high affinity. As MB is secreted into the environment, other microbes that require copper for their metabolism may be inhibited as MB may make copper unavailable; e.g., inhibition of denitrifiers as complete conversion nitrate to dinitrogen involves multiple enzymes, some of which are copper-dependent. Of key concern is inhibition of the copper-dependent nitrous oxide reductase (NosZ), the only known enzyme capable of converting nitrous oxide (N2O) to dinitrogen. Herein, we show that different forms of MB differentially affect copper uptake and N2O reduction by Pseudomonas stutzeri strain DCP-Ps1 (that expresses clade I NosZ) and Dechloromonas aromatica strain RCB (that expresses clade II NosZ). Specifically, in the presence of MB from Methylocystis sp. strain SB2 (SB2-MB), copper uptake and nosZ expression were more significantly reduced than in the presence of MB from Methylosinus trichosporium OB3b (OB3b-MB). Further, N2O accumulation increased more significantly for both P. stutzeri strain DCP-Ps1 and D. aromatica strain RCB in the presence of SB2-MB versus OB3b-MB. These data illustrate that copper competition between methanotrophs and denitrifying bacteria can be significant and that the extent of such competition is dependent on the form of MB that methanotrophs produce. IMPORTANCE Herein, it was demonstrated that the different forms of methanobactin differentially enhance N2O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. This study provides critical information for enhanced understanding of microbe-microbe interactions that are important for the development of better predictive models of net greenhouse gas emissions (i.e., methane and nitrous oxide) that are significantly controlled by microbial activity.
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Song S, Wang X, Wang Y, Li T, Huang J. NO 3- is an important driver of nitrite-dependent anaerobic methane oxidation bacteria and CH 4 fluxes in the reservoir riparian zone. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:16138-16151. [PMID: 34647205 DOI: 10.1007/s11356-021-16914-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (N-DAMO) is an important biological process that combines microbial nitrogen and carbon cycling and is mainly carried out by nitrite-dependent anaerobic methane-oxidizing bacteria. The discovery of this microbial process has changed the conventional view of methane oxidation and nitrogen loss. In this study, the abundance, diversity, and community structure of N-DAMO bacteria were investigated based on high-throughput sequencing and fluorescence quantitative PCR measurements. We examined environmental factors driving the variations of CH4 fluxes and N-DAMO bacterial using correlation analysis and redundancy analysis. We found low CH4 fluxes and abundant N-DAMO bacteria in the riparian zone. After decomposing the effects of single variables and exploring them, NO3- was the only significant factor that significantly correlated with the abundance and richness of the N-DAMO community and gas fluxes (p < 0.05). Under the influence of three different land use types, the increase in NO3- (grassland vs. woodland and sparse woods, + 132.81% and + 106.25%) caused structural changes in the composition of the N-DAMO bacterial community, increasing its abundance (- 9.58% and + 21.19%), thus promoting the oxidation of CH4 and reduced CH4 emissions (+ 4.78% and + 35.63%) from the riparian zone. Appropriate NO3- input helps maintain the existing low methane emission fluxes in the riparian zone of the reservoir.
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Affiliation(s)
- Shuang Song
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Xiaoyan Wang
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, 100048, China.
| | - Yubing Wang
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Tingting Li
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, 100048, China
| | - Jingyu Huang
- College of Resources, Environment and Tourism, Capital Normal University, Beijing, 100048, China
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18
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Gambelli L, Mesman R, Versantvoort W, Diebolder CA, Engel A, Evers W, Jetten MSM, Pabst M, Daum B, van Niftrik L. The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilis lanthanidiphila Bacteria. Front Microbiol 2021; 12:766527. [PMID: 34925275 PMCID: PMC8671808 DOI: 10.3389/fmicb.2021.766527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.
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Affiliation(s)
- Lavinia Gambelli
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands.,Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Rob Mesman
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Christoph A Diebolder
- Netherlands Centre for Electron Nanoscopy (NeCEN), Leiden University, Leiden, Netherlands
| | - Andreas Engel
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands
| | - Wiel Evers
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Department of Chemical Engineering, Delft University of Technology, Delft, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Laura van Niftrik
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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19
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Multispecies populations of methanotrophic Methyloprofundus and cultivation of a likely dominant species from the Iheya North deep-sea hydrothermal field. Appl Environ Microbiol 2021; 88:e0075821. [PMID: 34788070 PMCID: PMC8788690 DOI: 10.1128/aem.00758-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Methyloprofundus clade is represented by uncultivated methanotrophic bacterial endosymbionts of deep-sea bathymodiolin mussels, but only a single free-living species has been cultivated to date. This study reveals the existence of free-living Methyloprofundus variants in the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. A clade-targeted amplicon analysis of the particulate methane monooxygenase gene (pmoA) detected 647 amplicon sequence variants (ASVs) of the Methyloprofundus clade in microbial communities newly formed in in situ colonization systems. Such systems were deployed at colonies of bathymodiolin mussels and a galatheoid crab in diffuse-flow areas. These ASVs were classified into 161 species-like groups. The proportion of the species-like groups representing endosymbionts of mussels was unexpectedly low. A methanotrophic bacterium designated INp10, a likely dominant species in the Methyloprofundus population in this field, was enriched in a biofilm formed in a methane-fed cultivation system operated at 10°C. Genomic characterization with the gene transcription data set of INp10 from the biofilm suggested traits advantageous to niche competition in environments, such as mobility, chemotaxis, biofilm formation, offensive and defensive systems, and hypoxia tolerance. The notable metabolic traits that INp10 shares with some Methyloprofundus members are the use of lanthanide-dependent XoxF as the sole methanol dehydrogenase due to the absence of the canonical MxaFI, the glycolytic pathway using fructose-6-phosphate aldolase instead of fructose-1,6-bisphosphate aldolase, and the potential to perform partial denitrification from nitrate under oxygen-limited conditions. These findings help us better understand the ecological strategies of this possibly widespread marine-specific methanotrophic clade. IMPORTANCE The Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough is characterized by abundant methane derived from organic-rich sediments and diverse chemosynthetic animal species, including those harboring methanotrophic bacterial symbionts, such as bathymodiolin mussels Bathymodiolus japonicus and “Bathymodiolus” platifrons and a galatheoid crab, Shinkaia crosnieri. Symbiotic methanotrophs have attracted significant attention, and yet free-living methanotrophs in this environment have not been studied in detail. We focused on the free-living Methyloprofundus spp. that thrive in this hydrothermal field and identified an unexpectedly large number of species-like groups in this clade. Moreover, we enriched and characterized a methanotroph whose genome sequence indicated that it corresponds to a new species in the genus Methyloprofundus. This species might be a dominant member of the indigenous Methyloprofundus population. New information on free-living Methyloprofundus populations suggests that the hydrothermal field is a promising locale at which to investigate the adaptive capacity and associated genetic diversity of Methyloprofundus spp.
