1
|
Zhou J, Zheng Y, Hou L, Qi L, Mao T, Yin G, Liu M. Nitrogen input modulates the effects of coastal acidification on nitrification and associated N 2O emission. WATER RESEARCH 2024; 261:122041. [PMID: 38972235 DOI: 10.1016/j.watres.2024.122041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Acidification of coastal waters, synergistically driven by increasing atmospheric carbon dioxide (CO2) and intensive land-derived nutrient inputs, exerts significant stresses on the biogeochemical cycles of coastal ecosystem. However, the combined effects of anthropogenic nitrogen (N) inputs and aquatic acidification on nitrification, a critical process of N cycling, remains unclear in estuarine and coastal ecosystems. Here, we showed that increased loading of ammonium (NH4+) in estuarine and coastal waters alleviated the inhibitory effect of acidification on nitrification rates but intensified the production of the potent greenhouse gas nitrous oxide (N2O), thus accelerating global climate change. Metatranscriptomes and natural N2O isotopic signatures further suggested that the enhanced emission of N2O may mainly source from hydroxylamine (NH2OH) oxidation rather than from nitrite (NO2-) reduction pathway of nitrifying microbes. This study elucidates how anthropogenic N inputs regulate the effects of coastal acidification on nitrification and associated N2O emissions, thereby enhancing our ability to predict the feedbacks of estuarine and coastal ecosystems to climate change and human perturbations.
Collapse
Affiliation(s)
- Jie Zhou
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China.
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Tieqiang Mao
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| |
Collapse
|
2
|
Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
Collapse
Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
3
|
Li J, Zhao C, Li C, Xue B, Wang S, Zhang X, Yang X, Shen Z, Bo L, He X, Qiu Z, Wang J. Multidrug-resistant plasmid RP4 increases NO and N 2O yields via the electron transport system in Nitrosomonas europaea ammonia oxidation. WATER RESEARCH 2023; 242:120266. [PMID: 37421866 DOI: 10.1016/j.watres.2023.120266] [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: 01/03/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
Antibiotic resistance genes (ARGs) have recently become an important public health problem and therefore several studies have characterized ARG composition and distribution. However, few studies have assessed their impact on important functional microorganisms in the environment. Therefore, our study sought to investigate the mechanisms through which multidrug-resistant plasmid RP4 affected the ammonia oxidation capacity of ammonia-oxidizing bacteria, which play a key role in the nitrogen cycle. The ammonia oxidation capacity of N. europaea ATCC25978 (RP4) was significantly inhibited, and NO and N2O were produced instead of nitrite. Our findings demonstrated that the decrease in electrons from NH2OH decreased the ammonia monooxygenase (AMO) activity, leading to a decrease in ammonia consumption. In the ammonia oxidation process, N. europaea ATCC25978 (RP4) exhibited ATP and NADH accumulation. The corresponding mechanism was the overactivation of Complex Ⅰ, ATPase, and the TCA cycle by the RP4 plasmid. The genes encoding TCA cycle enzymes related to energy generation, including gltA, icd, sucD, and NE0773, were upregulated in N. europaea ATCC25978 (RP4). These results demonstrate the ecological risks of ARGs, including the inhibition of the ammonia oxidation process and an increased production of greenhouse gases such as NO and N2O.
Collapse
Affiliation(s)
- Jia Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhiqiang Shen
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Lin Bo
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Tiangong University, Tianjin, China
| | - Xinxin He
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
| |
Collapse
|
4
|
Zhang K, Qiu Y, Zhao Y, Wang S, Deng J, Chen M, Xu X, Wang H, Bai T, He T, Zhang Y, Chen H, Wang Y, Hu S. Moderate precipitation reduction enhances nitrogen cycling and soil nitrous oxide emissions in a semi-arid grassland. GLOBAL CHANGE BIOLOGY 2023; 29:3114-3129. [PMID: 36892227 DOI: 10.1111/gcb.16672] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 05/03/2023]
Abstract
The ongoing climate change is predicted to induce more weather extremes such as frequent drought and high-intensity precipitation events, causing more severe drying-rewetting cycles in soil. However, it remains largely unknown how these changes will affect soil nitrogen (N)-cycling microbes and the emissions of potent greenhouse gas nitrous oxide (N2 O). Utilizing a field precipitation manipulation in a semi-arid grassland on the Loess Plateau, we examined how precipitation reduction (ca. -30%) influenced soil N2 O and carbon dioxide (CO2 ) emissions in field, and in a complementary lab-incubation with simulated drying-rewetting cycles. Results obtained showed that precipitation reduction stimulated plant root turnover and N-cycling processes, enhancing soil N2 O and CO2 emissions in field, particularly after each rainfall event. Also, high-resolution isotopic analyses revealed that field soil N2 O emissions primarily originated from nitrification process. The incubation experiment further showed that in field soils under precipitation reduction, drying-rewetting stimulated N mineralization and ammonia-oxidizing bacteria in favor of genera Nitrosospira and Nitrosovibrio, increasing nitrification and N2 O emissions. These findings suggest that moderate precipitation reduction, accompanied with changes in drying-rewetting cycles under future precipitation scenarios, may enhance N cycling processes and soil N2 O emissions in semi-arid ecosystems, feeding positively back to the ongoing climate change.
Collapse
Affiliation(s)
- Kangcheng Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunfeng Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuhong Wang
- Ningxia Yunwu Mountains Grassland Natural Reserve Administration, Guyuan, 756000, China
| | - Jun Deng
- Ningxia Yunwu Mountains Grassland Natural Reserve Administration, Guyuan, 756000, China
| | - Mengfei Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tongshuo Bai
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tangqing He
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huaihai Chen
- School of Ecology, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yi Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Shuijin Hu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27695, USA
| |
Collapse
|
5
|
Bhattacharya R, Mazumder D. Performance evaluation of moving bed bioreactor for simultaneous nitrification denitrification and phosphorus removal from simulated fertilizer industry wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49060-49074. [PMID: 36763265 DOI: 10.1007/s11356-023-25708-z] [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: 11/04/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
With increasing demand for agricultural production, chemical fertilizers are now being intensively manufactured and used to provide readily available nutrients in larger quantities, which often leach out and contaminate the groundwater source. At the same time, effluents from fertilizer plants also pollute water bodies, when disposed of without proper treatment. The present study evaluates nitrogen and phosphorus removal efficiencies in a single-stage aerobic moving bed bioreactor (MBBR) from diammonium phosphate (DAP)-spiked wastewater containing no organic carbon. To date, no similar study has been undertaken that treats fertilizer plant effluent or agricultural runoff without the aid of external carbon, where organic carbon is hypothesized to be supplied from endogenous degradation of biomass. Both denitrification and phosphorus removal occurs in the anoxic zones of deeper layers of the biofilm. The present investigation demonstrates the feasibility of the processes with the requirement of a two-stage MBBR for effective simultaneous nitrification, denitrification, and phosphorus removal (SNDPr) together with a polishing technology to bring down the phosphorus concentration within limits. A novel bio-carrier designed for efficient SND was used in the study, with a carrier filling ratio of 35% that supported the formation of deep biofilms creating anoxic zones in the inner surface. Identification of the bacterial species reflects the occurrence of simultaneous nitrification, denitrification, and phosphorous removal (SNDPr) in the reactor. A maximum ammonium nitrogen removal efficiency of 98% was recorded with 95% total nitrogen removal, 69% phosphorus removal, and 85% SND efficiency, indicating the applicability of the process with a tertiary phosphorus removal unit to lower the nutrient concentration of effluents prior to disposal.
