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Li D, Meng M, Ren B, Ma X, Bai L, Li J, Bai G, Yao F, Tan C. Different responses of soil fungal and bacterial communities to nitrogen addition in a forest grassland ecotone. Front Microbiol 2023; 14:1211768. [PMID: 37736095 PMCID: PMC10510407 DOI: 10.3389/fmicb.2023.1211768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/14/2023] [Indexed: 09/23/2023] Open
Abstract
Introduction Continuous nitrogen deposition increases the nitrogen content of terrestrial ecosystem and affects the geochemical cycle of soil nitrogen. Forest-grassland ecotone is the interface area of forest and grassland and is sensitive to global climate change. However, the structure composition and diversity of soil microbial communities and their relationship with soil environmental factors at increasing nitrogen deposition have not been sufficiently studied in forest-grassland ecotone. Methods In this study, experiments were carried out with four nitrogen addition treatments (0 kgN·hm-2·a-1, 10 kgN·hm-2·a-1, 20 kgN·hm-2·a-1 and 40 kgN·hm-2·a-1) to simulate nitrogen deposition in a forest-grassland ecotone in northwest Liaoning Province, China. High-throughput sequencing and qPCR technologies were used to analyze the composition, structure, and diversity characteristics of the soil microbial communities under different levels of nitrogen addition. Results and discussion The results showed that soil pH decreased significantly at increasing nitrogen concentrations, and the total nitrogen and ammonium nitrogen contents first increased and then decreased, which were significantly higher in the N10 treatment than in other treatments (N:0.32 ~ 0.48 g/kg; NH4+-N: 11.54 ~ 13 mg/kg). With the increase in nitrogen concentration, the net nitrogen mineralization, nitrification, and ammoniation rates decreased. The addition of nitrogen had no significant effect on the diversity and structure of the fungal community, while the diversity of the bacterial community decreased significantly at increasing nitrogen concentrations. Ascomycetes and Actinomycetes were the dominant fungal and bacterial phyla, respectively. The relative abundance of Ascomycetes was negatively correlated with total nitrogen content, while that of Actinomycetes was positively correlated with soil pH. The fungal community diversity was significantly negatively correlated with nitrate nitrogen, while the diversity of the bacterial community was significantly positively correlated with soil pH. No significant differences in the abundance of functional genes related to soil nitrogen transformations under the different treatments were observed. Overall, the distribution pattern and driving factors were different in soil microbial communities in a forest-grassland ecotone in northwest Liaoning. Our study enriches research content related to factors that affect the forest-grassland ecotone.
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Affiliation(s)
- Daiyan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Meng Meng
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Baihui Ren
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xinwei Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Long Bai
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jiahuan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Guohua Bai
- Zhangwu County Forest and Grass Development Service Center, Fuxin, Liaoning, China
| | - Fengjun Yao
- Zhangwu County Forest and Grass Development Service Center, Fuxin, Liaoning, China
| | - Chunming Tan
- Zhangwu County Forest and Grass Development Service Center, Fuxin, Liaoning, China
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Li W, Siddique MS, Liu M, Graham N, Yu W. The migration and microbiological degradation of dissolved organic matter in riparian soils. WATER RESEARCH 2022; 224:119080. [PMID: 36113239 DOI: 10.1016/j.watres.2022.119080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Riparian zones are important natural means of water purification, by decreasing the aqueous concentration of terrestrial organic matter (OM) through adsorption and microbial degradation of the organic matter within the aquatic ecosystem. Limited studies have been reported so far concerning the migration of dissolved organic matter (DOM) in the horizontal and vertical planes of riparian zones. In this study, the migration of DOM in riparian zones, from forest soil to wetland soil, and with soil depth, were explored, based on a case study reservoir. Results showed that riparian wetlands can absorb the OM from the forest soils and adjacent reservoir, and act as a major OM sink through microbial action. Methylomirabilota and GAL15 bacteria increased with soil depth for the two soil systems, and the wetland soil system also contained microbial sulfates, nitrates and carbonates. These microorganisms successfully utilize the Fe3+, SO4-, and CO3- as electron acceptors in the wetland system, resulting in enhanced OM removal. Although the variation of soil DOM in the vertical direction was the same for both forest and wetland soils, the Chemical structure of the DOM was found to be significantly different. Furthermore, the soil was found to be the main source of DOM in the forest ecosystem, with lignin as the main ingredient. The lignin structure was gradually oxidized and decomposed, with an increase in carboxyl groups, as the lignin diffused down into the soil and the adjacent reservoir. PLS-PM analysis showed that the soil physicochemical properties were the main factors affecting DOM transformation. However, microbial metabolism was still the goes deeper affecting factor. This study will contribute to the analysis that migration and transform of soil organic matter in riparian zone.
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Affiliation(s)
- Weihua Li
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Muhammad Saboor Siddique
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mengjie Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Nigel Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
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Zhang RT, Liu YN, Zhong HX, Chen XW, Sui X. Effects of simulated nitrogen deposition on the soil microbial community diversity of a Deyeuxia angustifolia wetland in the Sanjiang Plain, Northeastern China. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01666-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
The soil microbial community is an important bioactive component of terrestrial ecosystems. Its structural and functional diversity directly affects carbon and nitrogen processes. This study aimed to investigate the variations in the diversity and composition of soil bacterial communities in a wetland with different nitrogen deposition conditions.
