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Tsujino S, Masuda R, Shimizu Y, Azuma Y, Kanada Y, Fujiwara T. Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification. Antonie Van Leeuwenhoek 2023; 116:1037-1055. [PMID: 37596503 DOI: 10.1007/s10482-023-01862-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023]
Abstract
Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.
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Affiliation(s)
- Shuhei Tsujino
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Ryota Masuda
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yoshiyuki Shimizu
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yuichi Azuma
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yutaro Kanada
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Taketomo Fujiwara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
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2
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Xie Y, Tian X, Liu Y, Zhao K, Li Y, Luo K, Wang B, Dong S. Nitrogen removal capability and mechanism of a novel heterotrophic nitrifying-aerobic denitrifying strain H1 as a potential candidate in mariculture wastewater treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:106366-106377. [PMID: 37728674 DOI: 10.1007/s11356-023-29666-4] [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: 04/12/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
The nitrogen removal performance and mechanisms of Bacillus subtilis H1 isolated from a mariculture environment were investigated. Strain H1 efficiently removed NH4+-N, NO2--N, and NO3--N in simulated wastewater with removal efficiencies of 85.61%, 90.58%, and 57.82%, respectively. Strain H1 also efficiently degraded mixed nitrogen (NH4+-N mixed with NO2--N and/or NO3--N) and had removal efficiencies ranging from 82.39 to 89.54%. Nitrogen balance analysis revealed that inorganic nitrogen was degraded by heterotrophic nitrification-aerobic denitrification (HN-AD) and assimilation. 15N isotope tracing indicated that N2O was the product of the HN-AD process, while N2 as the final product was only detected during the reduction of 15NO2--N. The nitrogen assimilation and dissimilation pathways by strain H1 were further clarified using complete genome sequencing, nitrification inhibitor addition, and enzymatic activity measurement, and the ammonium oxidation process was speculated as NH4+ → NH2OH → NO → N2O. These results showed the application prospect of B. subtilis H1 in treating mariculture wastewater.
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Affiliation(s)
- Yumeng Xie
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China.
| | - Yang Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kun Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Yongmei Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kai Luo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Bo Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Shuanglin Dong
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China
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Kim SK, Song J, Rajeev M, Kim SK, Kang I, Jang IK, Cho JC. Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp ( Litopenaeus vannamei) aquaculture system. Front Microbiol 2022; 13:995699. [PMID: 36204630 PMCID: PMC9531771 DOI: 10.3389/fmicb.2022.995699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented. In this study, the Pacific white shrimp, Litopenaeus vannamei was cultivated in a greenhouse-enclosed BFT system. Rearing water samples were collected on a weekly basis for 5 months (152 days) and water quality variables such as physicochemical parameters and inorganic nutrients were monitored. In parallel, 16S rRNA gene pyrosequencing was employed to investigate the temporal patterns of rearing-water microbiota. The productivity, survival rate, and feed conversion ratio were 3.2-4.4 kg/m3, 74%-89%, and 1.2-1.3, respectively, representing successful super-intensive cultures. The metataxonomic results indicated a highly dynamic bacterioplankton community, with two major shifts over the culture. Members of the phylum Planctomycetes dominated in rearing water during the early stages, while Actinobacteria dominated during the middle stages, and Chloroflexi and TM7 dominated during the late stages of culture. The bacterioplankton community fluctuated more in the beginning but stabilized as the culture progressed. Intriguingly, we observed that certain bacterioplankton groups dominated in a culture-stage-specific manner; these groups include Rhodobacteraceae, Flavobacteriaceae, Actinobacteria, and Chloroflexi, which either contribute to water quality regulation or possess probiotic potential. Altogether, our results indicate that an operationally successful BFT-based aquaculture system favors the growth and dynamics of specific microbial communities in rearing water. Our study expands the scientific understanding of the practical utilization of microbes in sustainable aquaculture. A thorough understanding of rearing-water microbiota and factors influencing their dynamics will help to establish effective management strategies.
