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Wu YJ, Wu JY, Hsieh CW, Chang BC, Whang LM. Biological treatment of N-methylpyrrolidone, cyclopentanone, and diethylene glycol monobutyl ether distilled residues and their effects on nitrogen removal in a full-scale wastewater treatment plant. CHEMOSPHERE 2024:142585. [PMID: 38866333 DOI: 10.1016/j.chemosphere.2024.142585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024]
Abstract
Manufacturing processes in semiconductor and photonics industries involve the use of a significant amount of organic solvents. Recycle and reuse of these solvents produce distillate residues and require treatment before being discharged. This study aimed to evaluate the performance of the biological treatment system in a full-scale wastewater treatment plant that treats wastewater containing distillate residues from the recycling of electronic chemicals. Batch experiments were conducted to investigate the optimal operational conditions for the full-scale wastewater treatment plant. To achieve good nitrogen removal efficiency with effluent ammonia and nitrate concentrations below 20 mg N/L and 50 mg N/L, respectively, it was suggested to control the ammonia concentration and pH of the influent below 500 mg N/L and 8.0, respectively. In addition, the biodegradability of N-methylpyrrolidone, diethylene glycol monobutyl ether, and cyclopentanone distillate residues from the electronic chemicals manufacturing process were evaluated under aerobic, anoxic, and anaerobic conditions. N-methylpyrrolidone and cyclopentanone distillate residues were suggested to be treated under anoxic condition. However, substrate inhibition occurred when using cyclopentanone distillate residue as a carbon source with chemical oxygen demand (COD) levels higher than 866 mg/L and nitrate levels higher than 415 mg N/L. Under aerobic condition, the COD from both N-methylpyrrolidone and cyclopentanone distillate residues could be easily degraded. Nevertheless, a negative effect on nitrification was observed, with a prolonged lag time for ammonia oxidation as the initial COD concentration increased. The specific ammonia oxidation rate and nitrate production rate decreased under high COD concentration contributed by N-methylpyrrolidone and cyclopentanone distillate residues. Furthermore, the biodegradability of diethylene glycol monobutyl ether distillate residue was found to be low under aerobic, anoxic, and anaerobic conditions. With respect to the abundance of nitrogen removal microorganisms in the wastewater treatment plant, results showed that Comammox may have an advantage over ammonia oxidizing bacteria under high pH conditions. In addition, Comammox may have higher resistance to environmental changes. Dominance of Comammox over ammonia oxidizing bacteria under high ammonia condition was first reported in this study.
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Affiliation(s)
- Yi-Ju Wu
- Department of Environmental Engineering
| | - Jie-Yu Wu
- Department of Environmental Engineering
| | | | | | - Liang-Ming Whang
- Department of Environmental Engineering; Sustainable Environment Research Laboratory (SERL), National Cheng Kung University (NCKU), No. 1, University Road, Tainan 701, Taiwan.
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2
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Loi JX, Syutsubo K, Rabuni MF, Takemura Y, Aoki M, Chua ASM. Downflow sponge biofilm reactors for polluted raw water treatment: Performance optimisation, kinetics, and microbial community. CHEMOSPHERE 2024; 358:142156. [PMID: 38679172 DOI: 10.1016/j.chemosphere.2024.142156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Water outages caused by elevated ammonium (NH4+-N) levels are a prevalent problem faced by conventional raw water treatment plants in developing countries. A treatment solution requires a short hydraulic retention time (HRT) to overcome nitrification rate limitation in oligotrophic conditions. In this study, the performance of polluted raw water treatment using a green downflow sponge biofilm (DSB) technology was evaluated. We operated two DSB reactors, DSB-1 and DSB-2 under different NH4+-N concentration ranges (DSB-1: 3.2-5.0 mg L-1; DSB-2: 1.7-2.6 mg L-1) over 360 days and monitored their performance under short HRT (60 min, 30 min, 20 min, and 15 min). The experimental results revealed vertical segregation of organic removal in the upper reactor depths and nitrification in the lower depths. Under the shortest HRT of 15 min, both DSB reactors achieved stable NH4+-N and chemical oxygen demand removal (≥95%) and produced minimal effluent nitrite (NO2--N). DSB system could facilitate complete NH4+-N oxidation to nitrate (NO3--N) without external aeration energy requirement. The 16S rRNA sequencing data revealed that nitrifying bacteria Nitrosomonas and Nitrospira in the reactor were stratified. Putative comammox bacteria with high ammonia affinity was successfully enriched in DSB-2 operating at a lower NH4+-N loading rate, which is advantageous in oligotrophic treatment. This study suggests that a high hydraulic rate DSB system with efficient ammonia removal could incorporate ammonia treatment capability into polluted raw water treatment process and ensure safe water supply in many developing countries.
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Affiliation(s)
- Jia Xing Loi
- Sustainable Process Engineering Centre, Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kazuaki Syutsubo
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan; Research Centre of Water Environment Technology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
| | - Mohamad Fairus Rabuni
- Sustainable Process Engineering Centre, Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yasuyuki Takemura
- Department of Civil Engineering, National Institute of Technology, Wakayama College, Gobo, Wakayama, 644-0023, Japan.
| | - Masataka Aoki
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan.
| | - Adeline Seak May Chua
- Sustainable Process Engineering Centre, Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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3
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Abasi S, Tarre S, Green M. Nitrous Oxide Emissions from Nitritation Reactors under Hypersaline Conditions. BIORESOURCE TECHNOLOGY 2024; 399:130639. [PMID: 38552863 DOI: 10.1016/j.biortech.2024.130639] [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: 12/13/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
This study focuses on nitrous oxide (N2O) emissions during hypersaline (4 % salinity) nitritation in continuously fed and mixed fixed bed reactors. In the presence of high concentrations of nitrite and ammonium, the percent yield of N2O emissions from ammonium removed decreased with increasing dissolved oxygen (DO). However, N2O production continued even at a high DO of 15 mg/L. Bulk ammonium concentration (not ammonia) was found to be the main controlling factor for N2O emissions under high and low DO during both nitritation and nitrification. Reducing bulk ammonium concentrations below 1 mg N/L in the nitritation reactor under both high and low DO conditions resulted in a reduction of N2O emissions of approximately 90 %. Under full nitrification and low DO, reducing nitrite concentrations below 0.3 mg N/L resulted in a 60 % reduction in N2O emissions. Similar results were observed in a low salinity reactor.
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Affiliation(s)
- Samah Abasi
- Faculty of Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - Sheldon Tarre
- Faculty of Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - Michal Green
- Faculty of Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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4
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Zheng R, Feng Y, Kong L, Wu X, Zhou J, Zhang L, Liu S. Blue-light irradiation induced partial nitrification. WATER RESEARCH 2024; 254:121381. [PMID: 38442606 DOI: 10.1016/j.watres.2024.121381] [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: 08/21/2023] [Revised: 12/08/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
The role of ray radiation from the sunlight acting on organisms has long-term been investigated. However, how the light with different wavelengths affects nitrification and the involved nitrifiers are still elusive. Here, we found more than 60 % of differentially expressed genes (DEGs) in nitrifiers were observed under irradiation of blue light with wavelengths of 440-480 nm, which were 13.4 % and 20.3 % under red light and white light irradiation respectively. Blue light was more helpful to achieve partial nitrification rather than white light or red light, where ammonium oxidization by ammonia-oxidizing archaea (AOA) with the increased relative abundance from 8.6 % to 14.2 % played a vital role. This was further evidenced by the enhanced TCA cycle, reactive oxygen species (ROS) scavenge and DNA repair capacity in AOA under blue-light irradiation. In contrast, nitrite-oxidizing bacteria (NOB) was inhibited severely to achieve partial nitrification, and the newly discovered encoded blue light photoreceptor proteins made them more sensitive to blue light and hindered cell activity. Ammonia-oxidizing bacteria (AOB) expressed genes for DNA repair capacity under blue-light irradiation, which ensured their tiny impact by light irradiation. This study provided valuable insights into the photosensitivity mechanism of nitrifiers and shed light on the diverse regulatory by light with different radiation wavelengths in artificial systems, broadening our comprehension of the nitrogen cycle on earth.