Collapse
Affiliation(s)
- Roumi Bhattacharya
- Civil Engineering Department, Indian Institute of Engineering Science and Technology, Shibpur, India.
| | - Debabrata Mazumder
- Civil Engineering Department, Indian Institute of Engineering Science and Technology, Shibpur, India
| |
Collapse
|
6
|
Yuan Y, Liu J, Gao B, Sillanpää M, Al-Farraj S. The effect of activated sludge treatment and catalytic ozonation on high concentration of ammonia nitrogen removal from landfill leachate. BIORESOURCE TECHNOLOGY 2022; 361:127668. [PMID: 35878770 DOI: 10.1016/j.biortech.2022.127668] [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: 06/27/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
This study adopted the combination of activated sludge treatment and catalytic ozonation technology to efficiently remove the high concentration of ammonia nitrogen from landfill leachate. Through optimizing the parameters continuously, the COD, NH4+-N, UV254 and colority respectively descended to 417.75 ± 6.72 mg/L, 9.77 mg/L, 1.98 ± 0.04 and 40 times, and 3D fluorescence also reduced significantly within 14 days. Target genes of AOB-amoA, nxrA, napA, nirS and nosZ analysis indicated that ammonia-oxidizing bacteria, nitrated bacteria, and denitrifying bacteria played a key role on nitrogen removal, aerobic denitrifying bacteria was dominated especially. The nitrogen removal process was as follows: catalytic ozonation converted nitrogen-containing organic matter into NH4+-N, then NH4+-N was converted into NO2--N and NO3--N with the action of ammonia oxidation, nitrification and catalytic ozonation. Finally, the denitrification microorganisms transformed NO3--N or NO2--N to N2. Therefore, this coupled process realized the nitrogen removal effectively from landfill leachate.
Collapse
Affiliation(s)
- Yuchen Yuan
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jiadong Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Bo Gao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Mika Sillanpää
- Department of Chemical Engineering, School of Mining, Metallurgy and Chemical Engineering, University of Johannesburg, P. O. Box 17011, Doornfontein 2028, South Africa; Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Zhejiang Rongsheng Environmental Protection Paper Co. LTD, NO. 588 East Zhennan Road, Pinghu Economic Development Zone, Zhejiang 314213, China; Department of Civil Engineering, University Centre for Research & Development, Chandigarh University, Gharuan, Mohali, Punjab, India; International Research Centre of Nanotechnology for Himalayan Sustainability (IRCNHS), Shoolini University, Solan 173212, Himachal Pradesh, India
| | - Saleh Al-Farraj
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
7
|
Irazoqui JM, Eberhardt MF, Adjad MM, Amadio AF. Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics. PeerJ 2022; 10:e12772. [PMID: 35310160 PMCID: PMC8929167 DOI: 10.7717/peerj.12772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/19/2021] [Indexed: 01/07/2023] Open
Abstract
Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.
Collapse
Affiliation(s)
- Jose M. Irazoqui
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria F. Eberhardt
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria M. Adjad
- Estacion Experimental Rafaela (INTA), Rafaela, Santa Fe, Argentina
| | - Ariel F. Amadio
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| |
Collapse
|
8
|
Clark IM, Hughes DJ, Fu Q, Abadie M, Hirsch PR. Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils. Sci Rep 2021; 11:15905. [PMID: 34354121 PMCID: PMC8342464 DOI: 10.1038/s41598-021-95100-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes-permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.
Collapse
Affiliation(s)
- Ian M Clark
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - David J Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Qingling Fu
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Maïder Abadie
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Penny R Hirsch
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK.
| |
Collapse
|
9
|
You Y, Aho K, Lohse KA, Schwabedissen SG, Ledbetter RN, Magnuson TS. Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem. Front Microbiol 2021; 12:569791. [PMID: 34025590 PMCID: PMC8134670 DOI: 10.3389/fmicb.2021.569791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 04/13/2021] [Indexed: 11/19/2022] Open
Abstract
Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.
Collapse
|
10
|
Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems. Sci Rep 2021; 11:7850. [PMID: 33846510 PMCID: PMC8041819 DOI: 10.1038/s41598-021-87184-0] [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] [Received: 12/23/2020] [Accepted: 03/22/2021] [Indexed: 11/08/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (15N/14N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor 15ε for the reduction of nitrite to N2 is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of 15ε for the oxidation of nitrite to nitrate (inverse isotope effect, - 16 to - 43‰) and for the reduction of ammonium to N2 (normal isotope effect, 19-32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.
Collapse
|
11
|
Jeong D, Bae H. Insight into functionally active bacteria in nitrification following Na + and Mg 2+ exposure based on 16S rDNA and 16S rRNA sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143592. [PMID: 33277005 DOI: 10.1016/j.scitotenv.2020.143592] [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: 08/10/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
Despite increasing interests in osmotic membrane bioreactors, the information regarding the bacterial toxicity effects of reversely transported draw solute (RTDS) is limited. In this study, two representative draw solutes (NaCl and MgCl2) were used at different concentrations (0, 2.5, 5.0, 7.5 and 10.0 g/L) to evaluate their toxicity in a continuous nitrifying bioreactor. Notably, Mg2+ selectively inhibited the activity of ammonia-oxidizing bacteria (AOB), which decreased to 11.3% at 7.5 g-Mg2+/L. The rRNA-based analysis was more effective than the rDNA-based analysis to elucidate the relationship between active communities of nitrifying bacteria and the actual nitrifying performance. Nitrosomonas europaea, a representative AOB, was vulnerable to Mg2+ in comparison to Na+. In contrast, the dominant nitrite-oxidizing bacteria (NOB), Nitrobacter winogradskyi and Nitrolancea hollandica, maintained a relevant level of relative abundance for achieving nitrite oxidation after exposure to 10 g/L Na+ and Mg2+. This fundamental inhibition information of the draw solute can be applied to set the operational regime preventing the critical solute concentration in mixed liquor of nitrifying OMBRs.