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Affiliation(s)
- Su-Kyoung Kim
- West Sea Mariculture Research Center, National Institute of Fisheries Science, Taean, South Korea
| | - Jaeho Song
- Division of Microbiology, Honam National Institute of Biological Resources, Mokpo, South Korea
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Meora Rajeev
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Su Kyoung Kim
- West Sea Mariculture Research Center, National Institute of Fisheries Science, Taean, South Korea
| | - Ilnam Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - In-Kwon Jang
- West Sea Mariculture Research Center, National Institute of Fisheries Science, Taean, South Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
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Cao Q, Li X, Xie Z, Li C, Huang S, Zhu B, Li D, Liu X. Compartmentation of microbial communities in structure and function for methane oxidation coupled to nitrification-denitrification. BIORESOURCE TECHNOLOGY 2021; 341:125761. [PMID: 34455252 DOI: 10.1016/j.biortech.2021.125761] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
A hollow-fiber membrane biofilm reactor was designed and constructed to achieve simultaneous nitrification-denitrification coupled to methane oxidation in low O2/CH4 ratio and high nitrogen removal rate. Three O2/CH4 ratio stages were operated. Ammonia removal rates reached 77.5 and 95 mg/(L·d) at the O2/CH4 ratio of 1.47 and 2.1, respectively. Microbial community analysis revealed that aeration through physical partition and O2/CH4 ratio stages achieved compartmentation of microbial community in structure and function. Combined functional genes analysis using qPCR, the aeration through gas distributer was proved to promote the enrichment of autotrophic ammonia oxidizers in the suspended liquid/mixed filler samples, and the aeration through hollow-fiber membrane favored the growth of methanotrophs and heterotrophic nitrification-aerobic denitrification bacteria. This study helps to develop effective regulatory strategies for high nitrogen removal based on the understanding of the community assembly process and the key driving factors.
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Affiliation(s)
- Qin Cao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiangzhen Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhijie Xie
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Chaonan Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Siyuan Huang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bingjian Zhu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Dong Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiaofeng Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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5
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Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification. Sci Rep 2021; 11:23105. [PMID: 34845321 PMCID: PMC8629993 DOI: 10.1038/s41598-021-02579-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
Alcaligenes faecalis is a heterotrophic nitrifying bacterium that oxidizes ammonia and generates nitrite and nitrate. When A. faecalis was cultivated in a medium containing pyruvate and ammonia as the sole carbon and nitrogen sources, respectively, high concentrations of nitrite accumulated in the medium whose carbon/nitrogen (C/N) ratio was lower than 10 during the exponential growth phase, while the accumulation was not observed in the medium whose C/N ratio was higher than 15. Comparative transcriptome analysis was performed using nitrifying and non-nitrifying cells of A. faecalis cultivated in media whose C/N ratios were 5 and 20, respectively, to evaluate the fluctuations of gene expression during induction of heterotrophic nitrification. Expression levels of genes involved in primary metabolism did not change significantly in the cells at the exponential growth phase under both conditions. We observed a significant increase in the expression levels of four gene clusters: pod cluster containing the gene encoding pyruvic oxime dioxygenase (POD), podh cluster containing the gene encoding a POD homolog (PODh), suf cluster involved in an iron-sulfur cluster biogenesis, and dnf cluster involved in a novel hydroxylamine oxidation pathway in the nitrifying cells. Our results provide valuable insight into the biochemical mechanism of heterotrophic nitrification.
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Kang CS, Dunfield PF, Semrau JD. The origin of aerobic methanotrophy within the Proteobacteria. FEMS Microbiol Lett 2020; 366:5485640. [PMID: 31054238 DOI: 10.1093/femsle/fnz096] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/02/2019] [Indexed: 11/13/2022] Open
Abstract
Aerobic methanotrophs play critical roles in the global carbon cycle, but despite their environmental ubiquity, they are phylogenetically restricted. Via bioinformatic analyses, it is shown that methanotrophy likely arose from methylotrophy from the lateral gene transfer of either of the two known forms of methane monooxygenase (particulate and soluble methane monooxygenases). Moreover, it appears that both known forms of pyrroloquinoline quinone-dependent methanol dehydrogenase (MeDH) found in methanotrophs-the calcium-containing Mxa-MeDH and the rare earth element-containing Xox-MeDH-were likely encoded in the genomes before the acquisition of the methane monooxygenases (MMOs), but that some methanotrophs subsequently received an additional copy of Xox-MeDH-encoding genes via lateral gene transfer. Further, data are presented that indicate the evolution of methanotrophy from methylotrophy not only required lateral transfer of genes encoding for methane monooxygenases, but also likely the pre-existence of a means of collecting copper. Given the emerging interest in valorizing methane via biological platforms, it is recommended that future strategies for heterologous expression of methane monooxygenase for conversion of methane to methanol also include cloning of genes encoding mechanism(s) of copper uptake, especially for expression of particulate methane monooxygenase.