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Affiliation(s)
- Ru Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Lingrui Kong
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Xiaogang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Jianhang Zhou
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Liguo Zhang
- School of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China.
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5
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Lian C, Xiang J, Cai H, Ke J, Ni H, Zhu J, Zheng Z, Lu K, Yang W. Microalgae Inoculation Significantly Shapes the Structure, Alters the Assembly Process, and Enhances the Stability of Bacterial Communities in Shrimp-Rearing Water. BIOLOGY 2024; 13:54. [PMID: 38275730 PMCID: PMC10813777 DOI: 10.3390/biology13010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Intensive shrimp farming may lead to adverse environmental consequences due to discharged water effluent. Inoculation of microalgae can moderate the adverse effect of shrimp-farming water. However, how bacterial communities with different lifestyles (free-living (FL) and particle-attached (PA)) respond to microalgal inoculation is unclear. In the present study, we investigated the effects of two microalgae (Nannochloropsis oculata and Thalassiosira weissflogii) alone or in combination in regulating microbial communities in shrimp-farmed water and their potential applications. PERMANOVA revealed significant differences among treatments in terms of time and lifestyle. Community diversity analysis showed that PA bacteria responded more sensitively to different microalgal treatments than FL bacteria. Redundancy analysis (RDA) indicated that the bacterial community was majorly influenced by environmental factors, compared to microalgal direct influence. Moreover, the neutral model analysis and the average variation degree (AVD) index indicated that the addition of microalgae affected the bacterial community structure and stability during the stochastic process, and the PA bacterial community was the most stable with the addition of T. weissflogii. Therefore, the present study revealed the effects of microalgae and nutrient salts on bacterial communities in shrimp aquaculture water by adding microalgae to control the process of community change. This study is important for understanding the microbial community assembly and interpreting complex interactions among zoo-, phyto-, and bacterioplankton in shrimp aquaculture ecosystems. Additionally, these findings may contribute to the sustainable development of shrimp aquaculture and ecosystem conservation.
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Affiliation(s)
- Chen Lian
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
| | - Jie Xiang
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
| | - Huifeng Cai
- Fishery Technical Management Service Station of Yinzhou District, Ningbo 315100, China;
| | - Jiangdong Ke
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
| | - Heng Ni
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
| | - Jinyong Zhu
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
| | - Zhongming Zheng
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
| | - Kaihong Lu
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
| | - Wen Yang
- School of Marine Sciences, Ningbo University, No. 169 Qixingnan Road, Beilun District, Ningbo 315832, China; (C.L.); (J.X.); (J.K.); (H.N.); (J.Z.); (Z.Z.); (K.L.)
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6
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Freeman CN, Russell JN, Yost CK. Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system. Microbiol Spectr 2024; 12:e0283223. [PMID: 38018980 PMCID: PMC10783093 DOI: 10.1128/spectrum.02832-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.
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Affiliation(s)
- Claire N. Freeman
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Chris K. Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
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7
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Adam-Beyer N, Laufer-Meiser K, Fuchs S, Schippers A, Indenbirken D, Garbe-Schönberg D, Petersen S, Perner M. Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge. Front Microbiol 2023; 14:1173613. [PMID: 37886064 PMCID: PMC10598711 DOI: 10.3389/fmicb.2023.1173613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.
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Affiliation(s)
- Nicole Adam-Beyer
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Katja Laufer-Meiser
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sebastian Fuchs
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | | | | | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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8
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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9
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Khanthong K, Jang H, Kadam R, Jo S, Lee J, Park J. Bioelectrochemical system for nitrogen removal: Fundamentals, current status, trends, and challenges. CHEMOSPHERE 2023; 339:139776. [PMID: 37567277 DOI: 10.1016/j.chemosphere.2023.139776] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Biological nitrogen removal (BNR) is essential for the treatment of nitrogen-containing wastewater. However, the requirement for aeration and the addition of external carbon sources, resulting in greenhouse gas emissions and additional costs, are disadvantages of the traditional BNR process. Alternative technologies have been devised to overcome these drawbacks. Bioelectrochemical nitrogen removal (BENR) has been proposed for efficient nitrogen removal, demonstrating flexibility and versatility. BENR can be performed by combining nitrification, denitrification, anaerobic ammonium oxidation (ANAMMOX), or organic carbon oxidation. Bioelectrochemical-ANAMMOX (BE-ANAMMOX) is the most promising method for nitrogen removal, as it can directly convert NH4+ to N2 and H2 in one step when the electrode is arranged as an electron acceptor. High-value-added hydrogen can potentially be recovered with efficient nitrogen removal using this concept, maximizing the benefits of BENR. Using alternative electron acceptors, such as electrodes and metal ions, for complete total nitrogen removal is a promising technology to substitute NO2- production from NH4+ oxidation by aeration. However, the requirement of electron donors for NO3- reduction, low NH4+ removal efficiency, and low competitiveness of exoelectrogenic bacteria still remain the main obstacles. The future direction for successful BENR should aim to achieve complete anaerobic NH4+ oxidation without any electron acceptor and to maximize selectivity in H2 production. Therefore, the bioelectrochemical pathways and balances between efficient nitrogen removal and high-value-added chemical production should be further studied for carbon and energy neutralities.
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Affiliation(s)
- Kamonwan Khanthong
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea.
| | - Heewon Jang
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Rahul Kadam
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Sangyeol Jo
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Jonghwa Lee
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Jungyu Park
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea.
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10
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Zhao W, Bi X, Bai M, Wang Y. Research advances of ammonia oxidation microorganisms in wastewater: metabolic characteristics, microbial community, influencing factors and process applications. Bioprocess Biosyst Eng 2023; 46:621-633. [PMID: 36988685 DOI: 10.1007/s00449-023-02866-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Ammonia oxidation carried out by ammonia-oxidizing microorganisms (AOMs) is a central step in the global nitrogen cycle. Aerobic AOMs comprise conventional ammonia-oxidizing bacteria (AOB), novel ammonia-oxidizing archaea (AOA), which could exist in complex and extreme conditions, and complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate within a single cell. Anaerobic AOMs mainly comprise anaerobic ammonia-oxidizing bacteria (AnAOB), which can transform NH4+-N and NO2--N into N2 under anaerobic conditions. In this review, the unique metabolic characteristics, microbial community of AOMs and the influencing factors are discussed. Process applications of nitrification/denitrification, nitritation/denitrification, nitritation/anammox and partial denitrification/anammox in wastewater treatment systems are emphasized. The future development of nitrogen removal processes using AOMs is expected, enrichment of comammox facilitates the complete nitrification performance, inhibiting the activity of comammox and NOB could achieve stable nitritation, and additionally, AnAOB conducting the anammox process in municipal wastewater is a promising development direction.
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Affiliation(s)
- Weihua Zhao
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China.
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, People's Republic of China.
- Qingdao University of Technology, Huangdao District, Qingdao, 266525, People's Republic of China.
| | - Xuejun Bi
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Meng Bai
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Yanyan Wang
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
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11
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Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4. Appl Environ Microbiol 2023; 89:e0196522. [PMID: 36719237 PMCID: PMC9973019 DOI: 10.1128/aem.01965-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.
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Ohbayashi T, Wang Y, Aoyagi LN, Hara S, Tago K, Hayatsu M. Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils. Microbes Environ 2023; 38:ME23068. [PMID: 38092410 PMCID: PMC10728637 DOI: 10.1264/jsme2.me23068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.