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Guerrero-Cruz S, Vaksmaa A, Horn MA, Niemann H, Pijuan M, Ho A. Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications. Front Microbiol 2021; 12:678057. [PMID: 34054786 PMCID: PMC8163242 DOI: 10.3389/fmicb.2021.678057] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
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Affiliation(s)
- Simon Guerrero-Cruz
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
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21
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Fischer PQ, Sánchez‐Andrea I, Stams AJM, Villanueva L, Sousa DZ. Anaerobic microbial methanol conversion in marine sediments. Environ Microbiol 2021; 23:1348-1362. [PMID: 33587796 PMCID: PMC8048578 DOI: 10.1111/1462-2920.15434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/15/2023]
Abstract
Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.
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Affiliation(s)
- Peter Q. Fischer
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
- Faculty of GeosciencesUtrecht University, Princetonlaan 8aUtrecht3584 CBThe Netherlands
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
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Ding J, Zeng RJ. Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143928. [PMID: 33316511 DOI: 10.1016/j.scitotenv.2020.143928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.
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Affiliation(s)
- Jing Ding
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China; Jiangsu Provincial Key Laboratory of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; CAS Key Laboratory for Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China.
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Zhong Q, Xue D, Chen H, Liu L, He Y, Zhu D, He Z. Structure and distribution of nitrite-dependent anaerobic methane oxidation bacteria vary with water tables in Zoige peatlands. FEMS Microbiol Ecol 2020; 96:5800981. [PMID: 32149349 DOI: 10.1093/femsec/fiaa039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/06/2020] [Indexed: 11/12/2022] Open
Abstract
The recently discovered nitrite-dependent anaerobic methane oxidation (n-damo) is an important methane sink in natural ecosystems performed by NC10 phylum bacteria. However, the effect of water table (WT) gradient due to global change on n-damo bacterial communities is not well studied in peatlands. Here, we analysed the vertical distribution (0-100 cm) of n-damo bacterial communities at three sites with different WTs of the Zoige peatlands in the Qinghai-Tibetan Plateau. Using an n-damo bacterial specific 16S rRNA gene clone library, we obtained 25 operational taxonomic units (OTUs) that could be divided into Groups A, B, C, D and E (dominated by A and B). The dominant group was Group B at the high (OTU14 and OTU20) and intermediate (OTU7 and OTU8) WT sites and Group A was dominant at the low WT site (OTU6 and OTU5). Using high-throughput sequencing, we observed that n-damo bacteria mainly distributed in subsurface soils (50-60 and 20-30 cm), and their relative abundances were higher at the low WT site than at the other two sites. In addition, we found that pH and nitrate were positively correlated with Group A, while total organic carbon, total nitrogen and ammonia were positively associated with Group B. Our study provides new insights into our understanding of the response of n-damo bacteria to WT gradient in peatlands, with important implications for global change.
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Affiliation(s)
- Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.,Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Dan Xue
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, China
| | - Liangfeng Liu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Yixin He
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Dan Zhu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
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Li Y, Wang J, Hua M, Yao X, Zhao Y, Hu J, Xi C, Hu B. Strategy for denitrifying anaerobic methane-oxidizing bacteria growing under the oxygen-present condition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140476. [PMID: 32629252 DOI: 10.1016/j.scitotenv.2020.140476] [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: 04/21/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Denitrifying anaerobic methane oxidizing (DAMO) bacteria are newly discovered microorganisms that use methane as the electron donor to reduce nitrite into dinitrogen. They have potential value on nitrogen removal from wastewater. However, the oxygen exposure in engineering is considered one of the bottlenecks for DAMO engineering application. In this work, we cultured DAMO bacteria under oxic and anoxic conditions in a gas-lift sequencing batch reactor (GLSBR) to explore DAMO bacterial response to oxygen stress. Under oxic conditions (7.5-8 mg O2/L), the extension of hydraulic retention time (HRT) from 2 days to 4 days increased DAMO bacterial abundance by 3.8 times. Under anoxic conditions (0.2-0.5 mg O2/L), DAMO bacterial abundance increased by 30.1 times and were kept over 2.0 × 1011 copies g-1 wet sludge. During the enrichment, microbial aggregates were formed and DAMO bacteria tended to be distributed inside the aggregates. Notably, aerobic methanotrophs existed in the whole process, capable of consuming oxygen and providing a suitable environment for DAMO bacterial growth. Finally, DAMO bacteria were enriched and the relative abundance was 16.16%. This work provides new insights into DAMO bacterial enrichment and their application in wastewater treatment.