Collapse
Affiliation(s)
- Dawoon Jeong
- Institute of Environmental Research, Kangwon National University, 1 Gangwondaehak-gil, Chuncheon-si, Gangwon-do 24341, Republic of Korea.
| | - Hyokwan Bae
- Department of Civil and Environmental Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
| |
Collapse
|
12
|
Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
Collapse
Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| |
Collapse
|
13
|
Xiao J, Huang J, Huang M, Chen M, Wang M. Application of basalt fiber in vertical flow constructed wetland for different pollution loads wastewater: Performance, substrate enzyme activity and microorganism community. BIORESOURCE TECHNOLOGY 2020; 318:124229. [PMID: 33091692 DOI: 10.1016/j.biortech.2020.124229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/27/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
The cost-effective and environmentally friendly substrates are vital for the design of constructed wetlands (CWs). This study explored the incorporation of basalt fiber (BF) into CWs as substrates for enhancing purification performance and comparative investigated the advantage of enzyme activities and microbial community of basalt fiber constructed wetland (BF-CW) compared with conventional constructed wetland (C-CW). It was found that the addition of BF obviously improved removal efficiencies of nitrogen and phosphorus around 10 ~ 25%, especially under high pollutant loading. Further substrate enzyme activity analysis showed that the dehydrogenase (DHA), urease (UA) and phosphatase (PST) activities of BF-CW were higher than those of C-CW. Moreover, high-throughput sequencing analysis revealed that the abundance of key functional bacteria was higher in BF-CW than C-CW, and the community structure in BF-CW was more resistant to changes in pollutant loadings. These results indicated that BF could be used as a new alternative substrate in CWs technology.
Collapse
Affiliation(s)
- Jun Xiao
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
| | - Juan Huang
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China.
| | - Minjie Huang
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
| | - Ming Chen
- Nanjing Research Institute of Environmental Protection, Nanjing, Jiangsu 210013, PR China
| | - Mingyu Wang
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 211189, PR China
| |
Collapse
|
14
|
Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. MICROBIAL ECOLOGY 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
Collapse
Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
| |
Collapse
|
15
|
Reyes C, Hodgskiss LH, Kerou M, Pribasnig T, Abby SS, Bayer B, Kraemer SM, Schleper C. Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation. THE ISME JOURNAL 2020; 14:2659-2674. [PMID: 32665710 PMCID: PMC7785015 DOI: 10.1038/s41396-020-0715-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/09/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.
Collapse
Affiliation(s)
- Carolina Reyes
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Sophie S Abby
- University Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Barbara Bayer
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Department of Limnology and Oceanography, Division of Bio-oceanography, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106-9620, USA
| | - Stephan M Kraemer
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Althanstrasse 14, UZA1, 1090, Vienna, Austria.
- Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, University of Vienna, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| |
Collapse
|
16
|
Xiang Y, Shao Z, Chai H, Ji F, He Q. Functional microorganisms and enzymes related nitrogen cycle in the biofilm performing simultaneous nitrification and denitrification. BIORESOURCE TECHNOLOGY 2020; 314:123697. [PMID: 32593105 DOI: 10.1016/j.biortech.2020.123697] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
Simultaneous nitrification and denitrification (SND) is a potential energy-saving process in wastewater treatment while the nitrogen removal mechanism is still unclear due to the lack of information about the functional microbes and enzymes. Sequencing batch biofilm reactors were implemented to achieve efficient SND. Eight nitrogen removal related microorganisms out of the top abundant 20 microbial community and reference species were used to construct a phylogenetic tree. Functional enzymes and modules analysis were investigated to reveal the SND pathway: in the aerobic part of the biofilm, ammonia oxidation was catalyzed by complete ammonia oxidizers while in the inner anoxic part, denitrification, dissimilatory nitrate reduction (DNRA) and nitrogen fixation (NF) cooperated to stimulate nitrate removal. These results provide a practical aeration control strategy to achieve SND and indicate that DNRA and NF are important nitrogen removal pathways that should not be ignored in the SND mechanism.
Collapse
Affiliation(s)
- Yu Xiang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Zhiyu Shao
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Hongxiang Chai
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China.
| | - Fangying Ji
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Qiang He
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| |
Collapse
|
17
|
Musiani F, Broll V, Evangelisti E, Ciurli S. The model structure of the copper-dependent ammonia monooxygenase. J Biol Inorg Chem 2020; 25:995-1007. [PMID: 32926231 PMCID: PMC7584546 DOI: 10.1007/s00775-020-01820-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022]
Abstract
Abstract Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01820-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| | - Valquiria Broll
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Elisa Evangelisti
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| |
Collapse
|
18
|
Sedlacek CJ. It Takes a Village: Discovering and Isolating the Nitrifiers. Front Microbiol 2020; 11:1900. [PMID: 32849473 PMCID: PMC7431685 DOI: 10.3389/fmicb.2020.01900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.
Collapse
Affiliation(s)
- Christopher J. Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| |
Collapse
|
19
|
Wang L, Lim CK, Klotz MG. High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. Microorganisms 2020; 8:E693. [PMID: 32397339 PMCID: PMC7285500 DOI: 10.3390/microorganisms8050693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022] Open
Abstract
The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world's oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C-107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.
Collapse
Affiliation(s)
- Lin Wang
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Chee Kent Lim
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Martin G. Klotz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
| |
Collapse
|
20
|
Sedlacek CJ, McGowan B, Suwa Y, Sayavedra-Soto L, Laanbroek HJ, Stein LY, Norton JM, Klotz MG, Bollmann A. A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria. MICROBIAL ECOLOGY 2019; 78:985-994. [PMID: 30976841 DOI: 10.1007/s00248-019-01378-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.