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Affiliation(s)
- Tsubasa Ohbayashi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Luciano Nobuhiro Aoyagi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Shintaro Hara
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
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Ye J, Wu J, Deng W, Li Y, Jiang C, Wang Y, Hong Y. Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea. MARINE POLLUTION BULLETIN 2022; 185:114351. [PMID: 36401947 DOI: 10.1016/j.marpolbul.2022.114351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/26/2022] [Accepted: 11/06/2022] [Indexed: 06/16/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.
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Affiliation(s)
- Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Wenfang Deng
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yiben Li
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Cuihong Jiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
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Xie C, Ma X, Zhao Y, Dai T, Song W, Qi Q, Feng J, Cui X, Zhou J, Huang X, Qi F, Zeng Y, Zhou J, Lin G, Yang Y. Nitrogen addition and warming rapidly alter microbial community compositions in the mangrove sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157992. [PMID: 35970461 DOI: 10.1016/j.scitotenv.2022.157992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The mangrove ecosystem is an important CO2 sink with an extraordinarily high primary productivity. However, it is vulnerable to the impact of climate warming and eutrophication. While there has been extensive research on plant growth and greenhouse gas emission in mangrove ecosystems, microbial communities, the primary biogeochemical cycling drivers, are much less understood. Here, we examined whether short-term experimental treatments: (1) eutrophication with a supplement of 185 g N m-2·year-1 (N), (2) 3°C warming (W), and (3) the dual treatment of N and W (NW) were sufficient to alter microbial communities in the sediment. After 4 months of experiments, most environmental factors remained unchanged. However, N had significant, strong effects on bacterial, fungal, and functional community compositions, while the effects of W on microbial communities were weaker. N increased bacterial richness, phylogenetic diversity, and evenness, owing to stronger stochastic processes induced by eutrophication. There were no interactive effects of N and W on bacterial, fungal, and functional community compositions, suggesting that joint effects of N and W were additive. Concomitant with higher N2O efflux induced by N, the relative abundances of most bacterial nitrogen cycling genes were increased or remained changed by N. In contrast, N decreased or did not change those of most bacterial carbon degradation genes, while W increased or did not change the relative abundances of most of bacterial and fungal carbon degradation genes, implying higher carbon degradation potentials. As the most abundant inorganic nitrogenous species in mangrove sediment, ammonium was a key factor in shaping microbial functional communities. Collectively, our findings showed that microbial community compositions in the mangrove sediment were highly sensitive to short-term N and W treatments, giving rise to ecological consequences such as higher N2O efflux.
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Affiliation(s)
- Changyi Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yan Zhao
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Tianjiao Dai
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weimin Song
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; The Yellow River Delta Ecology Research Station of Coastal Wetland, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianxiang Feng
- Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China; School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiaowei Cui
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Jian Zhou
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Fei Qi
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Guanghui Lin
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Urakawa H, Andrews GA, Lopez JV, Martens-Habbena W, Klotz MG, Stahl DA. Nitrosomonas supralitoralis sp. nov., an ammonia-oxidizing bacterium from beach sand in a supralittoral zone. Arch Microbiol 2022; 204:560. [PMID: 35978059 DOI: 10.1007/s00203-022-03173-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/24/2022]
Abstract
A betaproteobacterial chemolithotrophic ammonia-oxidizing bacterium designated APG5T was isolated from supralittoral sand of the Edmonds City Beach, WA, USA. Growth was observed at 10-35 °C (optimum, 30 °C), pH 5-9 (optimum, pH 8) and ammonia concentrations as high as 100 mM (optimum, 1-30 mM NH4Cl). The strain grows optimally in a freshwater medium but tolerates up to 400 mM NaCl. It is most closely related to 'Nitrosomonas ureae' (96.7% 16S rRNA and 92.4% amoA sequence identity). The 3.75-Mbp of AGP5T draft genome contained a single rRNA operon and all necessary tRNA genes and has the lowest G+C content (43.5%) when compared to the previously reported genomes of reference strains in cluster 6 Nitrosomonas. Based on an average nucleotide identity of 82% with its closest relative ('N. ureae' Nm10T) and the suggested species boundary of 95-96%, a new species Nitrosomonas supralitoralis sp. nov. is proposed. The type strain of Nitrosomonas supralitoralis is APG5T (= NCIMB 14870T = ATCC TSD-116T).
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Affiliation(s)
- Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA. .,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
| | - Gabrianna A Andrews
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Institute for Food and Agricultural Sciences, University of Florida, Davie, FL, USA.,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Martin G Klotz
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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Xu H, Deng Y, Zou J, Zhang K, Li X, Yang Y, Huang S, Liu ZQ, Wang Z, Hu C. Nitrification performance and bacterial community dynamics in a membrane bioreactor with elevated ammonia concentration: The combined inhibition effect of salinity, free ammonia and free nitrous acid on nitrification at high ammonia loading rates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154972. [PMID: 35367558 DOI: 10.1016/j.scitotenv.2022.154972] [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: 12/18/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The responses of the operational performance and bacterial community structure of a nitrification membrane bioreactor (MBR) to elevated ammonia loading rate (ALR) were investigated. Effective nitrification performance was achieved at high ALR up to 3.43 kg NH4+-N/m3·d, corresponding to influent NH4+-N concentration of 2000 mg/L. Further increasing influent NH4+-N concentration to 3000 mg/L, the MBR system finally became completely inefficient due to the combined inhibition effect of salinity, free ammonia and free nitrous acid on nitrification. Ammonia-oxidizing bacteria (AOB) Nitrosomonas were enriched with the increase of ALR. The relative abundance of Nitrosomonas in the sludge with ALR of 2.57 kg NH4+-N/m3·d was up to 14.82%, which were 9-fold and 53-fold higher than that in seed sludge and the sludge with ALR of 0.10 kg NH4+-N/m3·d, respectively. The phylogenetic analysis of AOB amoA genes showed that Nitrosomonas europaea/mobilis lineage are chiefly responsible for catalyzing ammonia oxidation at high ALRs.
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Affiliation(s)
- Huaihao Xu
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yuepeng Deng
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jie Zou
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Kaoming Zhang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiuying Li
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Shuangqiu Huang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Zhao-Qing Liu
- School of Chemistry and Chemical Engineering, Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou 510006, China
| | - Zhu Wang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Chun Hu
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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Nitrogen Removal of Water and Sediment in Grass Carp Aquaculture Ponds by Mixed Nitrifying and Denitrifying Bacteria and Its Effects on Bacterial Community. WATER 2022. [DOI: 10.3390/w14121855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Nitrification and denitrification are important for nitrogen (N) cycling in fish ponds culture, but the effects of nitrifying and denitrifying bacteria concentrations on pond water and sediments remain largely unknown. Here, we used 0, 0.15, 0.30, 0.60 mg/L different concentrations of mixed nitrifying and denitrifying bacteria to repair the pond substrate through an enclosure experiment lasting 15 days. The results showed that the purification effect of nitrifying and denitrifying bacteria was most obvious on pond nitrogen from day 4 to day 7. The optimal relative concentration was 0.60 mg/L for nitrifying and denitrifying bacteria; NH4+-N (ammonia nitrogen) decreased by 75.83%, NO2−-N (nitrite) by 93.09%, NO3−-N (nitrate) by 38.02%, and TN (total nitrogen) by 45.16% in this concentration group on pond water. In one cycle, C/N (carbon/nitrogen) ratio of both water body and bottom sediment significantly increased, but C/N ratio of water body increased more significantly than that of sediment. Water C/N ratio increased by 76.00%, and sediment C/N ratio increased by 51.96% in the 0.60 mg/L concentration group. Amplicon sequencing of pond sediment showed that the change in nitrifying and denitrifying bacterium diversity was consistent with that in water quality index. Dominant nitrifying bacteria had a relatively high percentage, with significant differences in dominant bacterium percentage across different bacterial addition groups, while dominant denitrifying bacterium percentage was not high without significant differences among different groups. The dominant species of nitrifying bacteria were, respectively, Nitrosomonas, Nitrosovibrio, Nitrosospira, and Aeromonas, and the dominant species of denitrifying bacteria were Thauera, Azoarcus, Magnetospirillum, Azospira, and Idiomarina. The correlation analyses showed an aerobic nitrification and facultative anaerobic denitrification in pond sediments. Research shows that the addition of exogenous nitrifying and denitrifying bacteria can effectively reduce the nitrogen load of pond water and sediment. At the concentration of 0.6 mg/L, the nitrogen load of pond water and sediment decreased most obviously, which had the best effect on pond purification.