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Affiliation(s)
- Christina S Kang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
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Silva LCF, Lima HS, Mendes TADO, Sartoratto A, Sousa MP, de Souza RS, de Paula SO, de Oliveira VM, Silva CC. Physicochemical characterization of Pseudomonas stutzeri UFV5 and analysis of its transcriptome under heterotrophic nitrification/aerobic denitrification pathway induction condition. Sci Rep 2020; 10:2215. [PMID: 32042029 PMCID: PMC7010759 DOI: 10.1038/s41598-020-59279-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/20/2020] [Indexed: 02/02/2023] Open
Abstract
Biological ammonium removal via heterotrophic nitrification/aerobic denitrification (HN/AD) presents several advantages in relation to conventional removal processes, but little is known about the microorganisms and metabolic pathways involved in this process. In this study, Pseudomonas stutzeri UFV5 was isolated from an activated sludge sample from oil wastewater treatment station and its ammonium removal via HN/AD was investigated by physicochemical and molecular approaches to better understand this process and optimize the biological ammonium removal in wastewater treatment plants. Results showed that P. stutzeri UFV5 removed all the ammonium in 48–72 hours using pyruvate, acetate, citrate or sodium succinate as carbon sources, C/N ratios 6, 8, 10 and 12, 3–6% salinities, pH 7–9 and temperatures of 20–40 °C. Comparative genomics and PCR revealed that genes encoding the enzymes involved in anaerobic denitrification process are present in P. stutzeri genome, but no gene that encodes enzymes involved in autotrophic nitrification was found. Furthermore, transcriptomics showed that none of the known enzymes of autotrophic nitrification and anaerobic denitrification had their expression differentiated and an upregulation of the biosynthesis machinery and protein translation was observed, besides several genes with unknown function, indicating a non-conventional mechanism involved in HN/AD process.
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Affiliation(s)
| | - Helena Santiago Lima
- Department of Microbiology, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | | | - Adilson Sartoratto
- Pluridisciplinary Center for Chemical, Biological and Agricultural Research, Campinas State University, Campinas, São Paulo, 13083-970, Brazil
| | - Maira Paula Sousa
- Petrobras - Research and Development Center (CENPES), Petrobras, Rio de Janeiro, 21941-915, Brazil
| | - Rodrigo Suhett de Souza
- Petrobras - Research and Development Center (CENPES), Petrobras, Rio de Janeiro, 21941-915, Brazil
| | - Sérgio Oliveira de Paula
- Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Valéria Maia de Oliveira
- Pluridisciplinary Center for Chemical, Biological and Agricultural Research, Campinas State University, Campinas, São Paulo, 13083-970, Brazil
| | - Cynthia Canedo Silva
- Department of Microbiology, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
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8
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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Methanotrophy across a natural permafrost thaw environment. ISME JOURNAL 2018; 12:2544-2558. [PMID: 29955139 PMCID: PMC6155033 DOI: 10.1038/s41396-018-0065-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 11/09/2022]
Abstract
The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ13C-CH4 isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.
