1
|
Intrator N, Jayakumar A, Ward BB. Aquatic nitrous oxide reductase gene ( nosZ) phylogeny and environmental distribution. Front Microbiol 2024; 15:1407573. [PMID: 38835481 PMCID: PMC11148229 DOI: 10.3389/fmicb.2024.1407573] [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: 03/26/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the gene nosZ. Organisms that contain nosZ are the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades of nosZ (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of nosZ containing organisms in the environment. A database of over 11,000 nosZ sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I nosZ genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I nosZ genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the nosZ gene displays regional and environmental separation. This study expands the known diversity of nosZ genes and provides a clearer picture of how the clades and phylogeny of nosZ organisms are distributed across diverse environments.
Collapse
Affiliation(s)
- Naomi Intrator
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| |
Collapse
|
2
|
Chen H, Tu Z, Wu S, Yu G, Du C, Wang H, Yang E, Zhou L, Deng B, Wang D, Li H. Recent advances in partial denitrification-anaerobic ammonium oxidation process for mainstream municipal wastewater treatment. CHEMOSPHERE 2021; 278:130436. [PMID: 33839386 DOI: 10.1016/j.chemosphere.2021.130436] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 05/05/2023]
Abstract
To solve the bottleneck of the unstable accumulation of nitrite in the partial nitrification (PN)-anammox (AMX) in municipal wastewater treatment, a novel process called partial denitrification (PD)-AMX has been developed. PD-AMX, which is known for cost-efficiency and environmental friendliness, has currently exhibited a promising potential for the removal of biological nitrogen from municipal wastewater and has attracted much research interest regarding its process mechanisms, as well as its practical applications. Here, we review the recent advances in the PD process and its coupling to the anammox process, including the development, basic principles, main characteristics, and critical process parameters of the stable operation of the PD-AMX process. We also explore the microbial community and its characteristics in the system and summarize the knowledge of the dominant bacteria to clarify the key factors affecting PD-AMX. Then, we introduce the engineering feasibility and economic feasibility as well as the potential challenges of the process. The induction and implementation of partial denitrification and maintenance of mainstream anammox are critical issues to be urgently solved. Meanwhile, the implementation of a full mainstream anammox application remains burdensome, while the mechanism of partial denitrification coupled to anammox needs to be further studied. Additionally, stable operation performance and process control1 methods need to be optimized or developed for the PD-AMX system for better engineering practice. This review can help to accelerate the research and application of the PD-AMX process for municipal wastewater treatment.
Collapse
Affiliation(s)
- Hong Chen
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Zhi Tu
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China; College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China
| | - Sha Wu
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China
| | - Guanlong Yu
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China
| | - Chunyan Du
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China
| | - Hong Wang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China; College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China
| | - Enzhe Yang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China; School of Energy Science and Engineering, Central South University, Changsha, 410083, China
| | - Lu Zhou
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China
| | - Bin Deng
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha, 410004, China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China.
| | - Hailong Li
- School of Energy Science and Engineering, Central South University, Changsha, 410083, China.
| |
Collapse
|
3
|
Miralles-Robledillo JM, Bernabeu E, Giani M, Martínez-Serna E, Martínez-Espinosa RM, Pire C. Distribution of Denitrification among Haloarchaea: A Comprehensive Study. Microorganisms 2021; 9:1669. [PMID: 34442748 PMCID: PMC8400030 DOI: 10.3390/microorganisms9081669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022] Open
Abstract
Microorganisms from the Halobacteria class, also known as haloarchaea, inhabit a wide range of ecosystems of which the main characteristic is the presence of high salt concentration. These environments together with their microbial communities are not well characterized, but some of the common features that they share are high sun radiation and low availability of oxygen. To overcome these stressful conditions, and more particularly to deal with oxygen limitation, some microorganisms drive alternative respiratory pathways such as denitrification. In this paper, denitrification in haloarchaea has been studied from a phylogenetic point of view. It has been demonstrated that the presence of denitrification enzymes is a quite common characteristic in Halobacteria class, being nitrite reductase and nitric oxide reductase the enzymes with higher co-occurrence, maybe due to their possible role not only in denitrification, but also in detoxification. Moreover, copper-nitrite reductase (NirK) is the only class of respiratory nitrite reductase detected in these microorganisms up to date. The distribution of this alternative respiratory pathway and their enzymes among the families of haloarchaea has also been discussed and related with the environment in which they constitute the major populations. Complete denitrification phenotype is more common in some families like Haloarculaceae and Haloferacaceae, whilst less common in families such as Natrialbaceae and Halorubraceae.