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Technologies for Biological and Bioelectrochemical Removal of Inorganic Nitrogen from Wastewater: A Review. NITROGEN 2022. [DOI: 10.3390/nitrogen3020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Water contamination due to various nitrogenous pollutants generated from wastewater treatment plants is a crucial and ubiquitous environmental problem now-a-days. Nitrogen contaminated water has manifold detrimental effects on human health as well as aquatic life. Consequently, various biological treatment processes are employed to transform the undesirable forms of nitrogen in wastewater to safer ones for subsequent discharge. In this review, an overview of various conventional biological treatment processes (viz. nitrification, denitrification, and anammox) have been presented along with recent novel bioelectrochemical methods (viz. microbial fuel cells and microbial electrolysis cells). Additionally, nitrogen is an indispensable nutrient necessary to produce artificial fertilizers by fixing dinitrogen gas from the atmosphere. Thus, this study also explored the potential capability of various nitrogen recovery processes from wastewater (like microalgae, cyanobacteria, struvite precipitation, stripping, and zeolites) that are used in industries. Further, the trade-offs, challenges posed by these processes have been dwelt on along with other biological processes like CANON, SHARON, OLAND, and others.
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Evaluating acute toxicity in enriched nitrifying cultures: Lessons learned. J Microbiol Methods 2021; 192:106377. [PMID: 34798174 DOI: 10.1016/j.mimet.2021.106377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 11/22/2022]
Abstract
Toxicological batch assays are essential to assess a compound's acute effect on microorganisms. This methodology is frequently employed to evaluate the effect of contaminants in sensitive microbial communities from wastewater treatment plants (WWTPs), such as autotrophic nitrifying populations. However, despite nitrifying batch assays being commonly mentioned in the literature, their experimental design criteria are rarely reported or overlooked. Here, we found that slight deviations in culture preparations and conditions impacted bacterial community performance and could skew assay results. From pre-experimental trials and experience, we determined how mishandling and treatment of cultures could affect nitrification activity. While media and biomass preparations are needed to establish baseline conditions (e.g., biomass washing), we found extensive centrifugation selectively destabilised nitrification activities. Further, it is paramount that the air supply is adjusted to minimise nitrite build-up in the culture and maintain suitable aeration levels without sparging ammonia. DMSO and acetone up to 0.03% (v/v) were suitable organic solvents with minimal impact on nitrification activity. In the nitrification assays with allylthiourea (ATU), dilute cultures exhibited more significant inhibition than concentrated cultures. So there were biomass-related effects; however, these differences minimally impacted the EC50 values. Using different nutrient-media compositions had a minimal effect; however, switching mineral media for the toxicity test from the original cultivation media is not recommended because it reduced the original biomass nitrification capacity. Our results demonstrated that these factors substantially impact the performance of the nitrifying inoculum used in acute bioassays, and consequently, affect the response of AOB-NOB populations during the toxicant exposure. These are not highlighted in operation standards, and unfortunately, they can have significant consequential impacts on the determinations of toxicological endpoints. Moreover, the practical procedures tested here could support other authors in developing testing methodologies, adding quality checks in the experimental framework with minimal waste of time and resources.
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Spieck E, Wegen S, Keuter S. Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems. Appl Microbiol Biotechnol 2021; 105:7123-7139. [PMID: 34508283 PMCID: PMC8494671 DOI: 10.1007/s00253-021-11487-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/10/2023]
Abstract
Abstract Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures. Key points • Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga • Comparison of the physiological features of Cand. Nitrotoga with those of other NOB • Identification of beneficial environmental/operational parameters for proliferation Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11487-5.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany.
| | - Simone Wegen
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
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21
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Gottshall EY, Bryson SJ, Cogert KI, Landreau M, Sedlacek CJ, Stahl DA, Daims H, Winkler M. Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria. WATER RESEARCH 2021; 202:117426. [PMID: 34274897 DOI: 10.1016/j.watres.2021.117426] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The discovery of anaerobic ammonia-oxidizing bacteria (Anammox) and, more recently, aerobic bacteria common in many natural and engineered systems that oxidize ammonia completely to nitrate (Comammox) have significantly altered our understanding of the global nitrogen cycle. A high affinity for ammonia (Km(app),NH3 ≈ 63nM) and oxygen place Comammox Nitrospira inopinata, the first described isolate, in the same trophic category as organisms such as some ammonia-oxidizing archaea. However, N. inopinata has a relatively low affinity for nitrite (Km,NO2 ≈ 449.2μM) suggesting it would be less competitive for nitrite than other nitrite-consuming aerobes and anaerobes. We examined the ecological relevance of the disparate substrate affinities by coupling it with the Anammox bacterium Candidatus Brocadia anammoxidans. Synthetic communities of the two were established in hydrogel granules in which Comammox grew in the aerobic outer layer to provide Anammox with nitrite in the inner anoxic core to form dinitrogen gas. This spatial organization was confirmed with FISH imaging, supporting a mutualistic or commensal relationship. The functional significance of interspecies spatial organization was informed by the hydrogel encapsulation format, broadening our limited understanding of the interplay between these two species. The resulting low nitrate formation and the competitiveness of Comammox over other aerobic ammonia- and nitrite-oxidizers sets this ecological cooperation apart and points to potential biotechnological applications. Since nitrate is an undesirable product of wastewater treatment effluents, the Comammox-Anammox symbiosis may be of economic and ecological importance to reduce nitrogen contamination of receiving waters.
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Affiliation(s)
- Ekaterina Y Gottshall
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States.
| | - Sam J Bryson
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Kathryn I Cogert
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Matthieu Landreau
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Christopher J Sedlacek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1010, Austria
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Holger Daims
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1010, Austria; The Comammox Research Platform. University of Vienna, 1010, Austria
| | - Mari Winkler
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
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22
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Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments. Appl Environ Microbiol 2021; 87:e0103821. [PMID: 34347515 DOI: 10.1128/aem.01038-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite - can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.
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Nejidat A, Diaz-Reck D, Gelfand I, Zaady E. Persistence and spread of tetracycline resistance genes and microbial community variations in the soil of animal corrals in a semi-arid planted forest. FEMS Microbiol Ecol 2021; 97:6323997. [PMID: 34279614 DOI: 10.1093/femsec/fiab106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/15/2021] [Indexed: 11/14/2022] Open
Abstract
At the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and the abundance of tetracycline resistance genes (TRGs) in active and abandoned corrals (1-10-years-old). Based on 16S rRNA gene sequences, the Proteobacteria and Actinobacteria phyla dominated the soil of all corrals. The Actinobacteria were less abundant in the active and 1-year-old corrals (23-26%) than in the other corrals and the control (33-38%). A principal component analysis showed that, the BCS in the active and the 1-year-old abandoned corrals was significantly different from that in the older corrals and the control. The Firmicutes phylum constituted 28% of the BCS in the active corrals, 12.5% in the 1-year-old corrals and 2% in the older corrals and the control. In contrast, the Acidobacteria phylum was hardly detected in the active and 1-year-old abandoned corrals and constituted 10% of the BCS in the older corrals. Genes conferring resistance to tetracycline were detected in high numbers. The tetG and tetW genes were detected in the active and abandoned corrals (1-10 years). The tetQ gene was detected only in the active and 1-year-old abandoned corrals. None of the genes were detected in the control soil. The three genes were detected outside an active corral, in the downstream section of an ephemeral tributary. The results prove that abandoned and unobserved periodic animal corrals are an environmental reservoir for TRGs.