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Diversity of culturable aerobic denitrifying bacteria in the sediment, water and biofilms in Liangshui River of Beijing, China. Sci Rep 2017; 7:10032. [PMID: 28855587 PMCID: PMC5577267 DOI: 10.1038/s41598-017-09556-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/24/2017] [Indexed: 01/17/2023] Open
Abstract
Aerobic denitrification is a process reducing the nitrate into gaseous nitrogen forms in the presence of oxygen gas, which makes the nitrification and denitrification performed simultaneously. However, little was known on the diversity of the culturable aerobic denitrifying bacteria in the surface water system. In this study, 116 strains of aerobic denitrifying bacteria were isolated from the sediment, water and biofilm samples in Liangshui River of Beijing. These bacteria were classified into 14 genera based on the 16 S rDNA, such as Pseudomonas, Rheinheimera, and Gemmobacter. The Pseudomonas sp., represented by the Pseudomonas stutzeri, Pseudomonas mendocina and Pseudomonas putida, composed the major culturable aerobic denitrifiers of the river, followed by Ochrobactrum sp. and Rheinheimera sp. The PCA plot showed the unclassified Pseudomonas sp. and Rheinheimera pacifica preferred to inhabit in biofilm phase while one unclassified Ochrobactrum sp. and Pseudomonas resinovorans had higher abundance in the sediment. In the overlying water, the Pseudomonas stutzeri and Ochrobactrum rhizosphaerae were found to have higher abundance, indicating these aerobic denitrifiers had different habitat-preferable characteristics among the 3 phases of river system. The findings may help select the niche to isolate the aerobic denitrifiers and facilitate the bioaugmentation-based purification of the nitrate polluted surface water.
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11
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Zhang P, Jia R, Zhang Y, Shi P, Chai T. Quinoline-degrading strain Pseudomonas aeruginosa KDQ4 isolated from coking activated sludge is capable of the simultaneous removal of phenol in a dual substrate system. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:1139-1148. [PMID: 27458688 DOI: 10.1080/10934529.2016.1206377] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Quinoline is a refractory organic compound in the treatment of coking wastewater. The isolation of high efficiency quinoline-degrading bacteria from activated sludge and the evaluation of their degradation characteristics in the presence of phenol or in the actual coking wastewater are important for the improvement of effluent quality. The novel bacterial strain Pseudomonas aeruginosa KDQ4 was isolated from a quinoline enrichment culture obtained from the activated sludge of a coking wastewater treatment plant. The optimum temperature and initial pH for quinoline degradation were 33-38°C and 8-9, respectively. KDQ4 completely degraded 400 mg/L of quinoline within 24 h and 800 mg/L of phenol within 30 h. In the dual-substrate system, the removal efficiencies of quinoline and phenol at the same initial concentration (200 mg/L) by KDQ4 were 89% and 100% within 24 h, respectively, indicating that KDQ4 could simultaneously and quickly degrade quinoline and phenol in a coexistence system. Moreover, KDQ4 was able to adapt to actual coking wastewater containing high quinoline and phenol concentrations and rapidly remove them. KDQ4 also exhibited heterotrophic nitrification and aerobic denitrification potential under aerobic conditions. These results suggested a potential bioaugmentation role for KDQ4 in the removal of nitrogen-heterocyclic compounds and phenolics from coking wastewater.
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Affiliation(s)
- Panhong Zhang
- a State Key Laboratory of Environmental Chemistry and Ecotoxicity , Research center for Eco-Environment of Sciences, Chinese Academy of Sciences , Beijing , PR China
- b Sino-Danish Center for Education and Research , Chinese Academy of Sciences , Beijing , PR China
| | - Rong Jia
- c Department of Environmental & Biological Engineering , School of Chemical & Environmental Engineering, China University of Mining & Technology (Beijing) , Beijing , PR China
| | - Yuxiu Zhang
- c Department of Environmental & Biological Engineering , School of Chemical & Environmental Engineering, China University of Mining & Technology (Beijing) , Beijing , PR China
| | - Peili Shi
- c Department of Environmental & Biological Engineering , School of Chemical & Environmental Engineering, China University of Mining & Technology (Beijing) , Beijing , PR China
| | - Tuanyao Chai
- d College of Life Science , University of Chinese Academy of Sciences , Beijing , PR China
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12
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Huang W, Li B, Zhang C, Zhang Z, Lei Z, Lu B, Zhou B. Effect of algae growth on aerobic granulation and nutrients removal from synthetic wastewater by using sequencing batch reactors. BIORESOURCE TECHNOLOGY 2015; 179:187-192. [PMID: 25544496 DOI: 10.1016/j.biortech.2014.12.024] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/07/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
The effect of algae growth on aerobic granulation and nutrients removal was studied in two identical sequencing batch reactors (SBRs). Sunlight exposure promoted the growth of algae in the SBR (Rs), forming an algal-bacterial symbiosis in aerobic granules. Compared to the control SBR (Rc), Rs had a slower granulation process with granules of loose structure and smaller particle size. Moreover, the specific oxygen uptake rate was significantly decreased for the granules from Rs with secretion of 25.7% and 22.5% less proteins and polysaccharides respectively in the extracellular polymeric substances. Although little impact was observed on chemical oxygen demand (COD) removal, algal-bacterial symbiosis deteriorated N and P removals, about 40.7-45.4% of total N and 44% of total P in Rs in contrast to 52.9-58.3% of TN and 90% of TP in Rc, respectively. In addition, the growth of algae altered the microbial community in Rs, especially unfavorable for Nitrospiraceae and Nitrosomonadaceae.