Methods
A long-term simulated nitrogen deposition experiment was conducted in the Ecological Locating Research Station of the Institute of Nature and Ecology of Heilongjiang Academy of Sciences. Three different treatments were evaluated, including low nitrogen (LK; 40 kg N·hm-2·a-1), high nitrogen (HN; 80 kg N·hm-2·a-1), and control (CK; 0 kg N·hm-2·a-1). Bacterial 16S rDNA was then sequenced and analyzed using the next-generation sequencing technology.
Result
Higher levels of N deposition resulted in an α-diversity increase followed by a decrease, with significant reductions in the HN treatment. Simulated nitrogen deposition resulted in changes in the structure and abundance of bacterial communities in wetland soils. The dominant phyla in all three plots were Proteobacteria and Acidobacteria. Compared with CK, the relative abundance of Chloroflexi increased significantly under the HN treatment (P < 0.05), whereas the relative abundance of Firmicutes and Bacteroidetes decreased significantly (P < 0.05). Nitrogen input changed the composition and relative abundance of the bacterial community, which was possibly due to N-induced soil acidification.
Conclusion
This study thus provides a theoretical basis for predicting the effects of atmospheric nitrogen deposition on soil microorganisms, as well as changes in the wetland ecosystem in Sanjiang Plain.
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Ma X, Song Y, Song C, Wang X, Wang N, Gao S, Cheng X, Liu Z, Gao J, Du Y. Effect of Nitrogen Addition on Soil Microbial Functional Gene Abundance and Community Diversity in Permafrost Peatland. Microorganisms 2021; 9:2498. [PMID: 34946100 PMCID: PMC8707234 DOI: 10.3390/microorganisms9122498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/25/2021] [Accepted: 12/01/2021] [Indexed: 12/03/2022] Open
Abstract
Nitrogen is the limiting nutrient for plant growth in peatland ecosystems. Nitrogen addition significantly affects the plant biomass, diversity and community structure in peatlands. However, the response of belowground microbe to nitrogen addition in peatland ecosystems remains largely unknown. In this study, we performed long-term nitrogen addition experiments in a permafrost peatland in the northwest slope of the Great Xing'an Mountains. The four nitrogen addition treatments applied in this study were 0 g N·m-2·year-1 (CK), 6 g N·m-2·year-1 (N1), 12 g N·m-2·year-1 (N2), and 24 g N·m-2·year-1 (N3). Effects of nitrogen addition over a period of nine growing seasons on the soil microbial abundance and community diversity in permafrost peatland were analyzed. The results showed that the abundances of soil bacteria, fungi, archaea, nitrogen-cycling genes (nifH and b-amoA), and mcrA increased in N1, N2, and N3 treatments compared to CK. This indicated that nitrogen addition promoted microbial decomposition of soil organic matter, nitrogen fixation, ammonia oxidation, nitrification, and methane production. Moreover, nitrogen addition altered the microbial community composition. At the phylum level, the relative abundance of Proteobacteria increased significantly in the N2 treatment. However, the relative abundances of Actinobacteria and Verrucifera in the N2 treatment and Patescibacteria in the N1 treatment decreased significantly. The heatmap showed that the dominant order composition of soil bacteria in N1, N2, and N3 treatments and the CK treatment were different, and the dominant order composition of soil fungi in CK and N3 treatments were different. The N1 treatment showed a significant increase in the Ace and Chao indices of bacteria and Simpson index of fungi. The outcomes of this study suggest that nitrogen addition altered the soil microbial abundance, community structure, and diversity, affecting the soil microbial carbon and nitrogen cycling in permafrost peatland. The results are helpful to understand the microbial mediation on ecological processes in response to N addition.
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Affiliation(s)
- Xiuyan Ma
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
| | - Yanyu Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
| | - Xianwei Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
| | - Nannan Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
| | - Siqi Gao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
- University of Chinese Academy Sciences, Beijing 100049, China
| | - Xiaofeng Cheng
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin 150025, China
| | - Zhendi Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
- University of Chinese Academy Sciences, Beijing 100049, China
| | - Jinli Gao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
| | - Yu Du
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.M.); (C.S.); (X.W.); (N.W.); (S.G.); (X.C.); (Z.L.); (J.G.); (Y.D.)
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Manirakiza B, Sirotkin AC. Bioaugmentation of nitrifying bacteria in up-flow biological aerated filter's microbial community for wastewater treatment and analysis of its microbial community. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Lai C, Sun Y, Guo Y, Cai Q, Yang P. A novel integrated bio-reactor of moving bed and constructed wetland (MBCW) for domestic wastewater treatment and its microbial community diversity. ENVIRONMENTAL TECHNOLOGY 2021; 42:2653-2668. [PMID: 31902307 DOI: 10.1080/09593330.2019.1709904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
An MBBR and CW combo bio-reactor (MBCW) was designed as a novel hybrid process for simultaneous organic, nitrogen and phosphate removal through the long-term operation. The effect of the internal recycling rate (IRR), hydraulic retention time (HRT) and chemical oxygen demand/total nitrogen (C/N) ratio were all discussed, and the recommended values were 5:1, 12 h and >6, respectively. A higher C/N ratio was a key factor for achieving a higher TN removal. The mixed biocarrier system was realized by inoculating porous polymer carriers (PPC) and cylindrical polyethylene carriers (CPC) and achieving a higher organic biodegradation and nitrification rate compared to a single carrier system. Microorganism activities and plants' uptake or utilization both contributed to the nutrient removal in a constructed wetland. High-throughput sequencing results revealed an abundant microbial diversity and a distinct microbial distribution in the whole system where Flavobacterium (14.2%), Acinetobacter (12.87%) and Rhodobacter (10.83%) dominated on PPC, Terrimonas (8.88%), Reyranella (6.61%) and Rubinisphaera (5.63%) dominated on CPC, Comamonas (4.18%), Gemmobacter (4.02%) and Hydrogenophaga (3.97%) dominated on CWs, as well as Citrobacter (53.13%) on suspended floc.