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Affiliation(s)
- Ali Nejidat
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel
| | - Damiana Diaz-Reck
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-G urion 84990, Israel
| | - Ilya Gelfand
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel
| | - Eli Zaady
- Department of Natural Resources, Gilat Research Center, Agriculture Research Organization, Mobile, Post Negev 8531100, Israel
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Xu H, Deng Y, Li X, Liu Y, Huang S, Yang Y, Wang Z, Hu C. Effect of Increasing C/N Ratio on Performance and Microbial Community Structure in a Membrane Bioreactor with a High Ammonia Load. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8070. [PMID: 34360363 PMCID: PMC8345800 DOI: 10.3390/ijerph18158070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 01/03/2023]
Abstract
Herein, the responses of the operational performance of a membrane bioreactor (MBR) with a high ammonium-nitrogen (NH4+-N) load and microbial community structure to increasing carbon to nitrogen (C/N) ratios were studied. Variation in the influent C/N ratio did not affect the removal efficiencies of chemical oxygen demand (COD) and NH4+-N but gradually abated the ammonia oxidization activity of sludge. The concentration of the sludge in the reactor at the end of the process increased four-fold compared with that of the seed sludge, ensuring the stable removal of NH4+-N. The increasing influent COD concentration resulted in an elevated production of humic acids in soluble microbial product (SMP) and accelerated the rate of membrane fouling. High-throughput sequencing analysis showed that the C/N ratio had selective effects on the microbial community structure. In the genus level, Methyloversatilis, Subsaxibacter, and Pseudomonas were enriched during the operation. However, the relative abundance of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) involved in nitrification declined gradually and were decreased by 86.54 and 90.17%, respectively, with influent COD increasing from 0 to 2000 mg/L. The present study offers a more in-depth insight into the control strategy of the C/N ratio in the operation of an MBR with a high NH4+-N load.
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Affiliation(s)
- Huaihao Xu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yuepeng Deng
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Xiuying Li
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yuxian Liu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
- Linköping University-Guangzhou University Research Center on Urban Sustainable Development, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Shuangqiu Huang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Zhu Wang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Chun Hu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
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25
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Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME JOURNAL 2021; 16:272-283. [PMID: 34316016 PMCID: PMC8692354 DOI: 10.1038/s41396-021-01064-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 02/04/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.
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26
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Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils. Appl Environ Microbiol 2021; 87:e0009221. [PMID: 33837020 DOI: 10.1128/aem.00092-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.
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27
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Zheng M, He S, Feng Y, Wang M, Liu YX, Dang C, Wang J. Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems. J Environ Sci (China) 2021; 102:273-282. [PMID: 33637253 DOI: 10.1016/j.jes.2020.09.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 05/04/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 108 copies g-1 dry sludge) were higher than those of AOA (averaged: 3.4 × 107 copies g-1 dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.
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Affiliation(s)
- Maosheng Zheng
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Shishi He
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yueqi Feng
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Mingyuan Wang
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yong-Xin Liu
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyuan Dang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jiawen Wang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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28
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Bernhard AE, Beltz J, Giblin AE, Roberts BJ. Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox. ISME COMMUNICATIONS 2021; 1:9. [PMID: 36717686 PMCID: PMC9723745 DOI: 10.1038/s43705-021-00008-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 02/03/2023]
Abstract
Few studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.
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Affiliation(s)
- A E Bernhard
- Department of Biology, Connecticut College, New London, CT, USA.
| | - J Beltz
- Department of Biology, Connecticut College, New London, CT, USA
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - A E Giblin
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - B J Roberts
- Louisiana Universities Marine Consortium, Chauvin, LA, USA
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29
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Hu H, Deng C, Wang X, Chen Z, Zhong Z, Wang R. Performance and mechanism of urea hydrolysis in partial nitritation system based on SBR. CHEMOSPHERE 2020; 258:127228. [PMID: 32535438 DOI: 10.1016/j.chemosphere.2020.127228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 04/14/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Urea hydrolysis in partial nitritation process forming nitrite and ammonia is advantageous to subsequent treatment with ANAMMOX for total nitrogen removal. In this study, stable partial nitritation for urea wastewater with urea increasing from 250 to 2000 mg L-1 were achieved in an aerobic SBR. Urea removal efficiency and nitrite accumulation percentage both kept above 98%, with nitrite production rate about 0.985 kg N·m-3·d-1. Urea hydrolysis mechanism in this aerobic system was described as, (1) massive urea in the bulk was absorbed into cell, (2) urea was hydrolyzed by intracellular urease inside cell, (3) produced ammonia then slowly diffused into the bulk through membrane, which is later converted by ammonia-oxidizing bacteria (AOB) into nitrite. Due to this mechanism, the activity of AOB could not be inhibited by high FA (free ammonia) value under high urea concentration condition while nitrite-oxidizing bacteria (NOB) remained to be inhibited. An uncultured genus belonging to poorly characterized phylum Gemmatimonadetes was found enriched in this process and became dominant genus. This genus was speculated to have same energy pathway like ureaplasma, by absorbing excessive urea from environment and utilize urea hydrolysis to generate energy. So it was believed to be responsible for urea hydrolysis mechanism mentioned above. This SBR showed stable partial nitritation and high urea removal efficiency for treating urea wastewater, which was obviously feasible as the pretreatment process for subsequent ANAMMOX.
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Affiliation(s)
- Haolin Hu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Cuilan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Xiaojun Wang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China.
| | - Zhenguo Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China; Hua an Biotech Co., Ltd., Foshan, 528300, China
| | - Zhong Zhong
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
| | - Ruixin Wang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China
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30
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Orschler L, Agrawal S, Lackner S. Lost in translation: the quest for Nitrosomonas cluster 7-specific amoA primers and TaqMan probes. Microb Biotechnol 2020; 13:2069-2076. [PMID: 32686322 PMCID: PMC7533338 DOI: 10.1111/1751-7915.13627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 11/30/2022] Open
Abstract
The choice of primer and TaqMan probes to quantify ammonia-oxidizing bacteria (AOB) in environmental samples is of crucial importance. The re-evaluation of primer pairs based on current genomic sequences used for quantification of the amoA gene revealed (1) significant misrepresentations of the AOB population in environmental samples, (2) and a lack of perfect match primer pairs for Nitrosomonas europaea and Nitrosomonas eutropha. We designed two new amoA cluster 7-specific primer pairs and TaqMan probes to quantify N. europaea (nerF/nerR/nerTaq) and N. eutropha (netF/netR/netTaq). Specificity and quantification biases of the newly designed primer sets were compared with the most popular primer pair (amoA1f/amoA2r) using DNA from various AOB cultures as individual templates as well as DNA mixtures and environmental samples. Based on the qPCR results, we found that the newly designed primer pairs and the most popular one performed similarly for individual templates but differed for the DNA mixtures and environmental samples. Using the popular primer pair introduced a high underestimation of AOB in environmental samples, especially for N. eutropha. Thus, there is a strong need for more specific primers and probes to understand the occurrence and competition between N. europaea and N. eutropha in different environments.