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Affiliation(s)
- Wenli Huang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Bing Li
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Chao Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhenya Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Baowang Lu
- Graduate School of Environmental and Life Sciences, Okayama University, 3-1-1 Tushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Beibei Zhou
- Shanghai Biotechnology Corporation, 121 Libing Road, Shanghai 201203, China
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13
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Hirsch PR, Mauchline TH. The Importance of the Microbial N Cycle in Soil for Crop Plant Nutrition. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:45-71. [PMID: 26505688 DOI: 10.1016/bs.aambs.2015.09.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nitrogen is crucial for living cells, and prior to the introduction of mineral N fertilizer, fixation of atmospheric N2 by diverse prokaryotes was the primary source of N in all ecosystems. Microorganisms drive the N cycle starting with N2 fixation to ammonia, through nitrification in which ammonia is oxidized to nitrate and denitrification where nitrate is reduced to N2 to complete the cycle, or partially reduced to generate the greenhouse gas nitrous oxide. Traditionally, agriculture has relied on rotations that exploited N fixed by symbiotic rhizobia in leguminous plants, and recycled wastes and manures that microbial activity mineralized to release ammonia or nitrate. Mineral N fertilizer provided by the Haber-Bosch process has become essential for modern agriculture to increase crop yields and replace N removed from the system at harvest. However, with the increasing global population and problems caused by unintended N wastage and pollution, more sustainable ways of managing the N cycle in soil and utilizing biological N2 fixation have become imperative. This review describes the biological N cycle and details the steps and organisms involved. The effects of various agricultural practices that exploit fixation, retard nitrification, and reduce denitrification are presented, together with strategies that minimize inorganic fertilizer applications and curtail losses. The development and implementation of new technologies together with rediscovering traditional practices are discussed to speculate how the grand challenge of feeding the world sustainably can be met.
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Affiliation(s)
- Penny R Hirsch
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Tim H Mauchline
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
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14
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Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture. Appl Environ Microbiol 2012; 78:2137-46. [PMID: 22267662 DOI: 10.1128/aem.06845-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.
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15
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Semrau JD, DiSpirito AA, Vuilleumier S. Facultative methanotrophy: false leads, true results, and suggestions for future research. FEMS Microbiol Lett 2011; 323:1-12. [DOI: 10.1111/j.1574-6968.2011.02315.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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16
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Quinoline biodegradation and its nitrogen transformation pathway by a Pseudomonas sp. strain. Biodegradation 2009; 21:335-44. [DOI: 10.1007/s10532-009-9304-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 10/13/2009] [Indexed: 10/20/2022]
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17
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Aerobic degradation of pyridine by a new bacterial strain, Shinella zoogloeoides BC026. J Ind Microbiol Biotechnol 2009; 36:1391-400. [DOI: 10.1007/s10295-009-0625-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
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18
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Ho KL, Chung YC, Tseng CP. Continuous deodorization and bacterial community analysis of a biofilter treating nitrogen-containing gases from swine waste storage pits. BIORESOURCE TECHNOLOGY 2008; 99:2757-65. [PMID: 17697773 DOI: 10.1016/j.biortech.2007.06.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 06/26/2007] [Accepted: 06/26/2007] [Indexed: 05/16/2023]
Abstract
A biofilter inoculated with Arthrobacter sp. was applied to the simultaneous elimination of trimethylamine (TMA) and ammonia (NH3) from the exhaust air of swine waste storage pits. The results showed that the biofilter achieved average removal efficiencies of 96.8+/-2.5% and 97.2+/-2.3% for TMA and NH3, respectively. A near-neutral pH (7.3-7.4) was maintained due to the accumulation of acid metabolites and the adsorption of alkaline NH3. Low moisture demand, low pressure drop and high biofilm stability in the system were other advantages. After long-term operation, the bacterial community structure showed that at least twenty-five bands were explicitly detected by a denaturing gradient gel electrophoresis (DGGE) method. However, the inoculated Arthrobacter sp. still maintained a dominant population (>50%). Paracoccus denitrificans' presence in the biofilter could play an important role in oxidizing NH3 and reducing nitrite by heterotrophic nitrification and anaerobic denitrification.