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Affiliation(s)
- Changmiao Lai
- College of Architecture and Environment, Sichuan University, Chengdu, People's Republic of China
| | - Yu Sun
- College of Architecture and Environment, Sichuan University, Chengdu, People's Republic of China
| | - Yong Guo
- School of Chemical Engineering, Sichuan University, Chengdu, People's Republic of China
| | - Qin Cai
- College of Architecture and Environment, Sichuan University, Chengdu, People's Republic of China
| | - Ping Yang
- College of Architecture and Environment, Sichuan University, Chengdu, People's Republic of China
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7
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Jia X, Gao Y, Li X, Zhao Y, Wang L, Zhang C. Effects of cadmium on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings under elevated atmospheric CO 2 scenarios. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145023. [PMID: 33581544 DOI: 10.1016/j.scitotenv.2021.145023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/02/2021] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
The individual impacts of elevated CO2 and heavy metals on soil nitrification have been widely reported. However, studies on the combined effects of elevated CO2 and heavy metals on soil nitrification are still limited. Here, a 135-day growth chamber experiment was conducted to investigate the impacts of elevated CO2 and cadmium (Cd) levels on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings. Elevated CO2 combined with Cd pollution generally stimulated ammonia monooxygenase (AMO), hydroxylamine oxidase (HAO), and nitrite oxidoreductase (NXR) activities. Compared to the control, the abundance of ammonia-oxidizing bacteria (AOB) at day 135 and ammonia-oxidizing archaea (AOA) increased significantly (p < 0.05) and the abundance of AOB at days 45 and 90 and that of the nitrite-oxidizing bacteria (NOB) decreased under elevated CO2 + Cd. Elevated CO2 mostly led to a significant (p < 0.05) decrease in soil nitrification intensity in the rhizosphere of R. pseudoacacia exposed to Cd. The effects of Cd, CO2, and their interaction on HAO and NXR activities were significant (p < 0.01). Soil pH, the C/N ratio, water-soluble organic carbon, water-soluble organic nitrogen (WSON), and total carbon were the dominant factors (p < 0.05) affecting nitrifying enzyme activities and nitrification intensity in rhizosphere soils. Elevated CO2 clearly affected AOA, AOB, and NOB community structures and dominant genera by shaping C/N ratio, pH, and Cd and WSON contents in rhizosphere soils under Cd exposure. Overall, the responses of pH, C/N ratio, WSON, and Cd to elevated CO2 led to changes in rhizosphere soil nitrification under the combination of elevated CO2 and Cd pollution.
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Affiliation(s)
- Xia Jia
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China.
| | - Yunfeng Gao
- Shaanxi Key Laboratory of Land Consolidation, School of Land Engineering, Chang'an University, Xi'an 710054, PR China
| | - Xiaodi Li
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
| | - Yonghua Zhao
- Shaanxi Key Laboratory of Land Consolidation, School of Land Engineering, Chang'an University, Xi'an 710054, PR China
| | - Lu Wang
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
| | - Chunyan Zhang
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
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Liang F, Wen Y, Dong X, Wang Y, Pan G, Jiang F, Luo H, Jin W, Wang J, Song H. Response of activity and community composition of nitrite-oxidizing bacteria to partial substitution of chemical fertilizer by organic fertilizer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:29332-29343. [PMID: 33559074 DOI: 10.1007/s11356-020-12038-7] [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: 09/20/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Nitrite oxidation as the second step of nitrification can become the determining step in disturbed soil systems. As a beneficial fertilization practice to maintain high crop yield and soil fertility, partial substitution of chemical fertilizer (CF) by organic fertilizer (OF) may exert a notable disturbance to soil systems. However, how nitrite oxidation responds to different proportions of CF to OF is still unclear. We sampled soils from a 4-year field experiment subject to a gradient of increasing proportions of OF to CF application. Activity, size, and structure of Nitrospira-like and Nitrobacter-like nitrite-oxidizing bacteria (NOB) community were measured. The results revealed that with increasing proportion of OF to CF application, potential nitrite oxidation activity (PNO) showed a marked decreasing trend. PNO was significantly correlated with the abundance of Nitrobacter-like but not Nitrospira-like NOB. The abundance of Nitrobacter-like was significantly influenced by soil organic matter, organic nitrogen (N), and available N. In addition, PNO was also affected by the structure of Nitrobacter-like NOB. The relative abundance of Nitrobacter hamburgensis, alkalicus, winogradskyi, and vulgaris responded differently to the proportions of OF to CF application. Organic N, organic matter, and available N were the main factor shaping their community structure. Overall, Nitrobacter-like NOB is more sensitive and plays a more important role than Nitrospira-like NOB in responding to different proportions of OF to CF application.