Collapse
Affiliation(s)
- Christopher J Sedlacek
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Brian McGowan
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA
| | - Yuichi Suwa
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Luis Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, 116 St. and 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Jeanette M Norton
- Department of Plants, Soil and Climate, Utah State University, Logan, UT, 84322-4820, USA
| | - Martin G Klotz
- School of Molecular Biosciences, Washington State University, Richland, WA, 99354, USA
| | - Annette Bollmann
- Department of Microbiology, Miami University, 501 East High St, Oxford, OH, 45056, USA.
| |
Collapse
|
21
|
Sharma PK, Sharma V, Sharma S, Bhatia G, Singh K, Sharma R. Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil. J Genet Eng Biotechnol 2019; 17:6. [PMID: 31659568 PMCID: PMC6821142 DOI: 10.1186/s43141-019-0006-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND Studying expression of genes by direct sequencing and analysis of metatranscriptomes at a particular time and space can disclose structural and functional insights about microbial communities. The present study reports comparative analysis of metatranscriptome from two distinct soil ecosystems referred as M1 (agriculture soil) and O1 (organic soil). RESULTS Analysis of sequencing reads revealed Proteobacteria as major dominant phyla in both soil types. The order of the top 3 abundant phyla in M1 sample was Proteobacteria > Ascomycota > Firmicutes, whereas in sample O1, the order was Proteobacteria > Cyanobacteria > Actinobacteria. Analysis of differentially expressed genes demonstrated high expression of transcripts related to copper-binding proteins, proteins involved in electron carrier activity, DNA integration, endonuclease activity, MFS transportation, and other uncharacterized proteins in M1 compared to O1. Of the particular interests, several transcripts related to nitrification, ammonification, stress response, and alternate carbon fixation pathways were highly expressed in M1. In-depth analysis of the sequencing data revealed that transcripts of archaeal origin had high expression in M1 compared to O1 indicating the active role of Archaea in metal- and pesticide-contaminated environment. In addition, transcripts encoding 4-hydroxyphenylpyruvate dioxygenase, glyoxalase/bleomycin resistance protein/dioxygenase, metapyrocatechase, and ring hydroxylating dioxygenases of aromatic hydrocarbon degradation pathways had high expression in M1. Altogether, this study provided important insights about the transcripts and pathways upregulating in the presence of pesticides and herbicides. CONCLUSION Altogether, this study claims a high expression of microbial transcripts in two ecosystems with a wide range of functions. It further provided clue about several molecular markers which could be a strong indicator of metal and pesticide contamination in soils. Interestingly, our study revealed that Archaea are playing a significant role in nitrification process as compared to bacteria in metal- and pesticide-contaminated soil. In particular, high expression of transcripts related to aromatic hydrocarbon degradation in M1 soil indicates their important role in biodegradation of pollutants, and therefore, further investigation is needed.
Collapse
Affiliation(s)
| | - Vinay Sharma
- Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407 India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Miyapur, Hyderabad, Telangana 500 049 India
| | - Garima Bhatia
- Department of Biotechnology, Panjab University, Chandigarh, 160014 India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, 160014 India
| | - Rohit Sharma
- Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407 India
| |
Collapse
|
22
|
Ferousi C, Lindhoud S, Baymann F, Hester ER, Reimann J, Kartal B. Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome. J Biol Chem 2019; 294:16953-16965. [PMID: 31582564 DOI: 10.1074/jbc.ra119.010568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/02/2019] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria convert nitrite and ammonium via nitric oxide (NO) and hydrazine into dinitrogen gas by using a diverse array of proteins, including numerous c-type cytochromes. Many new catalytic and spectroscopic properties of c-type cytochromes have been unraveled by studies on the biochemical pathways underlying the anammox process. The unique anammox intermediate hydrazine is produced by a multiheme cytochrome c protein, hydrazine synthase, through the comproportionation of ammonium and NO and the input of three electrons. It is unclear how these electrons are delivered to hydrazine synthase. Here, we report the discovery of a functional tetraheme c-type cytochrome from the anammox bacterium Kuenenia stuttgartiensis with a naturally-occurring contracted Cys-Lys-Cys-His (CKCH) heme-binding motif, which is encoded in the hydrazine synthase gene cluster. The purified tetraheme protein (named KsTH) exchanged electrons with hydrazine synthase. Complementary spectroscopic techniques revealed that this protein harbors four low-spin hexa-coordinated hemes with His/Lys (heme 1), His/Cys (heme 2), and two His/His ligations (hemes 3 and 4). A genomic database search revealed that c-type cytochromes with a contracted CXCH heme-binding motif are present throughout the bacterial and archaeal domains in the tree of life, suggesting that this heme recognition site may be employed by many different groups of microorganisms.
Collapse
Affiliation(s)
- Christina Ferousi
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Simon Lindhoud
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Frauke Baymann
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, Marseille Cedex 09, France
| | - Eric R Hester
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| |
Collapse
|
23
|
Lehtovirta-Morley LE. Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together. FEMS Microbiol Lett 2019; 365:4931719. [PMID: 29668934 DOI: 10.1093/femsle/fny058] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022] Open
Abstract
Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 -) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.
Collapse
Affiliation(s)
- Laura E Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| |
Collapse
|
24
|
Yoon S, Song B, Phillips RL, Chang J, Song MJ. Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems. FEMS Microbiol Ecol 2019; 95:5488431. [DOI: 10.1093/femsec/fiz066] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/10/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.