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Affiliation(s)
- Kuo-Ling Ho
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-chu, Taiwan, ROC
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19
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Ho KL, Chung YC, Lin YH, Tseng CP. Biofiltration of trimethylamine, dimethylamine, and methylamine by immobilized Paracoccus sp. CP2 and Arthrobacter sp. CP1. CHEMOSPHERE 2008; 72:250-256. [PMID: 18331754 DOI: 10.1016/j.chemosphere.2008.01.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 01/21/2008] [Accepted: 01/22/2008] [Indexed: 05/26/2023]
Abstract
A biofilter using granular activated carbon with immobilized Paracoccus sp. CP2 was applied to the elimination of 10-250 ppm of trimethylamine (TMA), dimethylamine (DMA), and methylamine (MA). The results indicated that the system effectively treated MA (>93%), DMA (>90%), and TMA (>85%) under high loading conditions, and the maximum degradation rates were 1.4, 1.2, and 0.9g-Nkg(-1) GAC d(-1). Among the three different amines treated, TMA was the most difficult to degrade and resulted in ammonia accumulation. Further study on TMA removal showed that the optimal pH was near neutral (6.0-8.0). The supply of high glucose (>0.1%) inhibited TMA removal, maybe due to substrate competition. However, complete TMA degradation was achieved under the co-immobilization of Paracoccus sp. CP2 and Arthrobacter sp. CP1 ( approximately 96%). Metabolite analysis results demonstrated that the metabolite NH(4)(+) concentrations decreased by a relatively small 27% while the metabolite NO(2)(-) apparently increased by heterotrophic nitrification of Arthrobacter sp. CP1 in the co-immobilization biofilter.
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Affiliation(s)
- Kuo-Ling Ho
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-chu, Taiwan, Republic of China
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20
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Bai Y, Sun Q, Zhao C, Wen D, Tang X. Microbial degradation and metabolic pathway of pyridine by a Paracoccus sp. strain BW001. Biodegradation 2008; 19:915-26. [PMID: 18437507 DOI: 10.1007/s10532-008-9193-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 04/04/2008] [Indexed: 11/24/2022]
Abstract
A bacterial strain using pyridine as sole carbon, nitrogen and energy source was isolated from the activated sludge of a coking wastewater treatment plant. By means of morphologic observation, physiological characteristics study and 16S rRNA gene sequence analysis, the strain was identified as the species of Paracoccus. The strain could degrade 2,614 mg l(-1) of pyridine completely within 49.5 h. Experiment designed to track the metabolic pathway showed that pyridine ring was cleaved between the C2 and N, then the mineralization of the carbonous intermediate products may comply with the early proposed pathway and the transformation of the nitrogen may proceed on a new pathway of simultaneous heterotrophic nitrification and aerobic denitrification. During the degradation, NH3-N occurred and increased along with the decrease of pyridine in the solution; but the total nitrogen decreased steadily and equaled to the quantity of NH3-N when pyridine was degraded completely. Adding glucose into the medium as the extra carbon source would expedite the biodegradation of pyridine and the transformation of the nitrogen. The fragments of nirS gene and nosZ gene were amplified which implied that the BW001 had the potential abilities to reduce NO2- to NO and/or N2O, and then to N2.