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Affiliation(s)
- Fei Liang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yongkang Wen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Xiao Dong
- School of Engineering, Anhui Agricultural University, Hefei, 230036, China
| | - Yiyao Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Guangyuan Pan
- Anhui General Station for Agricultural Technology Extension, Hefei, 230001, China
| | - Fangying Jiang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Huaying Luo
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjun Jin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - He Song
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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Abstract
In recent years, natural thermal mineral waters have been gaining the special attention of the scientific community, namely in the prevention and treatment of some diseases, due to the microbial properties that exist in these habitats. The aim of this work was to characterize the physicochemical composition and the microbial taxonomic communities present in three thermal waters of the Galician region in Spain and two samples of the northern region in Portugal. These collected water samples were analyzed for physicochemical characterization and the respective hydrogenome of the waters using next generation sequencing together with 16S rRNA gene sequencing. The sequencing showed a high diversity of microorganisms in all analyzed waters; however, there is a clear bacterial predominance of Proteobacteria phylum, followed by Firmicutes, Deinococcus-Thermus, Aquificae and Nitrospira. The main physicochemical parameters responsible for the clustering within the Spanish waters were sulfur compounds (SO32− and S2−), CO32− and neutral pH, and in the Portuguese waters were Mg, Ca and Sr, nitrogen compounds (NO3− and NH4+), Na, Rb, conductivity and dry residue. This work will allow for a better understanding of the microbial community’s composition and how these microorganisms interfere in the physicochemical constitution of these waters often associated with medicinal properties. Furthermore, the hydrogenome may be used as an auxiliary tool in the practice of medical hydrology, increasing the likelihood of safe use of these unique water types.
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Bayer B, Saito MA, McIlvin MR, Lücker S, Moran DM, Lankiewicz TS, Dupont CL, Santoro AE. Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. THE ISME JOURNAL 2021; 15:1025-1039. [PMID: 33230266 PMCID: PMC8115632 DOI: 10.1038/s41396-020-00828-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
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Affiliation(s)
- Barbara Bayer
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
| | - Mak A. Saito
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Matthew R. McIlvin
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands
| | - Dawn M. Moran
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Thomas S. Lankiewicz
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
| | | | - Alyson E. Santoro
- grid.133342.40000 0004 1936 9676Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA USA
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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12
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Lai C, Guo Y, Cai Q, Yang P. Enhanced nitrogen removal by simultaneous nitrification-denitrification and further denitrification (SND-DN) in a moving bed and constructed wetland (MBCW) integrated bioreactor. CHEMOSPHERE 2020; 261:127744. [PMID: 32739690 DOI: 10.1016/j.chemosphere.2020.127744] [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: 04/03/2020] [Revised: 07/04/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
With the main objective of improving the removal of nitrogen from domestic wastewater and more sustainably, a moving bed and constructed wetland (MBCW) integrated bioreactor was fabricated and evaluated with continuous and intermittent aeration operations. The hybrid system achieves average removal efficiencies up to 90.4 ± 0.8% of chemical oxygen demand (COD), 91.8 ± 1.2% of ammonia nitrogen (NH4+-N), and 77.0 ± 2.6% of total nitrogen (TN), respectively, through a simultaneous nitrification-denitrification and further denitrification (SND-DN) process. This occurs through an intermittent aeration operation followed by continuous aeration with a dissolved oxygen (DO) of 4.0 mg L-1 due to the complementary and coordinated action of mixed biocarriers. It has resulted in the improvement of the efficiency of SND from 5.9 to 35.3% and in the removal via wetland for DN, between 2.42 and 2.45 g m-2·d-1, respectively. The analysis of extracellular polymeric substances (EPS) and high-throughput sequencing demonstrated the enhanced SND mechanism and the evolution of microbial species within the biofilm structure. The total relative abundance of nitrifying bacteria, more aggregated outside the biofilm, decreased by 7.66% compared to denitrifying bacteria, mostly accumulated inside, which increased by 5.49%, respectively.
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Affiliation(s)
- Changmiao Lai
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China.
| | - Yong Guo
- School of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Qin Cai
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China.
| | - Ping Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China.
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13
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Beattie RE, Bandla A, Swarup S, Hristova KR. Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff. Front Microbiol 2020; 11:539921. [PMID: 33178143 PMCID: PMC7593329 DOI: 10.3389/fmicb.2020.539921] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023] Open
Abstract
Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances (p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira, and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher (p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii, two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.
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Affiliation(s)
- Rachelle E. Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Aditya Bandla
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Biological Science, National University of Singapore, Singapore, Singapore
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14
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Regulating soil bacterial diversity, community structure and enzyme activity using residues from golden apple snails. Sci Rep 2020; 10:16302. [PMID: 33004949 PMCID: PMC7530706 DOI: 10.1038/s41598-020-73184-z] [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: 11/07/2019] [Accepted: 09/10/2020] [Indexed: 11/08/2022] Open
Abstract
It has been shown that the golden apple snail (GAS, Pomacea canaliculata), which is a serious agricultural pest in Southeast Asia, can provide a soil amendment for the reversal of soil acidification and degradation. However, the impact of GAS residue (i.e., crushed, whole GAS) on soil bacterial diversity and community structure remains largely unknown. Here, a greenhouse pot experiment was conducted and 16S rRNA gene sequencing was used to measure bacterial abundance and community structure in soils amended with GAS residue and lime. The results suggest that adding GAS residue resulted in a significant variation in soil pH and nutrients (all P < 0.05), and resulted in a slightly alkaline (pH = 7.28-7.75) and nutrient-enriched soil, with amendment of 2.5-100 g kg-1 GAS residue. Soil nutrients (i.e., NO3-N and TN) and TOC contents were increased (by 132-912%), and some soil exocellular enzyme activities were enhanced (by 2-98%) in GAS residue amended soil, with amendment of 1.0-100 g kg-1 GAS residue. Bacterial OTU richness was 19% greater at the 2.5 g kg-1 GAS residue treatment than the control, while it was 40% and 53% lower at 100 g kg-1 of GAS residue and 50 g kg-1 of lime amended soils, respectively. Firmicutes (15-35%) was the most abundant phylum while Bacterioidetes (1-6%) was the lowest abundant one in GAS residue amended soils. RDA results suggest that the contents of soil nutrients (i.e., NO3-N and TN) and soil TOC explained much more of the variations of bacterial community than pH in GAS residue amended soil. Overuse of GAS residue would induce an anaerobic soil environment and reduce bacterial OTU richness. Soil nutrients and TOC rather than pH might be the main factors that are responsible for the changes of bacterial OTU richness and bacterial community structure in GAS residue amended soil.