Collapse
Affiliation(s)
- Sukhwan Yoon
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Sciences, College of William and Mary, 1375 Greate Rd, Gloucester Point, VA 23062, USA
| | - Rebecca L Phillips
- Ecological Insights Corporation, 130 69th Street SE, Hazelton, ND 58544, USA
| | - Jin Chang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| |
Collapse
|
25
|
Corregido MC, Asención Diez MD, Iglesias AÁ, Piattoni CV. New pieces to the carbon metabolism puzzle of Nitrosomonas europaea: Kinetic characterization of glyceraldehyde-3 phosphate and succinate semialdehyde dehydrogenases. Biochimie 2019; 158:238-245. [PMID: 30690134 DOI: 10.1016/j.biochi.2019.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/19/2019] [Indexed: 02/02/2023]
Abstract
Nitrosomonas europaea is a chemolithotroph that obtains energy through the oxidation of ammonia to hydroxylamine while assimilates atmospheric CO2 to cover the cell carbon demands for growth. This microorganism plays a relevant role in the nitrogen biogeochemical cycle on Earth but its carbon metabolism remains poorly characterized. Based on sequence homology, we identified two genes (cbbG and gabD) coding for redox enzymes in N. europaea. Cloning and expression of the genes in Escherichia coli, allowed the production of recombinant enzymes purified to determine their biochemical properties. The protein CbbG is a glyceraldehyde-3-phosphate (Ga3P) dehydrogenase (Ga3PDHase) catalyzing the reversible oxidation of Ga3P to 1,3-bis-phospho-glycerate (1,3bisPGA), using specifically NAD+/NADH as cofactor. CbbG showed ∼6-fold higher Km value for 1,3bisPGA but ∼5-fold higher kcat for the oxidation of Ga3P. The protein GabD irreversibly oxidizes Ga3P to 3Pglycerate using NAD+ or NADP+, thus resembling a non-phosphorylating Ga3PDHase. However, the enzyme showed ∼6-fold higher Km value and three orders of magnitude higher catalytic efficiency with succinate semialdehyde (SSA) and NADP+. Indeed, the GabD protein identity corresponds to an SSA dehydrogenase (SSADHase). CbbG seems to be the only Ga3PDHase present in N. europaea; which would be involved in reducing triose-P during autotrophic carbon fixation. Otherwise, in cells grown under conditions deprived of ammonia and oxygen, the enzyme could catalyze the glycolytic step of Ga3P oxidation producing NADH. As an SSADHase, GabD would physiologically act producing succinate and preferentially NADPH over NADH; thus being part of an alternative pathway of the tricarboxylic acid cycle converting α-ketoglutarate to succinate. The properties determined for these enzymes contribute to better identify metabolic steps in CO2 assimilation, glycolysis and the tricarboxylic acid cycle in N. europaea. Results are discussed in the framework of metabolic pathways that launch biosynthetic intermediates relevant in the microorganism to develop and fulfill its role in nature.
Collapse
Affiliation(s)
- María Cecilia Corregido
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina
| | - Matías Damián Asención Diez
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina
| | - Alberto Álvaro Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina.
| | - Claudia Vanesa Piattoni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina; Instituto Pasteur de Montevideo, Montevideo, Uruguay.
| |
Collapse
|
26
|
Khadka R, Clothier L, Wang L, Lim CK, Klotz MG, Dunfield PF. Evolutionary History of Copper Membrane Monooxygenases. Front Microbiol 2018; 9:2493. [PMID: 30420840 PMCID: PMC6215863 DOI: 10.3389/fmicb.2018.02493] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/28/2018] [Indexed: 11/30/2022] Open
Abstract
Copper membrane monooxygenases (CuMMOs) oxidize ammonia, methane and some short-chain alkanes and alkenes. They are encoded by three genes, usually in an operon of xmoCAB. We aligned xmo operons from 66 microbial genomes, including members of the Alpha-, Beta-, and Gamma-proteobacteria, Verrucomicrobia, Actinobacteria, Thaumarchaeota and the candidate phylum NC10. Phylogenetic and compositional analyses were used to reconstruct the evolutionary history of the enzyme and detect potential lateral gene transfer (LGT) events. The phylogenetic analyses showed at least 10 clusters corresponding to a combination of substrate specificity and bacterial taxonomy, but with no overriding structure based on either function or taxonomy alone. Adaptation of the enzyme to preferentially oxidize either ammonia or methane has occurred more than once. Individual phylogenies of all three genes, xmoA, xmoB and xmoC, closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in Verrucomicrobia, where the pmoB gene has a distinct phylogeny from pmoA and pmoC. Compositional analyses indicated that some clusters of xmoCAB operons (for example, the pmoCAB in gammaproteobacterial methanotrophs and the amoCAB in betaproteobacterial nitrifiers) were compositionally very different from their genomes, possibly indicating recent lateral transfer of these operons. The combined phylogenetic and compositional analyses support the hypothesis that an ancestor of the nitrifying bacterium Nitrosococcus was the donor of methane monooxygenase (pMMO) to both the alphaproteobacterial and gammaproteobacterial methanotrophs, but that before this event the gammaproteobacterial methanotrophs originally possessed another CuMMO (Pxm), which has since been lost in many species.
Collapse
Affiliation(s)
- Roshan Khadka
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lindsay Clothier
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lin Wang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Chee Kent Lim
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Martin G Klotz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Richland, WA, United States.,State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
27
|
Fisher OS, Kenney GE, Ross MO, Ro SY, Lemma BE, Batelu S, Thomas PM, Sosnowski VC, DeHart CJ, Kelleher NL, Stemmler TL, Hoffman BM, Rosenzweig AC. Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria. Nat Commun 2018; 9:4276. [PMID: 30323281 PMCID: PMC6189053 DOI: 10.1038/s41467-018-06681-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/20/2018] [Indexed: 12/24/2022] Open
Abstract
Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-dependent enzyme particulate methane monooxygenase (pMMO). Isolated pMMO exhibits lower activity than whole cells, however, suggesting that additional components may be required. A pMMO homolog, ammonia monooxygenase (AMO), converts ammonia to hydroxylamine in ammonia-oxidizing bacteria (AOB) which produce another potent greenhouse gas, nitrous oxide. Here we show that PmoD, a protein encoded within many pmo operons that is homologous to the AmoD proteins encoded within AOB amo operons, forms a copper center that exhibits the features of a well-defined CuA site using a previously unobserved ligand set derived from a cupredoxin homodimer. PmoD is critical for copper-dependent growth on methane, and genetic analyses strongly support a role directly related to pMMO and AMO. These findings identify a copper-binding protein that may represent a missing link in the function of enzymes critical to the global carbon and nitrogen cycles. Methane- and ammonia-oxidizing bacteria use the integral membrane, copper-dependent enzymes particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) to oxidize methane and ammonia. Here the authors structurally characterize the copper-binding protein PmoD, which contains an unusual CuA site and their genetic analyses strongly support a pMMO and AMO related function of PmoD.
Collapse
Affiliation(s)
- Oriana S Fisher
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Grace E Kenney
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Matthew O Ross
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Soo Y Ro
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Betelehem E Lemma
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Paul M Thomas
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Victoria C Sosnowski
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Caroline J DeHart
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Brian M Hoffman
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, 60208, IL, USA.
| |
Collapse
|
28
|
Zorz JK, Kozlowski JA, Stein LY, Strous M, Kleiner M. Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria. Front Microbiol 2018; 9:938. [PMID: 29867847 PMCID: PMC5960693 DOI: 10.3389/fmicb.2018.00938] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022] Open
Abstract
Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.