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Affiliation(s)
- Laura Orschler
- Institute IWARTechnical University of DarmstadtFranziska‐Braun‐Straße 7Darmstadt64287Germany
| | - Shelesh Agrawal
- Institute IWARTechnical University of DarmstadtFranziska‐Braun‐Straße 7Darmstadt64287Germany
| | - Susanne Lackner
- Institute IWARTechnical University of DarmstadtFranziska‐Braun‐Straße 7Darmstadt64287Germany
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31
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Lukumbuzya M, Kristensen JM, Kitzinger K, Pommerening-Röser A, Nielsen PH, Wagner M, Daims H, Pjevac P. A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria. WATER RESEARCH 2020; 186:116372. [PMID: 32916620 DOI: 10.1016/j.watres.2020.116372] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/12/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.
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Affiliation(s)
- Michael Lukumbuzya
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Jannie Munk Kristensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katharina Kitzinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Pommerening-Röser
- University of Hamburg, Institute of Plant Science and Microbiology, Microbiology and Biotechnology, Hamburg, Germany
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria; University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; University of Vienna, The Comammox Research Platform, Vienna, Austria.
| | - Petra Pjevac
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
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Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe. Sci Rep 2020; 10:17165. [PMID: 33051504 PMCID: PMC7555866 DOI: 10.1038/s41598-020-74163-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/24/2020] [Indexed: 11/25/2022] Open
Abstract
The community composition of betaproteobacterial ammonia-oxidizing bacteria (ß-AOB) in the River Elbe Estuary was investigated by high throughput sequencing of ammonia monooxygenase subunit A gene (amoA) amplicons. In the course of the seasons surface sediment samples from seven sites along the longitudinal profile of the upper Estuary of the Elbe were investigated. We observed striking shifts of the ß-AOB community composition according to space and time. Members of the Nitrosomonas oligotropha-lineage and the genus Nitrosospira were found to be the dominant ß-AOB within the river transect, investigated. However, continuous shifts of balance between members of both lineages along the longitudinal profile were determined. A noticeable feature was a substantial increase of proportion of Nitrosospira-like sequences in autumn and of sequences affiliated with the Nitrosomonas marina-lineage at downstream sites in spring and summer. Slightly raised relative abundances of sequences affiliated with the Nitrosomonas europaea/Nitrosomonas mobilis-lineage and the Nitrosomonas communis-lineage were found at sampling sites located in the port of Hamburg. Comparisons between environmental parameters and AOB-lineage (ecotype) composition revealed promising clues that processes happening in the fluvial to marine transition zone of the Elbe estuary are reflected by shifts in the relative proportion of ammonia monooxygenase sequence abundance, and hence, we propose ß-AOB as appropriate indicators for environmental dynamics and the ecological condition of the Elbe Estuary.
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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.
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Affiliation(s)
- Christopher J. Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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34
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Dynamics of nitrogenous compounds and their control in biofloc technology (BFT) systems: A review. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Zhang X, Li S, Zheng S, Duan S. Impact of dissolved oxygen and loading rate on NH 3 oxidation and N 2 production mechanisms in activated sludge treatment of sewage. Microb Biotechnol 2020; 14:419-429. [PMID: 32488999 PMCID: PMC7936313 DOI: 10.1111/1751-7915.13599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/19/2023] Open
Abstract
Microaerobic activated sludge (MAS) is a one-stage process operated at 0.5-1.0 mg l-1 dissolved oxygen (DO) aiming at simultaneous nitrification and denitrification. We used molecular techniques and a comprehensive nitrogen (N)-transformation activity test to investigate the dominant NH3 -oxidizing and N2 -producing mechanism as well as the dominant ammonia-oxidizing bacteria (AOB) species in sludge samples individually collected from an MAS system and a conventional anoxic/oxic (A/O) system; both systems were operated at a normal loading rate (i.e. 1.0 kg chemical oxygen demand (COD) m-3 day-1 and 0.1 kg NH4 + -N m-3 day-1 ) in our previous studies. The DO levels in both systems (aerobic: conventional A/O system; microaerobic: MAS system) did not affect the dominant NH3 -oxidizing mechanism or the dominant AOB species. This study further demonstrated the feasibility of a higher loading rate (i.e. 2.30 kg COD m-3 day-1 and 0.34 kg NH4 + -N m-3 day-1 ) with the MAS process during sewage treatment, which achieved a 40% reduction in aeration energy consumption than that obtained in the conventional A/O system. The increase in loading rates in the MAS system did not affect the dominant NH3 -oxidizing mechanism but did impact the dominant AOB species. Besides, N2 was predominantly produced by microaerobic denitrification in the MAS system at the two loading rates.
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Affiliation(s)
- Xueyu Zhang
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Shida Li
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Shaokui Zheng
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Shoupeng Duan
- MOE Key Laboratory of Water and Sediment Sciences/State Key Lab of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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36
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Jo Y, Cho K, Choi H, Lee C. Treatment of low-strength ammonia wastewater by single-stage partial nitritation and anammox using upflow dual-bed gel-carrier reactor (UDGR). BIORESOURCE TECHNOLOGY 2020; 304:123023. [PMID: 32088631 DOI: 10.1016/j.biortech.2020.123023] [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: 12/31/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
This study investigated the single-stage partial nitritation and anammox (S-PNA) treatment of low-strength ammonia wastewater (≤140 mg NH4+-N/L). Upflow dual-bed gel-carrier reactor (UDGR) with polyvinyl alcohol cryogel biocarriers, developed in this study, was employed for the anammox biomass enrichment from conventional activated sludge and subsequent S-PNA experiments. Anammox biomass was successfully enriched from conventional activated sludge. The enriched anammox carriers were inoculated together with gel carriers containing nitrifying sludge into the S-PNA reactors. S-PNA activity developed rapidly, and the nitrogen removal efficiency and rate reached up to 90.1% (with complete ammonia removal) and 0.15 kg N/m3⋅d, respectively, under low nitrogen loading conditions (0.10-0.17 kg N/m3⋅d). The microbial community structure changed significantly while adapting to anammox and S-PNA conditions. Anammox was likely driven solely by a Candidatus Jettenia population accounting for ≤49.4% of bacterial 16S rRNA genes. The results demonstrate that the UDGR-based S-PNA is suitable for treating low-strength wastewater.
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Affiliation(s)
- Yeadam Jo
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Kyungjin Cho
- Water Cycle Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Hyungmin Choi
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea.
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37
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Navada S, Knutsen MF, Bakke I, Vadstein O. Nitrifying biofilms deprived of organic carbon show higher functional resilience to increases in carbon supply. Sci Rep 2020; 10:7121. [PMID: 32346018 PMCID: PMC7189377 DOI: 10.1038/s41598-020-64027-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/08/2020] [Indexed: 11/09/2022] Open
Abstract
In nitrifying biofilms, the organic carbon to ammonia nitrogen (C/N) supply ratio can influence resource competition between heterotrophic and nitrifying bacteria for oxygen and space. We investigated the impact of acute and chronic changes in carbon supply on inter-guild competition in two moving bed biofilm reactors (MBBR), operated with (R1) and without (R0) external organic carbon supply. The microbial and nitrifying community composition of the reactors differed significantly. Interestingly, acute increases in the dissolved organic carbon inhibited nitrification in R1 ten times more than in R0. A sustained increase in the carbon supply decreased nitrification efficiency and increased denitrification activity to a greater extent in R1, and also increased the proportion of potential denitrifiers in both bioreactors. The findings suggest that autotrophic biofilms subjected to increases in carbon supply show higher nitrification and lower denitrification activity than carbon-fed biofilms. This has significant implications for the design of nitrifying bioreactors. Specifically, efficient removal of organic matter before the nitrification unit can improve the robustness of the bioreactor to varying influent quality. Thus, maintaining a low C/N ratio is important in nitrifying biofilters when acute carbon stress is expected or when anoxic activity (e.g. denitrification or H2S production) is undesirable, such as in recirculating aquaculture systems (RAS).