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15
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Jiang R, Wang JG, Zhu T, Zou B, Wang DQ, Rhee SK, An D, Ji ZY, Quan ZX. Use of Newly Designed Primers for Quantification of Complete Ammonia-Oxidizing (Comammox) Bacterial Clades and Strict Nitrite Oxidizers in the Genus Nitrospira. Appl Environ Microbiol 2020; 86:e01775-20. [PMID: 32826214 PMCID: PMC7531962 DOI: 10.1128/aem.01775-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/08/2020] [Indexed: 02/01/2023] Open
Abstract
Complete ammonia-oxidizing (comammox) bacteria play key roles in environmental nitrogen cycling and all belong to the genus Nitrospira, which was originally believed to include only strict nitrite-oxidizing bacteria (sNOB). Thus, differential estimation of sNOB abundance from that of comammox Nitrospira has become problematic, since both contain nitrite oxidoreductase genes that serve as common targets for sNOB detection. Herein, we developed novel comammox Nitrospira clade A- and B-specific primer sets targeting the α-subunit of the ammonia monooxygenase gene (amoA) and a sNOB-specific primer set targeting the cyanase gene (cynS) for quantitative PCR (qPCR). The high coverage and specificity of these primers were checked by use of metagenome and metatranscriptome data sets. Efficient and specific amplification with these primers was demonstrated using various environmental samples. Using the newly designed primers, we successfully estimated the abundances of comammox Nitrospira and sNOB in samples from two chloramination-treated drinking water systems and found that, in most samples, comammox Nitrospira clade A was the dominant type of Nitrospira and also served as the primary ammonia oxidizer. Compared with other ammonia oxidizers, comammox Nitrospira had a higher abundance in process water samples in these two drinking water systems. We also demonstrated that sNOB can be readily misrepresented by an earlier method, calculated by subtracting the comammox Nitrospira abundance from the total Nitrospira abundance, especially when the comammox Nitrospira proportion is relatively high. The new primer sets were successfully applied to comammox Nitrospira and sNOB quantification, which may prove useful in understanding the roles of Nitrospira in nitrification in various ecosystems.IMPORTANCENitrospira is a dominant nitrite-oxidizing bacterium in many artificial and natural environments. The discovery of complete ammonia oxidizers in the genus Nitrospira prevents the use of previously identified primers targeting the Nitrospira 16S rRNA gene or nitrite oxidoreductase (nxr) gene for differential determination of strict nitrite-oxidizing bacteria (sNOB) in the genus Nitrospira and among comammox bacteria in this genus. We designed three novel primer sets that enabled quantification of comammox Nitrospira clades A and B and sNOB with high coverage, specificity, and accuracy in various environments. With the designed primer sets, sNOB and comammox Nitrospira were differentially estimated in drinking water systems, and we found that comammox clade A predominated over sNOB and other ammonia oxidizers in process water samples. Accurate quantification of comammox Nitrospira and sNOB by use of the newly designed primers will provide essential information for evaluating the contribution of Nitrospira to nitrification in various ecosystems.
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Affiliation(s)
- Ran Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Jian-Gong Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Dan-Qi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Dong An
- Department of Environmental Science and Engineering, Fudan University, Shanghai, China
| | - Zhi-Yuan Ji
- Hangzhou Water Holding Group Co., Ltd., Hangzhou, China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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16
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Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinfeder M, Schwarz J, Zechmeister T, Karst SM, Albertsen M, Nielsen PH, Wagner M, Daims H. Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira. ISME JOURNAL 2020; 14:2967-2979. [PMID: 32709974 PMCID: PMC7784846 DOI: 10.1038/s41396-020-0724-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/01/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.
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Affiliation(s)
- Anne Daebeler
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
| | - Katharina Kitzinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.,Max Planck Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Hanna Koch
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.,Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela Steinfeder
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Jasmin Schwarz
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria. .,University of Vienna, The Comammox Research Platform, Vienna, Austria.