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Affiliation(s)
- Yufen Li
- Department of Environmental Engineering, College of Environmental &Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiaqi Wang
- Department of Environmental Engineering, College of Environmental &Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Miaolian Hua
- Department of Environmental Engineering, College of Environmental &Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiangwu Yao
- Department of Environmental Engineering, College of Environmental &Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, College of Environmental &Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiajie Hu
- Department of Environmental Engineering, College of Environmental &Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Baolan Hu
- Department of Environmental Engineering, College of Environmental &Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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Zhang M, Huang JC, Sun S, Rehman MMU, He S. Depth-specific distribution and significance of nitrite-dependent anaerobic methane oxidation process in tidal flow constructed wetlands used for treating river water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:137054. [PMID: 32036140 DOI: 10.1016/j.scitotenv.2020.137054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Tidal flow constructed wetlands (TF CWs) have been considered an effective approach to treat contaminated river water, as well as a significant role in global matter cycles, especially for carbon and nitrogen. Notably, it has been thought that methane oxidation was completely catalyzed by the aerobic process, ignoring the anaerobic methane oxidation, such as the nitrite-dependent anaerobic methane oxidation (n-damo) process. In our current work, therefore, we used molecular and stable isotopes to investigate the biodiversity, quantity and potential rate of n-damo bacteria in the TF CWs located in the Xisha Wetland Park in the Yangtze River estuary, China. The results revealed that n-damo process was active in the collected soil cores, with a decreasing trend along water depths and rates ranging from 8.48 to 23.45 nmol CO2 g-1 dry soil d-1. The n-damo bacterial contributions to CH4 oxidation and N2 production in TF CWs reached 9.49-26.26% and 20.73-47.11%, respectively, suggesting that n-damo bacteria was an important nitrogen and methane sink in the TF CWs, but had been previously overlooked. The copy numbers of total bacterial 16S rRNA and pmoA genes were 1.84-11.21 × 109 and 0.59-2.72 × 106 copies g-1 ds, respectively, as the higher abundance was found in the soil at lower water levels during tidal submergence. Diverse n-damo bacterial 16S rRNA gene sequences belonged to group B, C and D were measured, and it was found that group B and C were the most frequently measured n-damo clusters in the TF CWs. In addition, nitrite was the key factor regulating the n-damo bacterial distribution in the TF CWs. This study would broaden our horizons and help us better understand the nitrogen and methane cycles in tidal ecosystems.
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Affiliation(s)
- Manping Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jung-Chen Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Shanshan Sun
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Muhammad Muneeb Ur Rehman
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
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Wang W, Zhang RC, Huang ZQ, Chen C, Xu XJ, Zhou X, Yin TM, Wang AJ, Lee DJ, Ren NQ. Performance of a novel IAHD-DSR process with methane and sulfide as co-electron donors. JOURNAL OF HAZARDOUS MATERIALS 2020; 386:121657. [PMID: 31784129 DOI: 10.1016/j.jhazmat.2019.121657] [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: 09/02/2019] [Revised: 11/09/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
A novel integrated autotrophic and heterotrophic denitrification- denitrifying sulfide removal (IAHD-DSR) process was established in this study for biogas desulfurization to simultaneously remove nitrogen in wastewater. The study demonstrated that the system could utilize methane and sulfide as co-electron donors to replace organic carbon source in IAHD process. Three batch tests (B1, B2 and B3) were set up with IAHD sludge to explore how the novel process works. According to mass balance in B2, methane oxidation and sulfide oxidation contributed 18.75 % and 71.25 % to nitrate removal, respectively; however, the contribution of methane oxidation to total nitrogen (TN) removal reached 84.36 %. Sulfide was mainly responsible for the reduction of nitrate to nitrite, while the methane was for nitrite to nitrogen gas in the presence of insufficient sulfide as electron donors. The TN removal in B2 was almost the same as in normal IAHD-DSR process B3-C. The functional genes mcrA and pmoA responsible for methane oxidation were detected in all three batches, with the abundance of 2.23 ×106 copies/(g dry soil) for mcrA in B1 being the highest in three batches. The sulfide addition in B2 increased the abundance of gene pmoA, indicating the enhancement of nitrite reduction coupled with methane oxidation.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China
| | - Ruo-Chen Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China
| | - Zi-Qing Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China.
| | - Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China
| | - Xu Zhou
- Engineering Laboratory of Microalgal Bioenergy, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Tian-Ming Yin
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, HeiLongjiang Province 150090, China.
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Hu J, Liu S, Yang W, He Z, Wang J, Liu H, Zheng P, Xi C, Ma F, Hu B. Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone. MICROBIAL ECOLOGY 2019; 78:555-564. [PMID: 30903203 DOI: 10.1007/s00248-019-01359-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (107-108amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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Geochemical Evidence of Metal-Driven Anaerobic Oxidation of Methane in the Shenhu Area, the South China Sea. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16193559. [PMID: 31547583 PMCID: PMC6801726 DOI: 10.3390/ijerph16193559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/04/2019] [Accepted: 09/10/2019] [Indexed: 11/16/2022]
Abstract
Anaerobic oxidation of methane (AOM) is a common biochemical process in the ocean and it plays an important role in global climate change, elemental circulation, and atmospheric evolution over geological time. In this paper, we analyzed of δ34S, Fe, Mn, Ca/Ti, and Sr/Ti ratios, and the date of carbon and sulfur from the site SH3 of Shenhu area. Result showed that (1) 0-6 mbsf (meter blow the sea floor) was mainly affected by OSR (anaerobic oxidation of organic matters) and 7-15 mbsf was a paleo-SMTZ (sulfate-methane transition zone) position. The modern SMTZ was mainly distributed at 19-25 mbsf. The barium sulfate precipitation above the modern SMTZ indicating that the current methane leakage was stable and lasted longer during geological history. (2) By studying the change of magnetic and the different carbonate minerals, results showed that there were two AOM stages. During the early stage, Fe2+ were mainly produced by sulfide abiotic reductive dissolution. During the later stage, Fe2+ were mainly produced by the metal-AOM. (3) Study of the mineral characteristics of the paleo-SMTZ and the modern SMTZ showed that the modern SMTZ carbonate minerals were mainly low-Mg calcite and aragonite, while the paleo-SMTZ carbon minerals were mainly high Mg minerals. The reason for this difference is that the modern SMTZ layer was only experienced the first stage of anaerobic oxidation of methane. In the paleo-SMTZ layer, it has experienced two stage of anaerobic oxidation of methane. During the last stage of metal-AOM, the low Mg carbonate minerals were converted into high Mg carbonate minerals. This research confirms the presence of metal-driven methane anaerobic oxidation at the bottom of sulfate-driven methane anaerobic oxidation and during the metal-driven methane anaerobic oxidation, methane and metal oxides or hydroxides would couple to convert the in situ metal oxides or hydroxides into metal ions, meanwhile the phosphorus adsorbed on the surface of the metal oxides is released into adjacent pore water, and convert to new P-bearing minerals under suitable conditions.