Collapse
Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Elena Martínez-Serna
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| |
Collapse
|
4
|
Wang L, Shao Z. Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis. Front Microbiol 2021; 12:652766. [PMID: 33815342 PMCID: PMC8014003 DOI: 10.3389/fmicb.2021.652766] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.
Collapse
Affiliation(s)
- Liping Wang
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
5
|
Liu RR, Tian Y, Zhou EM, Xiong MJ, Xiao M, Li WJ. Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462 T Improved Environmental Adaptability. MICROBIAL ECOLOGY 2020; 80:614-626. [PMID: 32474659 DOI: 10.1007/s00248-020-01528-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/14/2020] [Indexed: 05/21/2023]
Abstract
Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2-) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462T were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462T. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.
Collapse
Affiliation(s)
- Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - En-Min Zhou
- School of Resource Environment and Earth Science, Yunnan Institute of Geography, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Jie Xiong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| |
Collapse
|
6
|
Community structures and comparison of nosZ and 16S rRNA genes from culturable denitrifying bacteria. Folia Microbiol (Praha) 2019; 65:497-510. [DOI: 10.1007/s12223-019-00754-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 10/14/2019] [Indexed: 10/25/2022]
|
7
|
Ma Y, Zilles JL, Kent AD. An evaluation of primers for detecting denitrifiers via their functional genes. Environ Microbiol 2019; 21:1196-1210. [PMID: 30724437 DOI: 10.1111/1462-2920.14555] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022]
Abstract
Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.
Collapse
Affiliation(s)
- Yanjun Ma
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julie L Zilles
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
8
|
Effects of the natural restoration time of abandoned farmland in a semiarid region on the soil denitrification rates and abundance and community structure of denitrifying bacteria. Appl Microbiol Biotechnol 2019; 103:1939-1951. [DOI: 10.1007/s00253-018-09575-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 12/11/2022]
|
9
|
Wang L, Zheng B, Nan B, Hu P. Diversity of bacterial community and detection of nirS- and nirK-encoding denitrifying bacteria in sandy intertidal sediments along Laizhou Bay of Bohai Sea, China. MARINE POLLUTION BULLETIN 2014; 88:215-223. [PMID: 25256298 DOI: 10.1016/j.marpolbul.2014.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/29/2014] [Accepted: 09/06/2014] [Indexed: 06/03/2023]
Abstract
The microbial community and the nirS- and nirK-encoding denitrifiers in the intertidal sediments along Laizhou Bay in China were studied using pyrosequencing and real-time quantitative PCR (qPCR), respectively. There were three primary intertidal zones: Laizhou (La), Weifang Harbor (We), and Dongying (Do). Significant differences in composition and abundances at the different taxonomic levels were observed among the three bacterial communities. The qPCR results indicated that the nirS gene abundance varied from 8.67 × 10(5) to 5.68 × 10(6)copies/gwet weight (ww), whereas the nirK gene abundance varied from 1.26 × 10(5) to 1.89 × 10(6)copies/gww. The canonical correlation analysis (CCA) indicated that the sand percentage was the most important factor in shaping the bacterial community followed by silt percentage, NO2(-), TOC, DO, pH, and clay percentage, whereas the clay percentage, pH, NO3(-), DO, NO2(-), TOC, silt percentage, and sand percentage were the most important factors associated with regulating the abundance of nirS- and nirK-encoding denitrifiers.