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17
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Laffite A, Florio A, Andrianarisoa KS, Creuze des Chatelliers C, Schloter‐Hai B, Ndaw SM, Periot C, Schloter M, Zeller B, Poly F, Le Roux X. Biological inhibition of soil nitrification by forest tree species affectsNitrobacterpopulations. Environ Microbiol 2020; 22:1141-1153. [DOI: 10.1111/1462-2920.14905] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/25/2019] [Accepted: 12/18/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Amandine Laffite
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Alessandro Florio
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | | | - Charline Creuze des Chatelliers
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Brigitte Schloter‐Hai
- Research Unit for Comparative Microbiome AnalysisHelmholtz Zentrum München D‐85764 Ingolstädter Landstraße 1 Neuherberg Germany
| | - Sidy M. Ndaw
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Charlotte Periot
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Michael Schloter
- Research Unit for Comparative Microbiome AnalysisHelmholtz Zentrum München D‐85764 Ingolstädter Landstraße 1 Neuherberg Germany
| | - Bernd Zeller
- Biogéochimie des Ecosystèmes ForestiersINRA Grand‐EST Nancy UR 1138 Route d'Amance, 54280 Champenoux France
| | - Franck Poly
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
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18
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Variations in the Compositions of Soil Bacterial and Fungal Communities Due to Microhabitat Effects Induced by Simulated Nitrogen Deposition of a Bamboo Forest in Wetland. FORESTS 2019. [DOI: 10.3390/f10121098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although numerous studies have been published on nitrogen (N) deposition, little is known about its impact on microbial communities in wetland forests. Here, we used simulated nitrogen deposition (SND) to analyze the importance of differences in soil microhabitats in promoting the diversity of soil bacteria and fungi. We compared various levels of SND (control (CK), low N (N30), medium N (N60), and high N (N90)) and found that these were associated with changes in soil microhabitats. Additionally, SND affected soil pH, clay and sand content of the soil, and specific surface area (SSA). Bacteria and fungi responded differently to increased SND levels. The alpha diversity of bacteria decreased with an increased SND level, while fungal abundance, diversity, and community evenness reached their maximum values at the N60 threshold. Principal coordinates analysis (PCoA), nonparametric multivariate analysis of variance (PERMANOVA), and linear discriminant analysis (LDA) coupled with effect size measurements (LefSe) also confirmed that the bacterial composition was different at N90 compared to other levels of SND while that of fungi was different at N60. A higher discriminant level (LDA score ≥4) may be a valuable index of selecting indicator microbial clades sensitive to SND for wetland management. Further, an increased pH was associated with a greater abundance of bacteria and fungi. In addition, the volume contents of clay and SSA were negatively correlated with bacteria but fungi are associated with soil specific gravity (SSG). Overall, in a neutral soil pH environment, pH fluctuation is the main influencing factor in terms of bacterial and fungal abundance and diversity. The diversity of fungi is more dependent on the type and relative content of solid phase components in soil than that of bacteria, implying the presence of species-specific niches for bacteria and fungi. These results demonstrate that changes in SND can induce short-term microbial and microhabitat changes.
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19
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Bacteria with Different Assemblages in the Soil Profile Drive the Diverse Nutrient Cycles in the Sugarcane Straw Retention Ecosystem. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11100194] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.
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20
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Norton J, Ouyang Y. Controls and Adaptive Management of Nitrification in Agricultural Soils. Front Microbiol 2019; 10:1931. [PMID: 31543867 PMCID: PMC6728921 DOI: 10.3389/fmicb.2019.01931] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.
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Affiliation(s)
- Jeanette Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
| | - Yang Ouyang
- Department of Microbiology and Plant Biology, Institute of Environmental Genomics, University of Oklahoma, Norman, OK, United States
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21
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Du Y, Wang T, Wang C, Anane PS, Liu S, Paz-Ferreiro J. Nitrogen fertilizer is a key factor affecting the soil chemical and microbial communities in a Mollisol. Can J Microbiol 2019; 65:510-521. [PMID: 30901528 DOI: 10.1139/cjm-2018-0683] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.
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Affiliation(s)
- Yan Du
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Tianye Wang
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Chengyu Wang
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Paul-Simon Anane
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Shuxia Liu
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, Jilin Province 130118, P.R. China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, Jilin Province 130118, P.R. China
| | - Jorge Paz-Ferreiro
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne 3001, VIC, Australia
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22
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Kong Y, Ling N, Xue C, Chen H, Ruan Y, Guo J, Zhu C, Wang M, Shen Q, Guo S. Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing. Environ Microbiol 2019; 21:1224-1240. [PMID: 30724443 DOI: 10.1111/1462-2920.14553] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/19/2018] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Abstract
Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.
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Affiliation(s)
- Yali Kong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huan Chen
- Crop Research Institute, Anhui Academy of Agricultural Science, Hefei, 230031, China
| | - Yang Ruan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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23
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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: 47] [Impact Index Per Article: 9.4] [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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24
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Sakoula D, Nowka B, Spieck E, Daims H, Lücker S. The draft genome sequence of " Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge. Stand Genomic Sci 2018; 13:32. [PMID: 30498561 PMCID: PMC6251164 DOI: 10.1186/s40793-018-0338-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/10/2018] [Indexed: 11/10/2022] Open
Abstract
The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of "Nitrospira lenta" strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of "N. lenta" has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the "N. lenta" core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and "N. defluvii", despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of "N. lenta" provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.
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Affiliation(s)
- Dimitra Sakoula
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Boris Nowka
- Department of Microbiology & Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Eva Spieck
- Department of Microbiology & Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
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25
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Han S, Li X, Luo X, Wen S, Chen W, Huang Q. Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil. Front Microbiol 2018; 9:885. [PMID: 29867799 PMCID: PMC5951965 DOI: 10.3389/fmicb.2018.00885] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/17/2018] [Indexed: 11/25/2022] Open
Abstract
Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.