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Affiliation(s)
- Sharada Navada
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491, Trondheim, Norway. .,Krüger Kaldnes AS (Veolia Water Technologies), N-3241, Sandefjord, Norway.
| | - Maja F Knutsen
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, N-7491, Trondheim, Norway.,Oxy Solutions, Gaustadalleen 21, N-0349, Oslo, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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38
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Yang Z, Guan Y, Bello A, Wu Y, Ding J, Wang L, Ren Y, Chen G, Yang W. Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China. PeerJ 2020; 8:e8844. [PMID: 32341890 PMCID: PMC7182023 DOI: 10.7717/peerj.8844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/02/2020] [Indexed: 11/20/2022] Open
Abstract
Organic fertilizer application could have an impact on the nitrogen cycle mediated by microorganisms in arable soils. However, the dynamics of soil ammonia oxidizers and denitrifiers in response to compost addition are less understood. In this study, we examined the effect of four compost application rates (0, 11.25, 22.5 and 45 t/ha) on soil ammonia oxidizers and denitrifiers at soybean seedling, flowering and mature stage in a field experiment in Northeast China. As revealed by quantitative PCR, compost addition significantly enhanced the abundance of ammonia oxidizing bacteria (AOB) at seedling stage, while the abundance of ammonia oxidizing archaea was unaffected across the growing season. The abundance of genes involved in denitrification (nirS, nirK and nosZ) were generally increased along with compost rate at seedling and flowering stages, but not in mature stage. The non-metric multidimensional scaling analysis revealed that moderate and high level of compost addition consistently induced shift in AOB and nirS containing denitrifers community composition across the growing season. Among AOB lineages, Nitrosospira cluster 3a gradually decreased along with the compost rate across the growing season, while Nitrosomonas exhibited an opposite trend. Network analysis indicated that the complexity of AOB and nirS containing denitrifiers network gradually increased along with the compost rate. Our findings highlighted the positive effect of compost addition on the abundance of ammonia oxidizers and denitrifiers and emphasized that compost addition play crucial roles in shaping their community compositions and co-occurrence networks in black soil of Northeast China.
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Affiliation(s)
- Zhongzan Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yupeng Guan
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yanxiang Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jiayi Ding
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Leiqi Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yuqing Ren
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Guangxin Chen
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, Heilongjiang, China
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39
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Separating and Characterizing Functional Nitrogen Degraders via Magnetic Nanoparticle-Mediated Isolation. J CHEM-NY 2020. [DOI: 10.1155/2020/1841364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Magnetic nanoparticle-mediated isolation (MMI) is a new method for isolating active functional microbes from complex microorganisms without substrate labeling. In this study, the composition and properties of magnetic nanoparticles (MNPs) were characterized by a number of techniques, indicating that MNPs have characteristics such as microinterfaces and can be efficiently fixed on the surface of microbial cells. It also introduced the MMI technology in activated sludge after stable long-term treatment. With further addition of promotor carbon sources, the enrichment of the functional nitrogen degraders in MMI was significantly higher than in samples without MNPs, showing the advantages of MMI in identifying the active degraders. Redundancy analysis (RDA) also showed that the functional nitrogen degraders such as Comamonadaceae_unclassified and Thiobacillus absolutely dominated in situ ammonia degradation, and the change in dominant genera had the same trend as the degradation rate of ammonia nitrogen. In the magnetically functionalized system, the separated functional nitrogen degraders significantly improved ammonia nitrogen degradation efficiency, making it basically stable at more than 80%, up to 91.6%. These results prove that the complex flora created after the addition of MNPs is more adaptable to newly introduced pollutants, and MMI is a powerful tool for studying pollutant-degrading microorganisms under in situ conditions.
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40
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Tsuchiya Y, Nakagawa T, Takahashi R. Quantification and Phylogenetic Analysis of Ammonia Oxidizers on Biofilm Carriers in a Full-Scale Wastewater Treatment Plant. Microbes Environ 2020; 35. [PMID: 32249239 PMCID: PMC7308565 DOI: 10.1264/jsme2.me19140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biofilm carriers have been used to remove ammonia in several wastewater treatment plants (WWTPs) in Japan. However, the abundance and species of ammonia oxidizers in the biofilms formed on the surface of carriers in full-scale operational WWTP tanks remain unclear. In the present study, we conducted quantitative PCR and PCR cloning of the amoA genes of ammonia-oxidizing bacteria and archaea (AOB and AOA) and a complete ammonia oxidizer (comammox) in the biofilm formed on the carriers in a full-scale WWTP. The quantification of amoA genes showed that the abundance of AOB and comammox was markedly greater in the biofilm than in the activated sludge suspended in a tank solution of the WWTP, while AOA was not detected in the biofilm or the activated sludge. A phylogenetic analysis of amoA genes revealed that as-yet-uncultivated comammox Nitrospira and uncultured AOB Nitrosomonas were predominant in the biofilm. The present results suggest that the biofilm formed on the surface of carriers enable comammox Nitrospira and AOB Nitrosomonas to co-exist and remain in the full-scale WWTP tank surveyed in this study.
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41
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Kniggendorf AK, Nogueira R, Nasiri Bahmanabad S, Pommerening-Röser A, Roth BW. Small Sample Stress: Probing Oxygen-Deprived Ammonia-Oxidizing Bacteria with Raman Spectroscopy In Vivo. Microorganisms 2020; 8:microorganisms8030432. [PMID: 32204374 PMCID: PMC7143505 DOI: 10.3390/microorganisms8030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 11/16/2022] Open
Abstract
The stress response of ammonia-oxidizing bacteria (AOB) to oxygen deprivation limits AOB growth and leads to different nitrification pathways that cause the release of greenhouse gases. Measuring the stress response of AOB has proven to be a challenge due to the low growth rates of stressed AOB, making the sample volumes required to monitor the internal stress response of AOB prohibitive to repeated analysis. In a proof-of-concept study, confocal Raman microscopy with excitation resonant to the heme c moiety of cytochrome c was used to compare the cytochrome c content and activity of stressed and unstressed Nitrosomonas europaea (Nm 50), Nitrosomonas eutropha (Nm 57), Nitrosospira briensis (Nsp 10), and Nitrosospira sp. (Nsp 02) in vivo. Each analysis required no more than 1000 individual cells per sampling; thus, the monitoring of cultures with low cell concentrations was possible. The identified spectral marker delivered reproducible results within the signal-to-noise ratio of the underlying Raman spectra. Cytochrome c content was found to be elevated in oxygen-deprived and previously oxygen-deprived samples. In addition, cells with predominantly ferrous cytochrome c content were found in deprived Nitrosomonas eutropha and Nitrosospira samples, which may be indicative of ongoing electron storage at the time of measurement.
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Affiliation(s)
- Ann-Kathrin Kniggendorf
- Hannover Centre for Optical Technologies, Gottfried Wilhelm Leibniz University of Hannover, Nienburger Str. 17, 30167 Hannover, Germany
- Correspondence: (A.-K.K.); (R.N.); Tel.: +49-511-762-17910 (A.-K.K.)
| | - Regina Nogueira
- Institute for Sanitary Engineering and Waste Management, Gottfried Wilhelm Leibniz Universität Hannover, Welfengarten 1, 30167 Hannover, Germany
- Correspondence: (A.-K.K.); (R.N.); Tel.: +49-511-762-17910 (A.-K.K.)