Collapse
Affiliation(s)
- Liping Wang
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| | - Binghui Zheng
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Bingxu Nan
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Peilong Hu
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| |
Collapse
|
10
|
Liu B, Mao Y, Bergaust L, Bakken LR, Frostegård Å. Strains in the genusThaueraexhibit remarkably different denitrification regulatory phenotypes. Environ Microbiol 2013; 15:2816-28. [DOI: 10.1111/1462-2920.12142] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Binbin Liu
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; N-1432; Norway
| | | | | | - Lars R. Bakken
- Department of Plant and Environmental Sciences; Norwegian University of Life Sciences; Ås; N-1432; Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; N-1432; Norway
| |
Collapse
|
11
|
Ghirardi S, Dessaint F, Mazurier S, Corberand T, Raaijmakers JM, Meyer JM, Dessaux Y, Lemanceau P. Identification of traits shared by rhizosphere-competent strains of fluorescent pseudomonads. MICROBIAL ECOLOGY 2012; 64:725-737. [PMID: 22576821 DOI: 10.1007/s00248-012-0065-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 04/21/2012] [Indexed: 05/31/2023]
Abstract
Rhizosphere competence of fluorescent pseudomonads is a prerequisite for the expression of their beneficial effects on plant growth and health. To date, knowledge on bacterial traits involved in rhizosphere competence is fragmented and derived mostly from studies with model strains. Here, a population approach was taken by investigating a representative collection of 23 Pseudomonas species and strains from different origins for their ability to colonize the rhizosphere of tomato plants grown in natural soil. Rhizosphere competence of these strains was related to phenotypic traits including: (1) their carbon and energetic metabolism represented by the ability to use a wide range of organic compounds, as electron donors, and iron and nitrogen oxides, as electron acceptors, and (2) their ability to produce antibiotic compounds and N-acylhomoserine lactones (N-AHSL). All these data including origin of the strains (soil/rhizosphere), taxonomic identification, phenotypic cluster based on catabolic profiles, nitrogen dissimilating ability, siderovars, susceptibility to iron starvation, antibiotic and N-AHSL production, and rhizosphere competence were submitted to multiple correspondence analyses. Colonization assays revealed a significant diversity in rhizosphere competence with survival rates ranging from approximately 0.1 % to 61 %. Multiple correspondence analyses indicated that rhizosphere competence was associated with siderophore-mediated iron acquisition, substrate utilization, and denitrification. However, the catabolic profile of one rhizosphere-competent strain differed from the others and its competence was associated with its ability to produce antibiotics phenazines and N-AHSL. Taken together, these data suggest that competitive strains have developed two types of strategies to survive in the rhizosphere.
Collapse
Affiliation(s)
- Sandrine Ghirardi
- INRA, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065 Dijon Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Rojas-Oropeza M, Fernández FJ, Dendooven L, Cabirol N. Effect of methyl parathion on nitrous oxide production: a laboratory study. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2012; 95 Suppl:S25-S30. [PMID: 21295905 DOI: 10.1016/j.jenvman.2011.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 11/14/2010] [Accepted: 01/04/2011] [Indexed: 05/30/2023]
Abstract
We investigated the diversity of a denitrifying gene (nirK) and the emission of CO(2) and N(2)O, in a "chinampa" soil contaminated with methyl parathion. Soil at 40% of water holding capacity was spiked with methyl parathion at four concentrations (i.e. 0, 0.7, 1.47 and 4.27 g kg(-1) dry soil), while emission of N(2)O and CO(2) and nirK diversity was determined after 0, 1, 14, 30, 60 and 90 days. The emission of N(2)O on a daily base and the cumulative emission of CO(2) was not affected by the different concentrations of methyl parathion applied to soil. The diversity of the nirK gene, determined by using temperature gradient gel electrophoresis (TGGE), decreased with increased methyl parathion application. It was found that methyl parathion had effect on the emissions of N(2)O and CO(2), and reduced the diversity of the nirK gene. Consequently, the reduced diversity of the nirK gene could affect the emission of N(2)O.