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Affiliation(s)
- Yaohui Bai
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, People's Republic of China
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21
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Heterotrophic cultivation of Paracoccus denitrificans in a horizontal rotating tubular bioreactor. World J Microbiol Biotechnol 2006. [DOI: 10.1007/s11274-006-9324-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Comparison between the heterotrophic cultivation of Paracoccus denitrificans in continuous stirred tank reactor and horizontal rotating tubular bioreactor. Process Biochem 2006. [DOI: 10.1016/j.procbio.2006.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Levipan HA, Aspé E, Urrutia H. Molecular analysis of the community structure of nitrifying bacteria in a continuous-flow bioreactor. ENVIRONMENTAL TECHNOLOGY 2004; 25:261-272. [PMID: 15176741 DOI: 10.1080/09593330409355460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We herein report the diversity and relative abundance of chemolithotrophic nitrifying bacteria in a continuous-flow bioreactor using 16S-ribosomal RNA quantitative dot-blot hybridizations. About 14.9% of the total bacterial population, determined by epifluorescence microscopy in the bioreactor suspended phase, was represented by nitrifying bacteria. Of this fraction, ammonia- and nitrite-oxidizing bacteria accounted for 10% and 90%, respectively, the latter group being mostly Nitrospira-like. On the other hand, the nitrifiers adhesion/colonization capacity on polyethylene surfaces as evaluated by scanning electron microscopy and hybridizations analyses was 12.6% of the total bacterial community adhered. Finally, in spite of the relatively small contribution of nitrifiers to the total bacterial abundance in the bioreactor, we determined a mean ammonia removal rate of 170.48 +/- 8.29 mg N l(-1) d(-1); thus, the low percentage of ammonia-oxidizing bacteria, was not limiting the bioreactor performance.
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Affiliation(s)
- H A Levipan
- Departamento de Microbiologá, Casilla 160-C, Correo 3, Universidad de Concepción, Concepción, Chile
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24
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Nemergut DR, Schmidt SK. Disruption of narH, narJ, and moaE inhibits heterotrophic nitrification in Pseudomonas strain M19. Appl Environ Microbiol 2002; 68:6462-5. [PMID: 12450879 PMCID: PMC134400 DOI: 10.1128/aem.68.12.6462-6465.2002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Interruptions in three nitrate reductase-related genes, narH, narJ, and moaE, inhibited heterotrophic nitrification in Pseudomonas strain M19. No nitrate was detected in the medium, and nitrification proceeded in the presence of a nitrate reductase inhibitor. Heterotrophic nitrification was greatly stimulated by the addition of nitrate.
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Affiliation(s)
- D R Nemergut
- Department of Environmental, Population and Organismic Biology, University of Colorado, Boulder 80309, USA
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25
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Harms N, Reijnders WN, Koning S, van Spanning RJ. Two-component system that regulates methanol and formaldehyde oxidation in Paracoccus denitrificans. J Bacteriol 2001; 183:664-70. [PMID: 11133961 PMCID: PMC94923 DOI: 10.1128/jb.183.2.664-670.2001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A chromosomal region encoding a two-component regulatory system, FlhRS, has been isolated from Paracoccus denitrificans. FlhRS-deficient mutants were unable to grow on methanol, methylamine, or choline as the carbon and energy source. Expression of the gene encoding glutathione-dependent formaldehyde dehydrogenase (fhlA) was undetectable in the mutant, and expression of the S-formylglutathione hydrolase gene (fghA) was reduced in the mutant background. In addition, methanol dehydrogenase was immunologically undetectable in cell extracts of FhlRS mutants. These results indicate that the FlhRS sensor-regulator pair is involved in the regulation of formaldehyde, methanol, and methylamine oxidation. The effect that the FlhRS proteins exert on the regulation of C(1) metabolism might be essential to maintain the internal concentration of formaldehyde below toxic levels.