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Versantvoort W, Guerrero-Castillo S, Wessels HJCT, van Niftrik L, Jetten MSM, Brandt U, Reimann J, Kartal B. Complexome analysis of the nitrite-dependent methanotroph Methylomirabilis lanthanidiphila. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:734-744. [PMID: 31376363 DOI: 10.1016/j.bbabio.2019.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 01/31/2023]
Abstract
The atmospheric concentration of the potent greenhouse gases methane and nitrous oxide (N2O) has increased drastically during the last century. Methylomirabilis bacteria can play an important role in controlling the emission of these two gases from natural ecosystems, by oxidizing methane to CO2 and reducing nitrite to N2 without producing N2O. These bacteria have an anaerobic metabolism, but are proposed to possess an oxygen-dependent pathway for methane activation. Methylomirabilis bacteria reduce nitrite to NO, and are proposed to dismutate NO into O2 and N2 by a putative NO dismutase (NO-D). The O2 produced in the cell can then be used to activate methane by a particulate methane monooxygenase. So far, the metabolic model of Methylomirabilis bacteria was based mainly on (meta)genomics and physiological experiments. Here we applied a complexome profiling approach to determine which of the proposed enzymes are actually expressed in Methylomirabilis lanthanidiphila. To validate the proposed metabolic model, we focused on enzymes involved in respiration, as well as nitrogen and carbon transformation. All complexes suggested to be involved in nitrite-dependent methane oxidation, were identified in M. lanthanidiphila, including the putative NO-D. Furthermore, several complexes involved in nitrate reduction/nitrite oxidation and NO reduction were detected, which likely play a role in detoxification and redox homeostasis. In conclusion, complexome profiling validated the expression and composition of enzymes hypothesized to be involved in the energy, methane and nitrogen metabolism of M. lanthanidiphila, thereby further corroborating their unique metabolism involved in the environmentally relevant process of nitrite-dependent methane oxidation.
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Affiliation(s)
- Wouter Versantvoort
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands.
| | - Sergio Guerrero-Castillo
- Molecular Bioenergetics Group, Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Laura van Niftrik
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Molecular Bioenergetics Group, Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; KPA Aging-Associated Diseases, CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Joachim Reimann
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Zhu B, Wang J, Bradford LM, Ettwig K, Hu B, Lueders T. Nitric Oxide Dismutase ( nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers. Front Microbiol 2019; 10:1577. [PMID: 31354671 PMCID: PMC6636425 DOI: 10.3389/fmicb.2019.01577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.
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Affiliation(s)
- Baoli Zhu
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, Netherlands.,Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Lauren M Bradford
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany
| | - Katharina Ettwig
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Munich, Germany.,Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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31
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He Z, Zhang Q, Wei Z, Wang S, Pan X. Multiple-pathway arsenic oxidation and removal from wastewater by a novel manganese-oxidizing aerobic granular sludge. WATER RESEARCH 2019; 157:83-93. [PMID: 30953858 DOI: 10.1016/j.watres.2019.03.064] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/03/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Aerobic granular sludge (AGS) is a powerful biotechnology to remove various heavy metal(loid)s from wastewater, but not including arsenic (As). In this study, a novel manganese-oxidizing aerobic granular sludge (Mn-AGS) was developed to remove As from organic wastewater. Eight sequencing batch reactors (SBRs) were operated in duplicate to investigate the feasibility of As removal by Mn-AGS. The immobilized As in the granular sludge was characterized by sequencing extraction, X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), and Raman spectroscopy. Oxidation pathways for As and their contributions in Mn-AGS were evaluated by seven batch experiments under different conditions. The results indicated that As removal efficiency was much higher by Mn-AGS than by AGS. In Mn-AGS, As(III) was efficiently oxidized into As(V) (74.6%-82.6%) and then mostly bound on amorphous ferrihydrite and biogenic Mn oxides (bio-MnOx) (56.2%-65.0%), while metal arsenates, such as ferric arsenate, were not detected. Importantly, As removal was greatly improved by a small addition of Fe(II) in Mn-AGS. This might be primarily caused by Fenton reactions, because this improvement was removed when H2O2, self-generated in Mn-AGS, was scavenged by exogenous catalase (CAT). This study provided a novel extension of the traditional AGS technology to treat As in organic wastewater with an acceptable degree of efficiency.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qingying Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Zhen Wei
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Shuo Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.