Collapse
Affiliation(s)
- Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jessica A Kozlowski
- Department of Ecogenomics and Systems Biology, Division Archaea Biology and Ecogenomics, University of Vienna, Vienna, Austria
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
29
|
Carini P, Dupont CL, Santoro AE. Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Environ Microbiol 2018; 20:2112-2124. [PMID: 29626379 DOI: 10.1111/1462-2920.14107] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 to ammonia limitation using RNA-Seq. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new strain capable of urea utilization. Ammonia limitation in CN25 resulted in reduced expression of transcripts coding for ammonia oxidation proteins, and increased expression of a gene coding an Hsp20-like chaperone. Despite significantly different transcript abundances across treatments, two ammonia monooxygenase subunits (amoAB), a nitrite reductase (nirK) and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells expressed a urea transporter 139-fold more than the urease catalytic subunit ureC. Gene coexpression networks derived from culture transcriptomes and 10 thaumarchaea-enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions and identified a module of coexpressed genes, including amoABC and nirK, that we hypothesize to represent the core ammonia oxidation machinery.
Collapse
Affiliation(s)
- Paul Carini
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | | | - Alyson E Santoro
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| |
Collapse
|
30
|
Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes. Appl Environ Microbiol 2018. [PMID: 29427421 DOI: 10.1128/aem.02615‐17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.
Collapse
|
31
|
Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes. Appl Environ Microbiol 2018; 84:AEM.02615-17. [PMID: 29427421 DOI: 10.1128/aem.02615-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/28/2018] [Indexed: 01/20/2023] Open
Abstract
Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.
Collapse
|
32
|
Phylogenomic analysis demonstrates a pattern of rare and long-lasting concerted evolution in prokaryotes. Commun Biol 2018; 1:12. [PMID: 30271899 PMCID: PMC6053082 DOI: 10.1038/s42003-018-0014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/11/2018] [Indexed: 12/15/2022] Open
Abstract
Concerted evolution, where paralogs in the same species show higher sequence similarity to each other than to orthologs in other species, is widely found in many species. However, cases of concerted evolution that last for hundreds of millions of years are very rare. By genome-wide analysis of a broad selection of prokaryotes, we provide strong evidence of recurrent concerted evolution in 26 genes, most of which have lasted more than ~500 million years. We find that most concertedly evolving genes are key members of important pathways, and encode proteins from the same complexes and/or pathways, suggesting coevolution of genes via concerted evolution to maintain gene balance. We also present LRCE-DB, a comprehensive online repository of long-lasting concerted evolution. Collectively, our study reveals that although most duplicated genes may diverge in sequence over a long period, on rare occasions this constraint can be breached, leading to unexpected long-lasting concerted evolution in a recurrent manner. Sishuo Wang and Youhua Chen present an analysis of concerted evolution in prokaryotes using a new computational pipeline, iSeeCE. They find evidence in 26 genes for recurrent concerted evolution, most of which last more than ~500 million years, and provide a database, LRCE-DB, for data exploration.
Collapse
|
33
|
Chen H, Li A, Cui D, Wang Q, Wu D, Cui C, Ma F. N-Acyl-homoserine lactones and autoinducer-2-mediated quorum sensing during wastewater treatment. Appl Microbiol Biotechnol 2017; 102:1119-1130. [DOI: 10.1007/s00253-017-8697-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/16/2022]
|
34
|
Yang W, Wang Y, Tago K, Tokuda S, Hayatsu M. Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols. Front Microbiol 2017; 8:2226. [PMID: 29184545 PMCID: PMC5694480 DOI: 10.3389/fmicb.2017.02226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/30/2017] [Indexed: 11/13/2022] Open
Abstract
Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.
Collapse
Affiliation(s)
- Wenjie Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, China
| | - Yong Wang
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kanako Tago
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Shinichi Tokuda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Kyoto, Japan
| | - Masahito Hayatsu
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| |
Collapse
|
35
|
Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
Collapse
Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
| |
Collapse
|
36
|
Moitinho-Silva L, Díez-Vives C, Batani G, Esteves AIS, Jahn MT, Thomas T. Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics. THE ISME JOURNAL 2017; 11:1651-1666. [PMID: 28338677 PMCID: PMC5520145 DOI: 10.1038/ismej.2017.25] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/10/2017] [Accepted: 01/19/2017] [Indexed: 12/21/2022]
Abstract
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales. Gene expression was estimated by mapping C. concentrica metatranscriptomic reads. Our analyses indicated that CcPhy is heterotrophic, while CcNi and CcThau are chemolithoautotrophs. CcPhy expressed many transporters for the acquisition of dissolved organic compounds, likely available through the sponge's filtration activity and symbiotic carbon fixation. Coupled nitrification by CcThau and CcNi was reconstructed, supported by the observed close proximity of the cells in fluorescence in situ hybridization. CcPhy facultative anaerobic respiration and assimilation by diatoms may consume the resulting nitrate. Transcriptional analysis of diatom and sponge functions indicated that these organisms are likely sources of organic compounds, for example, creatine/creatinine and dissolved organic carbon, for other members of the symbiosis. Our results suggest that organic nitrogen compounds, for example, creatine, creatinine, urea and cyanate, fuel the nitrogen cycle within the sponge. This study provides an unprecedented view of the metabolic interactions within sponge-microbe symbiosis, bridging the gap between cell- and community-level knowledge.
Collapse
Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Cristina Díez-Vives
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Giampiero Batani
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Ana IS Esteves
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Martin T Jahn
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
37
|
Wang Y, Ma L, Mao Y, Jiang X, Xia Y, Yu K, Li B, Zhang T. Comammox in drinking water systems. WATER RESEARCH 2017; 116:332-341. [PMID: 28390307 DOI: 10.1016/j.watres.2017.03.042] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 03/18/2017] [Accepted: 03/18/2017] [Indexed: 05/04/2023]
Abstract
The discovery of complete ammonia oxidizer (comammox) has fundamentally upended our perception of the global nitrogen cycle. Here, we reported four metagenome assembled genomes (MAGs) of comammox Nitrospira that were retrieved from metagenome datasets of tap water in Singapore (SG-bin1 and SG-bin2), Hainan province, China (HN-bin3) and Stanford, CA, USA (ST-bin4). Genes of phylogenetically distinct ammonia monooxygenase subunit A (amoA) and hydroxylamine dehydrogenase (hao) were identified in these four MAGs. Phylogenetic analysis based on ribosomal proteins, AmoA, hao and nitrite oxidoreductase (subunits nxrA and nxrB) sequences indicated their close relationships with published comammox Nitrospira. Canonical ammonia-oxidizing microbes (AOM) were also identified in the three tap water samples, ammonia-oxidizing bacteria (AOB) in Singapore's and Stanford's samples and ammonia-oxidizing archaea (AOA) in Hainan's sample. The comammox amoA-like sequences were also detected from some other drinking water systems, and even outnumbered the AOA and AOB amoA-like sequences. The findings of MAGs and the occurrences of AOM in different drinking water systems provided a significant clue that comammox are widely distributed in drinking water systems.