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Affiliation(s)
- N Harms
- Department of Molecular Cell Physiology, Vrije Universiteit, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
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26
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Shearer N, Hinsley AP, Van Spanning RJ, Spiro S. Anaerobic growth of Paracoccus denitrificans requires cobalamin: characterization of cobK and cobJ genes. J Bacteriol 1999; 181:6907-13. [PMID: 10559155 PMCID: PMC94164 DOI: 10.1128/jb.181.22.6907-6913.1999] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A pleiotropic mutant of Paracoccus denitrificans, which has a severe defect that affects its anaerobic growth when either nitrate, nitrite, or nitrous oxide is used as the terminal electron acceptor and which is also unable to use ethanolamine as a carbon and energy source for aerobic growth, was isolated. This phenotype of the mutant is expressed only during growth on minimal media and can be reversed by addition of cobalamin (vitamin B(12)) or cobinamide to the media or by growth on rich media. Sequence analysis revealed the mutation causing this phenotype to be in a gene homologous to cobK of Pseudomonas denitrificans, which encodes precorrin-6x reductase of the cobalamin biosynthesis pathway. Convergently transcribed with cobK is a gene homologous to cobJ of Pseudomonas denitrificans, which encodes precorrin-3b methyltransferase. The inability of the cobalamin auxotroph to grow aerobically on ethanolamine implies that wild-type P. denitrificans (which can grow on ethanolamine) expresses a cobalamin-dependent ethanolamine ammonia lyase and that this organism synthesizes cobalamin under both aerobic and anaerobic growth conditions. Comparison of the cobK and cobJ genes with their orthologues suggests that P. denitrificans uses the aerobic pathway for cobalamin synthesis. It is paradoxical that under anaerobic growth conditions, P. denitrificans appears to use the aerobic (oxygen-requiring) pathway for cobalamin synthesis. Anaerobic growth of the cobalamin auxotroph could be restored by the addition of deoxyribonucleosides to minimal media. These observations provide evidence that P. denitrificans expresses a cobalamin-dependent ribonucleotide reductase, which is essential for growth only under anaerobic conditions.
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Affiliation(s)
- N Shearer
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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27
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Krasko A, Schröder HC, Perovic S, Steffen R, Kruse M, Reichert W, Müller IM, Müller WE. Ethylene modulates gene expression in cells of the marine sponge Suberites domuncula and reduces the degree of apoptosis. J Biol Chem 1999; 274:31524-30. [PMID: 10531355 DOI: 10.1074/jbc.274.44.31524] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sponges (phylum Porifera) live in an aqueous milieu that contains dissolved organic carbon. This is degraded photochemically by ultraviolet radiation to alkenes, particularly to ethylene. This study demonstrates that sponge cells (here the demosponge Suberites domuncula has been used), which have assembled to primmorphs, react to 5 microM ethylene with a significant up-regulation of intracellular Ca(2+) concentration and with a reduction of starvation-induced apoptosis. In primmorphs from S. domuncula the expression of two genes is up-regulated after exposure to ethylene. The cDNA of the first gene (SDERR) isolated from S. domuncula encodes a potential ethylene-responsive protein, termed ERR_SUBDO; its putative M(r) is 32,704. Data bank search revealed that the sponge polypeptide shares high similarity (82% on amino acid level) with the corresponding plant molecule, the ethylene-inducible protein from Hevea brasiliensis. Until now no other metazoan ethylene-responsive proteins have been identified. The second gene, whose expression is up-regulated in response to ethylene is a Ca(2+)/calmodulin-dependent protein kinase II. Its cDNA, SDCCdPK, encodes a M(r) 54,863 putative kinase that shares 69% similarity with the corresponding enzyme from Drosophila melanogaster. The expression of both genes in primmorphs from S. domuncula is increased by approximately 5-fold after a 3-day incubation period with ethylene. It is concluded that also metazoan cells, with sponge cells as a model, may react to ethylene with an activation of cell metabolism including gene induction.
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Affiliation(s)
- A Krasko
- Institut für Physiologische Chemie, Abteilung Angewandte Molekularbiologie, Universität, Duesbergweg 6, D-55099 Mainz, Germany
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28
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Abstract
The minimal nitrogen cycle involves five reduction reactions and three oxidation reactions, each of which poses interesting problems in bioinorganic chemistry, energy transduction and protein structure/function relationships. Many of the major recent developments in this field have depended on the acquisition of protein crystal structures, including structures of enzymes with bound substrates or products and in protein-protein complexes. These enzymes include nitrogenase, nitrite reductases, hydroxylamine oxidoreductase and a fungal nitric oxide reductase.
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Affiliation(s)
- S J Ferguson
- Department of Biochemistry, Oxford Centre for Molecular Sciences, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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