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32
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He Z, Li Z, Zhang Q, Wei Z, Duo J, Pan X. Simultaneous remediation of As(III) and dibutyl phthalate (DBP) in soil by a manganese-oxidizing bacterium and its mechanisms. CHEMOSPHERE 2019; 220:837-844. [PMID: 30612053 DOI: 10.1016/j.chemosphere.2018.12.213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/13/2018] [Accepted: 12/31/2018] [Indexed: 05/26/2023]
Abstract
Soils are experiencing increasing pollution with arsenic (As) and phthalate esters (PAEs), which is threatening human health. In this study, the feasibility of simultaneous remediation of soil As(III) and a PAE, dibutyl phthalate (DBP), by a manganese-oxidizing bacterium (MnOB) was evaluated. As immobilization and DBP degradation were simultaneously enhanced by MnOB addition. The effects of initial concentrations of As(III), DBP, and Mn(II), and moisture content on the removal of As(III) and DBP were investigated. The results indicated that there was a competitive interaction between As(III) and DBP removal, and 40 mg/kg of Mn(II) dosage and 20%-30% soil moisture content were recommended for optimal and simultaneous removal of As(III) and DBP. Microbial community analysis revealed that community structure and diversity were not changed significantly by MnOB addition. Taken together, the findings from this study indicated that DBP was degraded primarily by microorganisms, whereas As(III) was removed largely by biogenic Mn oxides and immobilized by adsorption onto Mg/Fe oxides and/or formation of metal arsenate precipitates/co-precipitates. This study offers a novel and high-efficiency strategy to remediate the combined contamination of As and PAEs in soils.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zeya Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qingying Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhen Wei
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jia Duo
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.
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33
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Wang J, Cai C, Li Y, Hua M, Wang J, Yang H, Zheng P, Hu B. Denitrifying Anaerobic Methane Oxidation: A Previously Overlooked Methane Sink in Intertidal Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:203-212. [PMID: 30457852 DOI: 10.1021/acs.est.8b05742] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The intertidal zone is an open ecosystem rich in organic matter and plays an important role in global biogeochemical cycles. It was previously considered that methane was mainly removed by sulfate-dependent anaerobic methane oxidation (sulfate-AOM) process in marine ecosystems while other anaerobic methane oxidation processes were ignored. Recent researches have demonstrated that denitrifying anaerobic methane oxidation (DAMO), consisting of nitrite-dependent anaerobic methane oxidation (nitrite-AOM) and nitrate-dependent anaerobic methane oxidation (nitrate-AOM), can also oxidize methane. In this work, the community structure, quantity and potential methane oxidizing rate of DAMO archaea and bacteria in the intertidal zone were studied by high-throughput sequencing, qPCR and stable isotope tracing method. The results showed that nitrate-AOM and nitrite-AOM were both active in the intertidal zone and showed approximate methane oxidation rates. The copy number of 16S rRNA gene of DAMO archaea and DAMO bacteria were 104 ∼ 105 copies g-1 (dry sediment), whereas NC10 bacteria were slightly higher. The contribution rate of DAMO process to total anaerobic methane removal in the intertidal zone reached 65.6% ∼ 100%, which indicates that DAMO process is an important methane sink in intertidal ecosystem. Laboratory incubations also indicated that DAMO archaea were more sensitive to oxygen and preferred a more anoxic environment. These results help us draw a more complete picture of methane and nitrogen cycles in natural habitats.
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Affiliation(s)
- Jiaqi Wang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Chaoyang Cai
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Yufen Li
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Miaolian Hua
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Junren Wang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Hongrui Yang
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Ping Zheng
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
| | - Baolan Hu
- Department of Environmental Engineering , Zhejiang University , Hangzhou 310058 , China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety , Hangzhou , China
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He Z, Wang J, Hu J, Yu H, Jetten MSM, Liu H, Cai C, Liu Y, Ren H, Zhang X, Hua M, Xu X, Zheng P, Hu B. Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 244:228-237. [PMID: 30342364 DOI: 10.1016/j.envpol.2018.10.057] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/29/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
Coastal wetlands are widely recognized as atmospheric methane sources. However, recent field studies suggest that some coastal wetlands could also act as methane sinks, but the mechanism is not yet clear. Here, we investigated methane oxidation with different electron acceptors (i.e., oxygen, nitrate/nitrite, sulfate, Fe(III) and Mn(IV)) in four coastal wetlands in China using a combination of molecular biology methods and isotopic tracing technologies. The geochemical profiles and in situ Gibbs free energies suggest that there was significant nitrite-dependent anaerobic oxidation of methane (nitrite-AOM) in the sub-surface sediments; this was subsequently experimentally verified by both the microbial abundance and activity. Remarkably, the methanotrophic communities seemed to exist in the sediments as layered structures, and the surface aerobic methane-oxidizing bacteria were able to take up atmospheric methane at a rate of 0.10-0.18 nmol CH4 day-1 cm-2, while most, if not all, sedimentary methane was being completely consumed by anaerobic methanotrophs (23-58% by methane oxidizers in phylum NC10). These results suggest that coastal methane sinks might be governed by diverse microbial communities where NC10 methane oxidizers contributed significantly. This finding helps to better understand and predict the coastal methane cycle and reduce uncertainties in the estimations of the global methane flux.
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Affiliation(s)
- Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Hanqing Yu
- Department of Chemistry, University of Science & Technology of China, Hefei, China
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chaoyang Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Hongxing Ren
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xu Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Miaolian Hua
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xinhua Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou, China.