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Affiliation(s)
- Shun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Shilin Wen
- Hengyang Red Soil Experimental Station, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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26
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Zhang X, Zhou Y, Ma Y, Zhang N, Zhao S, Zhang R, Zhang J, Zhang H. Effect of inorganic carbon concentration on the stability and nitrite-oxidizing bacteria community structure of the CANON process in a membrane bioreactor. ENVIRONMENTAL TECHNOLOGY 2018; 39:457-463. [PMID: 28327080 DOI: 10.1080/09593330.2017.1302996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 02/05/2017] [Indexed: 06/06/2023]
Abstract
In the completely autotrophic nitrogen removal over nitrite (CANON) process, the nitrite-oxidizing bacteria (NOB) should be effectively suppressed or thoroughly washed out. In this study, the nitrate production and the structure of NOB community under different inorganic carbon (IC) concentrations were investigated using denaturing gradient gel electrophoresis (DGGE) in a membrane bioreactor (MBR). Results showed that IC decrease correspondingly lowered the nitrogen removal, and simultaneously induced the nitrate production by NOB. DGGE results indicated the IC deficit led to the biodiversity increasing of both Nitrobacter-like NOB and Nitrospira-like NOB. An equation fitted between the ratio of nitrate production to ammonia consumption ([Formula: see text]) and the ratio of influent IC to ammonia concentration ([Formula: see text]) indicated the influent [Formula: see text] should be controlled between 1.6 and 2.3 to ensure the stable operation of the CANON process. A small amount addition of organic material could be used as an effective strategy to suppress NOB when the [Formula: see text] ratio was not appropriate.
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Affiliation(s)
- Xiaojing Zhang
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
| | - Yue Zhou
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
| | - Yongpeng Ma
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
| | - Nan Zhang
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
| | - Siyu Zhao
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
| | - Rongrong Zhang
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
| | - Jun Zhang
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
| | - Hongzhong Zhang
- a Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, School of Material and Chemical Engineering , Zhengzhou University of Light Industry , Zhengzhou , People's Republic of China
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27
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Giguere AT, Taylor AE, Myrold DD, Mellbye BL, Sayavedra-Soto LA, Bottomley PJ. Nitrite-oxidizing activity responds to nitrite accumulation in soil. FEMS Microbiol Ecol 2018; 94:4817529. [DOI: 10.1093/femsec/fiy008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/18/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Andrew T Giguere
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-4501, USA
| | - Anne E Taylor
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-4501, USA
| | - David D Myrold
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-4501, USA
| | - Brett L Mellbye
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-4501, USA
| | - Luis A Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-4501, USA
| | - Peter J Bottomley
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-4501, USA
- Department of Microbiology, Oregon State University, Corvallis, OR 97331-4501, USA
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28
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Ushiki N, Fujitani H, Shimada Y, Morohoshi T, Sekiguchi Y, Tsuneda S. Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity. Front Microbiol 2018; 8:2637. [PMID: 29375506 PMCID: PMC5767232 DOI: 10.3389/fmicb.2017.02637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/18/2017] [Indexed: 02/02/2023] Open
Abstract
The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira, we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10–C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira.
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Affiliation(s)
- Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yu Shimada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, Tochigi, Japan
| | - Yuji Sekiguchi
- Bio-Measurement Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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29
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Yao Q, Peng DC. Nitrite oxidizing bacteria (NOB) dominating in nitrifying community in full-scale biological nutrient removal wastewater treatment plants. AMB Express 2017; 7:25. [PMID: 28116698 PMCID: PMC5256632 DOI: 10.1186/s13568-017-0328-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/10/2022] Open
Abstract
Nitrification activities and microbial populations of ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were investigated in 10 full-scale biological nutrient removal wastewater treatment plants in Xi’an, China. Aerobic batch tests were used to determine the nitrifying activities while fluorescence in situ hybridization was used to quantify the fractions of AOB and NOB in the activated sludge. The results showed that nitrifying bacteria accounted for 1–10% of the total population. Nitrosomonas and Nitrospira were the dominant bacteria for AOB and NOB respectively. Moreover, the average percentage of AOB was 1.27% and that of NOB was 4.02%. The numerical ratios of NOB/AOB varied between 1.72 and 5.87. The average ammonium uptake rate and nitrite uptake rate were 3.25 ± 0.52 mg (NH4+–N)/g(VSS) h and 4.49 ± 0.49 mg (NO2−–N)/g(VSS) h, respectively. Correspondingly, the activity of NOB was 1.08–2.00 times higher than that of AOB. Thus, NOB was the dominating bacteria in nitrifying communities. The year-round data of Dianzicun (W6) also expressed a similar trend. Since NOB had higher activities than that of AOB, a large nitrite oxidation pool could be formed, which guaranteed that no nitrite would be accumulated. Therefore, stable nitrification could be achieved. A conceptual model was proposed to describe the population variation of AOB and NOB in a nitrifying community.
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30
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Adaptation of soil nitrifiers to very low nitrogen level jeopardizes the efficiency of chemical fertilization in west african moist savannas. Sci Rep 2017; 7:10275. [PMID: 28860500 PMCID: PMC5578973 DOI: 10.1038/s41598-017-10185-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/07/2017] [Indexed: 12/05/2022] Open
Abstract
The moist savanna zone covers 0.5 × 106 km2 in West Africa and is characterized by very low soil N levels limiting primary production, but the ecology of nitrifiers in these (agro)ecosystems is largely unknown. We compared the effects of six agricultural practices on nitrifier activity, abundance and diversity at nine sites in central Ivory Coast. Treatments, including repeated fertilization with ammonium and urea, had no effect on nitrification and crop N status after 3 to 5 crop cycles. Nitrification was actually higher at low than medium ammonium level. The nitrifying community was always dominated by ammonia oxidizing archaea and Nitrospira. However, the abundances of ammonia oxidizing bacteria, AOB, and Nitrobacter increased with fertilization after 5 crop cycles. Several AOB populations, some affiliated to Nitrosospira strains with urease activity or adapted to fluctuating ammonium levels, emerged in fertilized plots, which was correlated to nitrifying community ability to benefit from fertilization. In these soils, dominant nitrifiers adapted to very low ammonium levels have to be replaced by high-N nitrifiers before fertilization can stimulate nitrification. Our results show that the delay required for this replacement is much longer than ever observed for other terrestrial ecosystems, i.e. > 5 crop cycles, and demonstrate for the first time that nitrifier characteristics jeopardize the efficiency of fertilization in moist savanna soils.