Collapse
Affiliation(s)
- Marcelo Rojas-Oropeza
- Facultad de Ciencias, Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 México D.F., Mexico
| | | | | | | |
Collapse
|
13
|
Zribi K, Djébali N, Mrabet M, Khayat N, Smaoui A, Mlayah A, Aouani ME. Physiological responses to cadmium, copper, lead, and zinc of Sinorhizobium sp. strains nodulating Medicago sativa grown in Tunisian mining soils. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0358-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
14
|
Assessment of genetic and functional relationship of antagonistic fluorescent pseudomonads of rice rhizosphere by repetitive sequence, protein coding sequence and functional gene analyses. J Microbiol 2011; 48:715-27. [DOI: 10.1007/s12275-010-0064-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 06/30/2010] [Indexed: 10/18/2022]
|
15
|
Wu Z, Zou L, Lu D, Liu Z. Restoration of taxonomic and functional genes after bioaugmentation of petroleum contaminated soil. ACTA ACUST UNITED AC 2011; 13:2904-13. [DOI: 10.1039/c0em00761g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
Reyna L, Wunderlin DA, Genti-Raimondi S. Identification and quantification of a novel nitrate-reducing community in sediments of Suquía River basin along a nitrate gradient. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2010; 158:1608-1614. [PMID: 20045234 DOI: 10.1016/j.envpol.2009.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 12/01/2009] [Accepted: 12/06/2009] [Indexed: 05/28/2023]
Abstract
We evaluated the molecular diversity of narG gene from Suquía River sediments to assess the impact of the nitrate concentration and water quality on the composition and structure of the nitrate-reducing bacterial community. To this aim, a library of one of the six monitoring stations corresponding to the highest nitrate concentration was constructed and 118 narG clones were screened. Nucleotide sequences were associated to narG gene from alpha-, beta-, delta-, gammaproteobacteria and Thermus thermophilus. Remarkably, 18% of clones contained narG genes with less than 69% similarity to narG sequences available in databases. Thus, indicating the presence of nitrate-reducing bacteria with novel narG genes, which were quantified by real-time PCR. Results show a variable number of narG copies, ranging from less than 1.0 x 10(2) to 5.0 x 10(4) copies per ng of DNA, which were associated with a decreased water quality index monitored along the basin at different times.
Collapse
Affiliation(s)
- Luciana Reyna
- Universidad Nacional de Córdoba-CONICET, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica-CIBICI, Haya de la Torre y Medina Allende, Ciudad Universitaria, 5000 Córdoba, Argentina
| | | | | |
Collapse
|
17
|
Denitrification as an important taxonomic marker within the genus Halomonas. Syst Appl Microbiol 2010; 33:85-93. [DOI: 10.1016/j.syapm.2009.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 12/15/2009] [Accepted: 12/16/2009] [Indexed: 11/17/2022]
|
18
|
Throbäck IN, Enwall K, Jarvis A, Hallin S. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol 2009; 49:401-17. [PMID: 19712290 DOI: 10.1016/j.femsec.2004.04.011] [Citation(s) in RCA: 626] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We re-evaluated PCR primers targeting nirS, nirK and nosZ genes for denaturing gradient gel electrophoresis as a tool to survey denitrifying community composition in environmental samples. New primers for both nirS and nosZ were combined with existing primers, while for nirK the previously published F1aCu:R3Cu set was chosen for denaturing electrophoresis. All three sets yielded amplicons smaller than 500 bp and amplified the correct fragment in all environmental samples. The denaturing gradient gel electrophoresis worked satisfactorily for nirK and nosZ, but not for nirS. This was probably due to the multiple melting domains in this particular nirS fragment. From the excised and sequenced bands, only sequences related to the target genes were detected and tree analysis showed that the selected primers acted as broad range primers for each of the three genes. By use of the new nirS primers it was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers.