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35
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He Z, Feng J, Wei Z, Wu S, Zou J, Pan X. Optimization of methane-dependent oxygenic denitrification in sequencing batch reactors by insights into the microbial interactions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:623-631. [PMID: 29957429 DOI: 10.1016/j.scitotenv.2018.06.238] [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: 04/22/2018] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Abstract
Methane-dependent oxygenic denitrification (O2DN) is a promising technology used for reducing greenhouse gas emissions of nitrous oxide (N2O) during wastewater treatment. Heterotrophic bacteria are associated with methane-dependent O2DN bacteria, and it has been proposed that metabolic cross-feeding occurs between the two populations above. In this study, a mathematical model was developed to describe the microbial processes and interactions between methane-dependent O2DN bacteria and associated heterotrophic bacteria in a sequencing batch reactor (SBR). A growth factor-dependent decoupling of metabolism and growth of methane-dependent O2DN bacteria was introduced into the model. Effects of influent substrates, operating parameters, and initial biomass on microbial community and reactor performance were then investigated, and the above parameters were optimized using the model. Results surprisingly show that organic matter in the influent greatly stimulated the growth of methane-dependent O2DN bacteria but slightly limited the increase of heterotrophic bacteria. This effect could be explained by the increased excretion of growth factors by heterotrophic bacteria and the intensified competition for nitrite when methane-dependent O2DN bacteria increased. These results will assist in providing a new understanding of microbial interactions in methane-dependent O2DN systems and offer a new and efficient strategy for operating methane-dependent O2DN reactors.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jieni Feng
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Zhen Wei
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Shuyun Wu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jinte Zou
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China.
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36
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Vuillemin A, Horn F, Friese A, Winkel M, Alawi M, Wagner D, Henny C, Orsi WD, Crowe SA, Kallmeyer J. Metabolic potential of microbial communities from ferruginous sediments. Environ Microbiol 2018; 20:4297-4313. [PMID: 29968357 DOI: 10.1111/1462-2920.14343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 06/25/2018] [Indexed: 01/22/2023]
Abstract
Ferruginous (Fe-rich, SO4 -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.
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Affiliation(s)
- Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - André Friese
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute of Earth and Environmental Sciences, Potsdam, Germany
| | - Cynthia Henny
- Research Center for Limnology (LIPI), Indonesian Institute of Sciences, Division of Inland Waterways Dynamics, Cibinong-Bogor, Indonesia
| | - William D Orsi
- Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Geobio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.,Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
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37
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Versantvoort W, Guerrero-Cruz S, Speth DR, Frank J, Gambelli L, Cremers G, van Alen T, Jetten MSM, Kartal B, Op den Camp HJM, Reimann J. Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila. Front Microbiol 2018; 9:1672. [PMID: 30140258 PMCID: PMC6094997 DOI: 10.3389/fmicb.2018.01672] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/04/2018] [Indexed: 11/18/2022] Open
Abstract
Methane is a potent greenhouse gas, which can be converted by microorganism at the expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium ‘Candidatus Methylomirabilis oxyfera,’ a member of the NC10 phylum, is capable of nitrite-dependent anaerobic methane oxidation. Prolonged enrichment of ‘Ca. M. oxyfera’ with cerium added as trace element and without nitrate resulted in the shift of the dominant species. Here, we present a high quality draft genome of the new species ‘Candidatus Methylomirabilis lanthanidiphila’ and use comparative genomics to analyze its metabolic potential in both nitrogen and carbon cycling. To distinguish between gene content specific for the ‘Ca. Methylomirabilis’ genus and the NC10 phylum, the genome of a distantly related NC10 phylum member, CSP1-5, an aerobic methylotroph, is included in the analysis. All genes for the conversion of nitrite to N2 identified in ‘Ca. M. oxyfera’ are conserved in ‘Ca. M. lanthanidiphila,’ including the two putative genes for NO dismutase. In addition both species have several heme-copper oxidases potentially involved in NO and O2 respiration. For the oxidation of methane ‘Ca. Methylomirabilis’ species encode a membrane bound methane monooxygenase. CSP1-5 can act as a methylotroph, but lacks the ability to activate methane. In contrast to ‘Ca. M. oxyfera,’ which harbors three methanol dehydrogenases (MDH), both CSP1-5 and ‘Ca. M. lanthanidiphila’ only encode a lanthanide-dependent XoxF-type MDH, once more underlining the importance of rare earth elements for methylotrophic bacteria. The pathways for the subsequent oxidation of formaldehyde to carbon dioxide and for the Calvin–Benson–Bassham cycle are conserved in all species. Furthermore, CSP1-5 can only interconvert nitrate and nitrite, but lacks subsequent nitrite or NO reductases. Thus, it appears that although the conversion of methanol to carbon dioxide is present in several NC10 phylum bacteria, the coupling of nitrite reduction to the oxidation of methane is a trait so far unique to the genus ‘Ca. Methylomirabilis.’
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Affiliation(s)
- Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Simon Guerrero-Cruz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Jeroen Frank
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lavinia Gambelli
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Theo van Alen
- 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.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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He Z, Feng Y, Zhang S, Wang X, Wu S, Pan X. Oxygenic denitrification for nitrogen removal with less greenhouse gas emissions: Microbiology and potential applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:453-464. [PMID: 29195194 DOI: 10.1016/j.scitotenv.2017.11.280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/24/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen pollution is a worldwide problem and has been extensively treated by canonical denitrification (CDN) process. However, the CDN process generates several issues such as intensive greenhouse gas (GHG) emissions. In the past years, a novel biological nitrogen removal (BNR) process of oxygenic denitrification (O2DN) has been proposed as a promising alternative to the CDN process. The classic denitrification four steps are simplified to three steps by O2DN bacteria without producing and releasing the intermediate nitrous oxide (N2O), a potent GHG. In this article, we summarized the findings in previous literatures as well as our results, including involved microorganisms and metabolic mechanisms, functional genes and microbial detection, kinetics and influencing factors and their potential applications in wastewater treatment. Based on our knowledge and experience, the benefits and limitations of the current O2DN process were analyzed. Since O2DN is a new field in wastewater treatment, more research and application is required, especially the development of integrated processes and the quantitative assessment of the contribution of O2DN process in natural habitats and engineered systems.