| | - Somayeh Nasiri Bahmanabad
- Institute for Sanitary Engineering and Waste Management, Gottfried Wilhelm Leibniz Universität Hannover, Welfengarten 1, 30167 Hannover, Germany
| | | | - Bernhard Wilhelm Roth
- Hannover Centre for Optical Technologies, Gottfried Wilhelm Leibniz University of Hannover, Nienburger Str. 17, 30167 Hannover, Germany
- Cluster of Excellence PhoenixD (Photonics, Optics, and Engineering – Innovation Across Disciplines), Welfengarten 1, 30167 Hannover, Germany
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42
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Zhang L, Okabe S. Ecological niche differentiation among anammox bacteria. WATER RESEARCH 2020; 171:115468. [PMID: 31926373 DOI: 10.1016/j.watres.2020.115468] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/03/2019] [Accepted: 01/02/2020] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria can directly convert ammonium and nitrite to nitrogen gas anaerobically and were responsible for a substantial part of the fixed nitrogen loss and re-oxidation of nitrite to nitrate in freshwater and marine ecosystems. Although a wide variety of studies have been undertaken to investigate the abundance and biodiversity of anammox bacteria so far, ecological niche differentiation of anammox bacteria is still not fully understood. To assess their growth behavior and consequent population dynamics at a given environment, the Monod model is often used. Here, we summarize the Monod kinetic parameters such as the maximum specific growth rate (μmax) and the half-saturation constant for nitrite (KNO2-) and ammonium (KNH4+) of five known candidatus genera of anammox bacteria. We also discuss potential pivotal environmental factors and metabolic flexibility that influence the community compositions of anammox bacteria. Particularly biodiversity of the genus "Scalindua" might have been largely underestimated. Several anammox bacteria have been successfully enriched from various source of biomass. We reevaluate their enrichment methods and culture medium compositions to gain a clue of niche differentiation of anammox bacteria. Furthermore, we formulate the current issues that must be addressed. Overall this review re-emphasizes the importance of enrichment cultures (preferably pure cultures), physiological characterization and direct microbial competition studies using enrichment cultures in laboratories.
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Affiliation(s)
- Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan.
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43
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Isshiki R, Fujitani H, Tsuneda S. Transcriptome Analysis of the Ammonia-Oxidizing Bacterium Nitrosomonas mobilis Ms1 Reveals Division of Labor between Aggregates and Free-living Cells. Microbes Environ 2020; 35. [PMID: 32115437 PMCID: PMC7308568 DOI: 10.1264/jsme2.me19148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacteria change their metabolic states to increase survival by forming aggregates. Ammonia-oxidizing bacteria also form aggregates in response to environmental stresses. Nitrosomonas mobilis, an ammonia-oxidizing bacterium with high stress tolerance, often forms aggregates mainly in wastewater treatment systems. Despite the high frequency of aggregate formation by N. mobilis, its relationship with survival currently remains unclear. In the present study, aggregates were formed in the late stage of culture with the accumulation of nitrite as a growth inhibitor. To clarify the significance of aggregate formation in N. mobilis Ms1, a transcriptome analysis was performed. Comparisons of the early and late stages of culture revealed that the expression of stress response genes (chaperones and proteases) increased in the early stage. Aggregate formation may lead to stress avoidance because stress response genes were not up-regulated in the late stage of culture during which aggregates formed. Furthermore, comparisons of free-living cells with aggregates in the early stage of culture showed differences in gene expression related to biosynthesis (ATP synthase and ribosomal proteins) and motility and adhesion (flagella, pilus, and chemotaxis). Biosynthesis genes for growth were up-regulated in free-living cells, while motility and adhesion genes for adaptation were up-regulated in aggregates. These results indicate that N. mobilis Ms1 cells adapt to an unfavorable environment and grow through the division of labor between aggregates and free-living cells.
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Affiliation(s)
- Rino Isshiki
- Department of Life Science and Medical Bioscience, Waseda University
| | - Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology.,Research Organization for Nano & Life Innovation, Waseda University
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University.,Research Organization for Nano & Life Innovation, Waseda University
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44
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Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities. Microorganisms 2019; 8:microorganisms8010009. [PMID: 31861554 PMCID: PMC7022406 DOI: 10.3390/microorganisms8010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 11/17/2022] Open
Abstract
We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.
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Sanders T, Fiencke C, Hüpeden J, Pfeiffer EM, Spieck E. Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia. Microorganisms 2019; 7:E699. [PMID: 31847402 PMCID: PMC6955795 DOI: 10.3390/microorganisms7120699] [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: 09/25/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 01/01/2023] Open
Abstract
Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.
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Affiliation(s)
- Tina Sanders
- Helmholtz Zentrum Geesthacht, Institut für Küstenforschung, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Claudia Fiencke
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Jennifer Hüpeden
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
| | - Eva Maria Pfeiffer
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Eva Spieck
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
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Christiaens ME, De Paepe J, Ilgrande C, De Vrieze J, Barys J, Teirlinck P, Meerbergen K, Lievens B, Boon N, Clauwaert P, Vlaeminck SE. Urine nitrification with a synthetic microbial community. Syst Appl Microbiol 2019; 42:126021. [DOI: 10.1016/j.syapm.2019.126021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 08/14/2019] [Accepted: 08/30/2019] [Indexed: 01/23/2023]
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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.
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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.
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Norton J, Ouyang Y. Controls and Adaptive Management of Nitrification in Agricultural Soils. Front Microbiol 2019; 10:1931. [PMID: 31543867 PMCID: PMC6728921 DOI: 10.3389/fmicb.2019.01931] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.
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Affiliation(s)
- Jeanette Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
| | - Yang Ouyang
- Department of Microbiology and Plant Biology, Institute of Environmental Genomics, University of Oklahoma, Norman, OK, United States
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Widner B, Fuchsman CA, Chang BX, Rocap G, Mulholland MR. Utilization of urea and cyanate in waters overlying and within the eastern tropical north Pacific oxygen deficient zone. FEMS Microbiol Ecol 2019; 94:5055141. [PMID: 30016420 DOI: 10.1093/femsec/fiy138] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 07/16/2018] [Indexed: 11/15/2022] Open
Abstract
In marine oxygen deficient zones (ODZs), which contribute up to half of marine N loss, microbes use nitrogen (N) for assimilatory and dissimilatory processes. Here, we examine N utilization above and within the ODZ of the Eastern Tropical North Pacific Ocean, focusing on distribution, uptake and genes for the utilization of two simple organic N compounds, urea and cyanate. Ammonium, urea and cyanate concentrations generally peaked in the oxycline while uptake rates were highest in the surface. Within the ODZ, concentrations were lower, but urea N and C and cyanate C were taken up. All identified autotrophs had an N assimilation pathway that did not require external ammonium: ODZ Prochlorococcus possessed genes to assimilate nitrate, nitrite and urea; nitrite oxidizers (Nitrospina) possessed genes to assimilate nitrite, urea and cyanate; anammox bacteria (Scalindua) possessed genes to utilize cyanate; and ammonia-oxidizing Thaumarchaeota possessed genes to utilize urea. Urease genes were present in 20% of microbes, including SAR11, suggesting the urea utilization capacity was widespread. In the ODZ core, cyanate genes were largely (∼95%) associated with Scalindua, suggesting that, within this ODZ, cyanate N is primarily used for N loss via anammox (cyanammox), and that anammox does not require ammonium for N loss.
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Affiliation(s)
- Brittany Widner
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, USA
| | - Clara A Fuchsman
- University of Washington, School of Oceanography, Seattle, USA.,Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, USA
| | - Bonnie X Chang
- Joint Institute for the Study of the Atmosphere and Ocean, University of Washington, Seattle, USA.,Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, Seattle, USA
| | - Gabrielle Rocap
- University of Washington, School of Oceanography, Seattle, USA
| | - Margaret R Mulholland
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, USA
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Kong Y, Ling N, Xue C, Chen H, Ruan Y, Guo J, Zhu C, Wang M, Shen Q, Guo S. Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing. Environ Microbiol 2019; 21:1224-1240. [PMID: 30724443 DOI: 10.1111/1462-2920.14553] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/19/2018] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Abstract
Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.
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Affiliation(s)
- Yali Kong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huan Chen
- Crop Research Institute, Anhui Academy of Agricultural Science, Hefei, 230031, China
| | - Yang Ruan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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