Collapse
Affiliation(s)
- Ingela Noredal Throbäck
- Department of Microbiology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
| | | | | | | |
Collapse
|
19
|
Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers. Appl Environ Microbiol 2009; 75:5170-4. [PMID: 19502444 DOI: 10.1128/aem.00254-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of > or =97% had a narG or nosZ similarity of > or =67% or > or =80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent.
Collapse
|
20
|
Purification and properties of a heat-stable enzyme of Pseudomonas fluorescens Rm12 from raw milk. Eur Food Res Technol 2008. [DOI: 10.1007/s00217-008-0983-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
21
|
Jones CM, Stres B, Rosenquist M, Hallin S. Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 2008; 25:1955-66. [PMID: 18614527 DOI: 10.1093/molbev/msn146] [Citation(s) in RCA: 263] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Denitrification is a facultative respiratory pathway in which nitrite (NO2(-)), nitric oxide (NO), and nitrous oxide (N2O) are successively reduced to nitrogen gas (N(2)), effectively closing the nitrogen cycle. The ability to denitrify is widely dispersed among prokaryotes, and this polyphyletic distribution has raised the possibility of horizontal gene transfer (HGT) having a substantial role in the evolution of denitrification. Comparisons of 16S rRNA and denitrification gene phylogenies in recent studies support this possibility; however, these results remain speculative as they are based on visual comparisons of phylogenies from partial sequences. We reanalyzed publicly available nirS, nirK, norB, and nosZ partial sequences using Bayesian and maximum likelihood phylogenetic inference. Concomitant analysis of denitrification genes with 16S rRNA sequences from the same organisms showed substantial differences between the trees, which were supported by examining the posterior probability of monophyletic constraints at different taxonomic levels. Although these differences suggest HGT of denitrification genes, the presence of structural variants for nirK, norB, and nosZ makes it difficult to determine HGT from other evolutionary events. Additional analysis using phylogenetic networks and likelihood ratio tests of phylogenies based on full-length sequences retrieved from genomes also revealed significant differences in tree topologies among denitrification and 16S rRNA gene phylogenies, with the exception of the nosZ gene phylogeny within the data set of the nirK-harboring genomes. However, inspection of codon usage and G + C content plots from complete genomes gave no evidence for recent HGT. Instead, the close proximity of denitrification gene copies in the genomes of several denitrifying bacteria suggests duplication. Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution of each denitrification gene.
Collapse
Affiliation(s)
- Christopher M Jones
- Department of Microbiology, Swedish Agricultural University, Uppsala, Sweden.
| | | | | | | |
Collapse
|
22
|
McSpadden Gardener BB. Diversity and Ecology of Biocontrol Pseudomonas spp. in Agricultural Systems. PHYTOPATHOLOGY 2007; 97:221-226. [PMID: 18944378 DOI: 10.1094/phyto-97-2-0221] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Diverse Pseudomonas spp. may act as biological controls of plant pathogens, but the ecology of those natural populations is not well understood. And, while biocontrol potential has been identified in multiple pseudomonad strains, the linkages between genotype and phenotype have yet to be fully delineated. However, intensive studies of one class of biocontrol strains, i.e., those that can produce 2,4-diacetylphloroglucionl (DAPG), have provided new insights into the diversity, distribution, and interactions of biocontrol pseudomonads. Those studies also laid the foundation for future research and development of pseudomonad-based biocontrol strategies. Over the past several years, numerous studies have also revealed that biocontrol pseudomonads are widely distributed in agricultural soils, and that multiple crop and soil factors can affect their abundance and activities. Recent work has shown that a variety of farm management practices that reduce soilborne disease pressure can also alter the rhizosphere abundance of DAPG producers in complex ways. Such studies provide support for the hypothesis of an ecological feedback mechanism whereby a native biocontrol population increase and subsequently reduce root disease severity following infection. It is well established that complex biological interactions can take place among bio-control pseudomonads, plant pathogens, their hosts, and other members of the microbial community. The net result of such interactions likely dilutes biocontrol efficacy at the field scale. Nonetheless, inoculation can be effective, and several successful applications of biocontrol pseudomonads have been developed. Future applications of microbial ecology research will hopefully improve the consistency and efficacy of bio-control mediated by Pseudomonas spp. Current applications and future opportunities for improving pseudomonad-based biological control are discussed.