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Affiliation(s)
- Zhanfei He
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Yudong Feng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Shijie Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiaonan Wang
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Shuyun Wu
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China.
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Xu S, Lu W, Muhammad FM, Liu Y, Guo H, Meng R, Wang H. New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches. J Environ Sci (China) 2018; 65:367-374. [PMID: 29548408 DOI: 10.1016/j.jes.2017.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/22/2017] [Accepted: 04/19/2017] [Indexed: 06/08/2023]
Abstract
The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (p<0.05). The redundancy analysis further revealed that the pH, volatile solid and nitrite nitrogen were the most important factors in shaping the NC10 bacterial structure (p=0.01) based on the variation inflation factors selection and Monte Carlo test (999 times). Results of this study extended the existing molecular tools for studying the NC10 bacterial community structures and provided new information on the ecological distributions of NC10 bacteria.
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Affiliation(s)
- Sai Xu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China.
| | | | - Yanting Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hanwen Guo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruihong Meng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongtao Wang
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China
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Molecular and stable isotopic evidence for the occurrence of nitrite-dependent anaerobic methane-oxidizing bacteria in the mangrove sediment of Zhangjiang Estuary, China. Appl Microbiol Biotechnol 2018; 102:2441-2454. [DOI: 10.1007/s00253-017-8718-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/18/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
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He Z, Zhang Q, Feng Y, Luo H, Pan X, Gadd GM. Microbiological and environmental significance of metal-dependent anaerobic oxidation of methane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:759-768. [PMID: 28830047 DOI: 10.1016/j.scitotenv.2017.08.140] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/22/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic oxidation of methane (AOM) can be coupled to the reduction of sulfate, nitrate and nitrite, which effectively reduces methane emission into the atmosphere. Recently, metal-dependent AOM (metal-AOM, AOM coupled to metal reduction) was demonstrated to occur in both environmental samples and enrichment cultures. Anaerobic methanotrophs are capable of respiration using Fe(III) or Mn(IV), whether they are in the form of soluble metal species or insoluble minerals. Given the wide distribution of Fe(III)/Mn(IV)-bearing minerals in aquatic methane-rich environments, metal-AOM is considered to be globally important, although it has generally been overlooked in previous studies. In this article, we discuss the discovery of this process, the microorganisms and mechanisms involved, environmental significance and factors influencing metal-AOM. Since metal-AOM is poorly studied to date, some discussion is included on the present understanding of sulfate- and nitrate-AOM and traditional metal reduction processes using organic substrates or hydrogen as electron donors. Metal-AOM is a relatively new research field, and therefore more studies are needed to fully characterize the process. This review summarizes current studies and discusses the many unanswered questions, which should be useful for future research in this field.
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Affiliation(s)
- Zhanfei He
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Qingying Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yudong Feng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Hongwei Luo
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China.
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Shen LD, Wu HS, Liu X, Li J. Cooccurrence and potential role of nitrite- and nitrate-dependent methanotrophs in freshwater marsh sediments. WATER RESEARCH 2017; 123:162-172. [PMID: 28668629 DOI: 10.1016/j.watres.2017.06.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 05/31/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
Nitrite- and nitrate-dependent anaerobic methane oxidation are mediated by the NC10 bacteria closely related to "Candidatus Methylomirabilis oxyfera" (M. oxyfera) and the ANME-2d archaea closely related to "Candidatus Methanoperedens nitroreducens" (M. nitroreducens), respectively. Here, we investigated the occurrence and activity of both M. oxyfera-like bacteria and M. nitroreducens-like archaea in the sediment of freshwater marshes in Eastern China. The presence of diverse M. oxyfera-like bacteria (>87% identity to M. oxyfera) and M. nitroreducens-like archaea (>96% identity to M. nitroreducens) was confirmed by using Illumina-based total bacterial and archaeal 16S rRNA gene sequencing, respectively. The recovered M. oxyfera-like bacterial sequences accounted for 1.6-4.3% of the total bacterial 16S rRNA pool, and M. nitroreducens-like archaeal sequences accounted for 0.2-1.8% of the total archaeal 16S rRNA pool. The detected numbers of OTUs of the 16S rRNA genes of M. oxyfera-like bacteria and M. nitroreducens-like archaea were 78 and 72, respectively, based on 3% sequence difference. Quantitative PCR showed that the 16S rRNA gene abundance of M. oxyfera-like bacteria (6.1 × 106-3.2 × 107 copies g-1 sediment) was 2-4 orders of magnitude higher than that of M. nitroreducens-like archaea (1.4 × 103-3.2 × 104 copies g-1 sediment). Stable isotope experiments showed that the addition of both nitrite and nitrate stimulated the anaerobic methane oxidation, while the stimulation by nitrite is more significant than nitrate. Our results provide the first evidence that the M. oxyfera-like bacteria play a more important role than the M. nitroreducens-like archaea in methane cycling in wetland systems.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China.