Collapse
Affiliation(s)
- Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Liping Ma
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yu Xia
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Ke Yu
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Bing Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong.
| |
Collapse
|
38
|
Oshiki M, Takagi R, Hatamoto M, Yamaguchi T, Araki N. High-cell-density cultivation of Nitrosomonas europaea in a membrane bioreactor for performing protein purification and characterization studies. J GEN APPL MICROBIOL 2017; 62:330-333. [PMID: 27773917 DOI: 10.2323/jgam.2016.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | | | | | | | | |
Collapse
|
39
|
Kozlowski JA, Kits KD, Stein LY. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria. Front Microbiol 2016; 7:1090. [PMID: 27462312 PMCID: PMC4940428 DOI: 10.3389/fmicb.2016.01090] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity.
Collapse
Affiliation(s)
- Jessica A Kozlowski
- Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada
| | - K Dimitri Kits
- Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada
| | - Lisa Y Stein
- Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada
| |
Collapse
|
40
|
Wagner FB, Nielsen PB, Boe-Hansen R, Albrechtsen HJ. Copper deficiency can limit nitrification in biological rapid sand filters for drinking water production. WATER RESEARCH 2016; 95:280-288. [PMID: 27010788 DOI: 10.1016/j.watres.2016.03.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 06/05/2023]
Abstract
Incomplete nitrification in biological filters during drinking water treatment is problematic, as it compromises drinking water quality. Nitrification problems can be caused by a lack of nutrients for the nitrifying microorganisms. Since copper is an important element in one of the essential enzymes in nitrification, we investigated the effect of copper dosing on nitrification in different biological rapid sand filters treating groundwater. A lab-scale column assay with filter material from a water works demonstrated that addition of a trace metal mixture, including copper, increased ammonium removal compared to a control without addition. Subsequently, another water works was investigated in full-scale, where copper influent concentrations were below 0.05 μg Cu L(-1) and nitrification was incomplete. Copper dosing of less than 5 μg Cu L(-1) to a full-scale filter stimulated ammonium removal within one day, and doubled the filter's removal from 0.22 to 0.46 g NH4-N m(-3) filter material h(-1) within 20 days. The location of ammonium and nitrite oxidation shifted upwards in the filter, with an almost 14-fold increase in ammonium removal rate in the filter's top 10 cm, within 57 days of dosing. To study the persistence of the stimulation, copper was dosed to another filter at the water works for 42 days. After dosing was stopped, nitrification remained complete for at least 238 days. Filter effluent concentrations of up to 1.3 μg Cu L(-1) confirmed that copper fully penetrated the filters, and determination of copper content on filter media revealed a buildup of copper during dosing. The amount of copper stored on filter material gradually decreased after dosing stopped; however at a slower rate than it accumulated. Continuous detection of copper in the filter effluent confirmed a release of copper to the bulk phase. Overall, copper dosing to poorly performing biological rapid sand filters increased ammonium removal rates significantly, achieving effluent concentrations of below 0.01 mg NH4-N L(-1), and had a long-term effect on nitrification performance.
Collapse
Affiliation(s)
- Florian B Wagner
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet, Building 115, 2800 Kgs. Lyngby, Denmark.
| | | | | | - Hans-Jørgen Albrechtsen
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet, Building 115, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
41
|
Wang L, Lim CK, Dang H, Hanson TE, Klotz MG. D1FHS, the Type Strain of the Ammonia-Oxidizing Bacterium Nitrosococcus wardiae spec. nov.: Enrichment, Isolation, Phylogenetic, and Growth Physiological Characterization. Front Microbiol 2016; 7:512. [PMID: 27148201 PMCID: PMC4830845 DOI: 10.3389/fmicb.2016.00512] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/29/2016] [Indexed: 11/30/2022] Open
Abstract
An ammonia-oxidizing bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4(T). The average nucleotide identity between the genomes of strain D1FHS and N. halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic ammonia-oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37°C in dark. Because pertinent conditions for other studied Nitrosococcus spp. are 100-200 mM ammonium and <700 mM NaCl at pH of 7.5 to 8.0 and at 28-32°C, D1FHS is physiologically distinct from other Nitrosococcus spp. in terms of substrate, salt, and thermal tolerance.
Collapse
Affiliation(s)
- Lin Wang
- Evolutionary and Genomic Microbiology, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
| | - Chee Kent Lim
- Evolutionary and Genomic Microbiology, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
- Joint Research Center for Carbon Sink: The Institute of Marine Microbes and Ecospheres, Xiamen University and the Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Thomas E. Hanson
- School of Marine Science and Policy, College of Earth, Ocean, and Environment, University of DelawareNewark, DE, USA
- Delaware Biotechnology Institute, University of DelawareNewark, DE, USA
| | - Martin G. Klotz
- Evolutionary and Genomic Microbiology, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
- Joint Research Center for Carbon Sink: The Institute of Marine Microbes and Ecospheres, Xiamen University and the Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
- Evolutionary and Genomic Microbiology, Department of Biology and School of Earth and Environmental Sciences, Queens College, The City University of New YorkFlushing, NY, USA
| |
Collapse
|
42
|
Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00094-16. [PMID: 26966201 PMCID: PMC4786657 DOI: 10.1128/genomea.00094-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome of Nitrosomonas ureae strain Nm10, a mesophilic betaproteobacterial ammonia oxidizer isolated from Mediterranean soils in Sardinia, Italy, is reported here. This genome represents a cluster 6a nitrosomonad.
Collapse
|
43
|
Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota. ISME JOURNAL 2016; 10:1836-45. [PMID: 26882267 DOI: 10.1038/ismej.2016.2] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 12/14/2015] [Accepted: 12/24/2015] [Indexed: 11/08/2022]
Abstract
Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76(T) exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196(T). In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions.
Collapse
|
44
|
Gagnon J, Clift MJD, Vanhecke D, Widnersson IE, Abram SL, Petri-Fink A, Caruso RA, Rothen-Rutishauser B, Fromm KM. Synthesis, characterization, antibacterial activity and cytotoxicity of hollow TiO2-coated CeO2nanocontainers encapsulating silver nanoparticles for controlled silver release. J Mater Chem B 2016; 4:1166-1174. [DOI: 10.1039/c5tb01917f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This novel type of nanocontainers offers the concept of potentially controlling silver delivery for the prevention of implant-associated infections.