Collapse
|
23
|
Dandie CE, Burton DL, Zebarth BJ, Trevors JT, Goyer C. Analysis of denitrification genes and comparison of nosZ, cnorB and 16S rDNA from culturable denitrifying bacteria in potato cropping systems. Syst Appl Microbiol 2006; 30:128-38. [PMID: 16793234 DOI: 10.1016/j.syapm.2006.05.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Indexed: 11/24/2022]
Abstract
Bacterial denitrification in agricultural soils is a major source of nitrous oxide, a potent greenhouse gas. This study examined the culturable bacterial population of denitrifiers in arable field soils in potato (Solanum tuberosum L.) production and denitrification genes (nir, nor and nos) and 16S rDNA in those isolates. Enrichments for culturable denitrifiers yielded 31 diverse isolates that were then analysed for denitrification genes. The nitrous oxide reductase (nosZ) gene was found in all isolates. The majority of isolates ( approximately 90%) contained the cnorB nitric oxide reductase gene, with the remainder containing the qnorB gene. Nitrite reductase genes (nirS and nirK) were amplifiable from most of the isolates, and were segregated between species similar to previously isolated denitrifiers. Isolated strains were preliminarily identified using fatty acid methyl ester analysis and further identified using 16S rDNA sequencing. The majority of isolates (21) were classified as Pseudomonas sp., with smaller groups of isolates being most similar to Bosea spp. (4), Achromobacter spp. (4) and two isolates closely related to Sinorhizobium/Ensifer spp. Phylogenetic trees were compared among nosZ, cnorB and 16S rDNA genes for a subset of Pseudomonas strains. The trees were mostly congruent, but some Pseudomonas sp. isolates grouped differently depending on the gene analysed, indicating potential horizontal gene transfer of denitrification genes. Although Bosea spp. are known denitrifiers, to the best of our knowledge this is the first report of isolation and sequencing of denitrification genes from this bacterial genus.
Collapse
Affiliation(s)
- C E Dandie
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada E3B 4Z7
| | | | | | | | | |
Collapse
|
24
|
Roussel-Delif L, Tarnawski S, Hamelin J, Philippot L, Aragno M, Fromin N. Frequency and diversity of nitrate reductase genes among nitrate-dissimilating Pseudomonas in the rhizosphere of perennial grasses grown in field conditions. MICROBIAL ECOLOGY 2005; 49:63-72. [PMID: 15650915 DOI: 10.1007/s00248-003-0228-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2003] [Accepted: 02/19/2004] [Indexed: 05/24/2023]
Abstract
A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO2 content (pCO2) at the Swiss FACE (Free Air CO2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil-associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO2. Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO2 treatment.
Collapse
Affiliation(s)
- L Roussel-Delif
- Laboratoire de Microbiologie, Université de Neuchâtel, rue Emile Argand 11, 2007, Neuchâtel, Switzerland
| | | | | | | | | | | |
Collapse
|
25
|
Mazurier S, Lemunier MÃ, Siblot SÃ, Mougel C, Lemanceau P. Distribution and diversity of type III secretion system-like genes in saprophytic and phytopathogenic fluorescent pseudomonads. FEMS Microbiol Ecol 2004; 49:455-67. [DOI: 10.1016/j.femsec.2004.04.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|