| | - Hong-Sheng Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xu Liu
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Ji Li
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
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Wang J, Shen L, He Z, Hu J, Cai Z, Zheng P, Hu B. Spatial and temporal distribution of nitrite-dependent anaerobic methane-oxidizing bacteria in an intertidal zone of the East China Sea. Appl Microbiol Biotechnol 2017; 101:8007-8014. [DOI: 10.1007/s00253-017-8521-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/21/2017] [Accepted: 09/06/2017] [Indexed: 12/18/2022]
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Hatamoto M, Sato T, Nemoto S, Yamaguchi T. Cultivation of denitrifying anaerobic methane-oxidizing microorganisms in a continuous-flow sponge bioreactor. Appl Microbiol Biotechnol 2017; 101:5881-5888. [PMID: 28484811 DOI: 10.1007/s00253-017-8315-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 11/29/2022]
Abstract
Anaerobic treatment of sewage has many advantages; however, the effluent contains high levels of dissolved methane. In this study, we investigated the use of a closed-type downflow hanging sponge (DHS) reactor for application of the denitrifying anaerobic methane oxidation (DAMO) reaction for nitrogen and dissolved methane removal. When using nitrate, the DAMO reaction achieved a denitrification rate of 84.4 g N m-3 day-1, which is close to that required for practical application of denitrification to anaerobic sewage treatment. The microbial community that developed in the DHS was investigated using16S rRNA, and novel species of DAMO bacteria affiliated with Group b of NC10 phylum were enriched. This contrasted with the results of previous studies in which the Candidatus Methylomirabilis oxyfera affiliated with Group a was enriched. The results obtained herein suggest that a post-treatment system for anaerobically treated sewage using a closed-type DHS reactor may become practical in the near future.
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Affiliation(s)
- Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan. .,Top Runner Incubation Center for Academia-Industry Fusion, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.
| | - Takafumi Sato
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Sho Nemoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.,Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
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Zhu B, Bradford L, Huang S, Szalay A, Leix C, Weissbach M, Táncsics A, Drewes JE, Lueders T. Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems. Appl Environ Microbiol 2017; 83:e02750-16. [PMID: 27986721 PMCID: PMC5288823 DOI: 10.1128/aem.02750-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/02/2016] [Indexed: 11/20/2022] Open
Abstract
It has recently been suggested that oxygenic dismutation of NO into N2 and O2 may occur in the anaerobic methanotrophic "Candidatus Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to "Ca Methylomirabilis oxyfera" and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from "Ca Methylomirabilis oxyfera" and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 107 to 5.2 × 1010 copies · g-1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. IMPORTANCE NO dismutation into N2 and O2 is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium "Ca Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of nod genes in environmental samples. A surprisingly high diversity and abundance of nod genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future.
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Affiliation(s)
- Baoli Zhu
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Lauren Bradford
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Sichao Huang
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Anna Szalay
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Carmen Leix
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Max Weissbach
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | | | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz-Zentrum München, Neuherberg, Germany
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Nitrogen source effects on the denitrifying anaerobic methane oxidation culture and anaerobic ammonium oxidation bacteria enrichment process. Appl Microbiol Biotechnol 2017; 101:3895-3906. [DOI: 10.1007/s00253-017-8163-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022]
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Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, Jetten MSM, Lüke C, Reimann J. Nitrate- and nitrite-dependent anaerobic oxidation of methane. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:941-955. [PMID: 27753265 DOI: 10.1111/1758-2229.12487] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N2 and O2 for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
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Chen J, Dick R, Lin JG, Gu JD. Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments. Appl Microbiol Biotechnol 2016; 100:9845-9860. [DOI: 10.1007/s00253-016-7853-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 09/11/2016] [Accepted: 09/13/2016] [Indexed: 11/29/2022]
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49
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He Z, Cai C, Wang J, Xu X, Zheng P, Jetten MSM, Hu B. A novel denitrifying methanotroph of the NC10 phylum and its microcolony. Sci Rep 2016; 6:32241. [PMID: 27582299 PMCID: PMC5007514 DOI: 10.1038/srep32241] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/02/2016] [Indexed: 12/03/2022] Open
Abstract
The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies.
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Affiliation(s)
- Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chaoyang Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xinhua Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
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50
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Shen LD, Hu BL, Liu S, Chai XP, He ZF, Ren HX, Liu Y, Geng S, Wang W, Tang JL, Wang YM, Lou LP, Xu XY, Zheng P. Anaerobic methane oxidation coupled to nitrite reduction can be a potential methane sink in coastal environments. Appl Microbiol Biotechnol 2016; 100:7171-80. [PMID: 27225473 DOI: 10.1007/s00253-016-7627-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/01/2016] [Accepted: 05/07/2016] [Indexed: 12/14/2022]
Abstract
In the current study, we investigated nitrite-dependent anaerobic methane oxidation (N-DAMO) as a potential methane sink in the Hangzhou Bay and the adjacent Zhoushan sea area. The potential activity of the N-DAMO process was primarily observed in Hangzhou Bay by means of (13)C-labeling experiments, whereas very low or no potential N-DAMO activity could be detected in the Zhoushan sea area. The measured potential N-DAMO rates ranged from 0.2 to 1.3 nmol (13)CO2 g(-1) (dry sediment) day(-1), and the N-DAMO potentially contributed 2.0-9.4 % to the total microbial methane oxidation in the examined sediments. This indicated that the N-DAMO process may be an alternative pathway in the coastal methane cycle. Phylogenetic analyses confirmed the presence of Candidatus Methylomirabilis oxyfera-like bacteria in all the examined sediments, while the group A members (the dominant bacteria responsible for N-DAMO) were found mainly in Hangzhou Bay. Quantitative PCR showed that the 16S rRNA gene abundance of Candidatus M. oxyfera-like bacteria varied from 5.4 × 10(6) to 5.0 × 10(7) copies g(-1) (dry sediment), with a higher abundance observed in Hangzhou Bay. In addition, the overlying water NO3 (-) concentration and salinity were identified as the most important factors influencing the abundance and potential activity of Candidatus M. oxyfera-like bacteria in the examined sediments. This study showed the evidence of N-DAMO in coastal environments and indicated the importance of N-DAMO as a potential methane sink in coastal environments.
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Affiliation(s)
- Li-Dong Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Bao-Lan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Ping Chai
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Zhan-Fei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hong-Xing Ren
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Sha Geng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Wei Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jing-Liang Tang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Yi-Ming Wang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, 316021, China
| | - Li-Ping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiang-Yang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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