Collapse
Affiliation(s)
- J. Gagnon
- Department of Chemistry and Fribourg Center for Nanomaterials
- University of Fribourg
- 1700 Fribourg
- Switzerland
- PFPC
| | - M. J. D. Clift
- Adolphe Merkle Institute
- University of Fribourg
- 1700 Fribourg
- Switzerland
| | - D. Vanhecke
- Adolphe Merkle Institute
- University of Fribourg
- 1700 Fribourg
- Switzerland
| | - I. E. Widnersson
- PFPC
- School of Chemistry
- The University of Melbourne
- Melbourne, Victoria 3010
- Australia
| | - S.-L. Abram
- Department of Chemistry and Fribourg Center for Nanomaterials
- University of Fribourg
- 1700 Fribourg
- Switzerland
| | - A. Petri-Fink
- Adolphe Merkle Institute
- University of Fribourg
- 1700 Fribourg
- Switzerland
| | - R. A. Caruso
- PFPC
- School of Chemistry
- The University of Melbourne
- Melbourne, Victoria 3010
- Australia
| | | | - K. M. Fromm
- Department of Chemistry and Fribourg Center for Nanomaterials
- University of Fribourg
- 1700 Fribourg
- Switzerland
| |
Collapse
|
45
|
Chang A, Peng Y, Li Z, Yu X, Hong K, Zhou S, Wu W. Assembly of polythiophenes on responsive polymer microgels for the highly selective detection of ammonia gas. Polym Chem 2016. [DOI: 10.1039/c5py02014j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel material that allows highly selective ammonia-to-conductance signal transduction is prepared by the assembly of polythiophenes on responsive polymer microgels.
Collapse
Affiliation(s)
- Aiping Chang
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- and Department of Chemistry
- College of Chemistry and Chemical Engineering
| | - Yahui Peng
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- and Department of Chemistry
- College of Chemistry and Chemical Engineering
| | - Zezhou Li
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- and Department of Chemistry
- College of Chemistry and Chemical Engineering
| | - Xiang Yu
- Chemical Sciences Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Center for Nanophase Materials Sciences
| | - Kunlun Hong
- Center for Nanophase Materials Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Shuiqin Zhou
- Department of Chemistry and The Center for Engineered Polymeric Materials of College of Staten Island
- and The Graduate Center
- The City University of New York
- Staten Island
- USA
| | - Weitai Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Collaborative Innovation Center of Chemistry for Energy Materials
- The Key Laboratory for Chemical Biology of Fujian Province
- and Department of Chemistry
- College of Chemistry and Chemical Engineering
| |
Collapse
|
46
|
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M. Complete nitrification by Nitrospira bacteria. Nature 2015; 528:504-9. [PMID: 26610024 PMCID: PMC5152751 DOI: 10.1038/nature16461] [Citation(s) in RCA: 1111] [Impact Index Per Article: 123.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/19/2015] [Indexed: 11/11/2022]
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
Collapse
Affiliation(s)
- Holger Daims
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Elena V. Lebedeva
- Winogradsky Institute of Microbiology, Research Center of
Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071
Moscow, Russia
| | - Petra Pjevac
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Ping Han
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Craig Herbold
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marton Palatinszky
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Julia Vierheilig
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Alexandr Bulaev
- Winogradsky Institute of Microbiology, Research Center of
Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071
Moscow, Russia
| | - Rasmus H. Kirkegaard
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Proteomics, Permoserstr. 15, 04318 Leipzig, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Department of
Metabolomics, Permoserstr. 15, 04318 Leipzig, Germany
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of
Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| | - Bernd Bendinger
- DVGW-Forschungsstelle TUHH, Hamburg University of Technology, 21073
Hamburg, Germany
| | - Per H. Nielsen
- Center for Microbial Communities, Department of Chemistry and
Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of
Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna,
Austria
| |
Collapse
|
47
|
Ni BJ, Yuan Z. Recent advances in mathematical modeling of nitrous oxides emissions from wastewater treatment processes. WATER RESEARCH 2015; 87:336-46. [PMID: 26451976 DOI: 10.1016/j.watres.2015.09.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/27/2015] [Accepted: 09/28/2015] [Indexed: 05/20/2023]
Abstract
Nitrous oxide (N2O) can be emitted from wastewater treatment contributing to its greenhouse gas footprint significantly. Mathematical modeling of N2O emissions is of great importance toward the understanding and reduction of the environmental impact of wastewater treatment systems. This article reviews the current status of the modeling of N2O emissions from wastewater treatment. The existing mathematical models describing all the known microbial pathways for N2O production are reviewed and discussed. These included N2O production by ammonia-oxidizing bacteria (AOB) through the hydroxylamine oxidation pathway and the AOB denitrification pathway, N2O production by heterotrophic denitrifiers through the denitrification pathway, and the integration of these pathways in single N2O models. The calibration and validation of these models using lab-scale and full-scale experimental data is also reviewed. We conclude that the mathematical modeling of N2O production, while is still being enhanced supported by new knowledge development, has reached a maturity that facilitates the estimation of site-specific N2O emissions and the development of mitigation strategies for a wastewater treatment plant taking into the specific design and operational conditions of the plant.
Collapse
Affiliation(s)
- Bing-Jie Ni
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia.
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| |
Collapse
|
48
|
Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns. Appl Microbiol Biotechnol 2015; 100:1843-1852. [DOI: 10.1007/s00253-015-7095-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/04/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
|
49
|
Zhou L, Wang S, Zou Y, Xia C, Zhu G. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China. Sci Rep 2015; 5:15969. [PMID: 26522086 PMCID: PMC4629152 DOI: 10.1038/srep15969] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/06/2015] [Indexed: 12/28/2022] Open
Abstract
Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.
Collapse
Affiliation(s)
- Leiliu Zhou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Yuxuan Zou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Chao Xia
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China.,Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Breme, Germany
| |
Collapse
|
50
|
Reis MP, Ávila MP, Keijzer RM, Barbosa FAR, Chartone-Souza E, Nascimento AMA, Laanbroek HJ. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Front Microbiol 2015; 6:898. [PMID: 26379659 PMCID: PMC4553384 DOI: 10.3389/fmicb.2015.00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
Collapse
Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| |
Collapse
|