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31
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Gu Y, Wang Y, Lu S, Xiang Q, Yu X, Zhao K, Zou L, Chen Q, Tu S, Zhang X. Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil. Front Microbiol 2017; 8:1516. [PMID: 28861048 PMCID: PMC5559540 DOI: 10.3389/fmicb.2017.01516] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/27/2017] [Indexed: 01/23/2023] Open
Abstract
Soil microbes provide important ecosystem services. Though the effects of changes in nutrient availability due to fertilization on the soil microbial communities in the topsoil (tilled layer, 0–20 cm) have been extensively explored, the effects on communities and their associations with soil nutrients in the subsoil (below 20 cm) which is rarely impacted by tillage are still unclear. 16S rRNA gene amplicon sequencing was used to investigate bacterial and archaeal communities in a Pup-Calric-Entisol soil treated for 32 years with chemical fertilizer (CF) and CF combined with farmyard manure (CFM), and to reveal links between soil properties and specific bacterial and archaeal taxa in both the top- and subsoil. The results showed that both CF and CFM treatments increased soil organic carbon (SOC), soil moisture (MO) and total nitrogen (TN) while decreased the nitrate_N content through the profile. Fertilizer applications also increased Olsen phosphorus (OP) content in most soil layers. Microbial communities in the topsoil were significantly different from those in subsoil. Compared to the CF treatment, taxa such as Nitrososphaera, Nitrospira, and several members of Acidobacteria in topsoil and Subdivision 3 genera incertae sedis, Leptolinea, and Bellilinea in subsoil were substantially more abundant in CFM. A co-occurrence based network analysis demonstrated that SOC and OP were the most important soil parameters that positively correlated with specific bacterial and archaeal taxa in topsoil and subsoil, respectively. Hydrogenophaga was identified as the keystone genus in the topsoil, while genera Phenylobacterium and Steroidobacter were identified as the keystone taxa in subsoil. The taxa identified above are involved in the decomposition of complex organic compounds and soil carbon, nitrogen, and phosphorus transformations. This study revealed that the spatial variability of soil properties due to long-term fertilization strongly shapes the bacterial and archaeal community composition and their interactions at both high and low taxonomic levels across the whole soil profile.
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Affiliation(s)
- Yunfu Gu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Yingyan Wang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Sheng'e Lu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Likou Zou
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Shihua Tu
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural SciencesChengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
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Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment. Appl Environ Microbiol 2017; 83:AEM.00549-17. [PMID: 28500038 DOI: 10.1128/aem.00549-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of "Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (Km ) and the generation time were determined to be 25 μM NO2- and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH4Cl but completely inhibited at 50 mM NH4Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of NitrotogaIMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification.
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Simonin M, Martins JM, Le Roux X, Uzu G, Calas A, Richaume A. Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose–response relationships. Nanotoxicology 2017; 11:247-255. [DOI: 10.1080/17435390.2017.1290845] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marie Simonin
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | | | - Xavier Le Roux
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
| | - Gaëlle Uzu
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | - Aude Calas
- University of Grenoble Alpes, CNRS, IRD, IGE, Grenoble, France
| | - Agnès Richaume
- CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Microbial Ecology Laboratory (LEM), UMR5557 CNRS, UMR1418 INRA, Villeurbanne, France
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Potential of Rhodobacter capsulatus Grown in Anaerobic-Light or Aerobic-Dark Conditions as Bioremediation Agent for Biological Wastewater Treatments. WATER 2017. [DOI: 10.3390/w9020108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Luo X, Han S, Lai S, Huang Q, Chen W. Long-term straw returning affectsNitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil. J Basic Microbiol 2016; 57:309-315. [DOI: 10.1002/jobm.201600400] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Xuesong Luo
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University; Wuhan China
| | - Shun Han
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
| | - Songsong Lai
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University; Wuhan China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology; Huazhong Agricultural University; Wuhan China
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Rughöft S, Herrmann M, Lazar CS, Cesarz S, Levick SR, Trumbore SE, Küsel K. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa. Front Microbiol 2016; 7:1638. [PMID: 27807431 PMCID: PMC5069293 DOI: 10.3389/fmicb.2016.01638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/30/2016] [Indexed: 11/13/2022] Open
Abstract
Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20-66%), Chloroflexi (9-29%), and Firmicutes (7-42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43-99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g-1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g-1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our results suggest a strong effect of the savanna soils' nutrient scarcity on all microbial communities, resulting in a distinct community structure that differs markedly from nutrient-rich, temperate grasslands, along with a high relevance of archaeal ammonia oxidation in savanna soils.
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Affiliation(s)
- Saskia Rughöft
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Martina Herrmann
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Cassandre S Lazar
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany; Institute of Biology, Leipzig UniversityLeipzig, Germany
| | - Shaun R Levick
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Susan E Trumbore
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Kirsten Küsel
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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Le Roux X, Bouskill NJ, Niboyet A, Barthes L, Dijkstra P, Field CB, Hungate BA, Lerondelle C, Pommier T, Tang J, Terada A, Tourna M, Poly F. Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach. Front Microbiol 2016; 7:628. [PMID: 27242680 PMCID: PMC4868854 DOI: 10.3389/fmicb.2016.00628] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the ‘High CO2+Nitrogen+Precipitation’ treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.
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Affiliation(s)
- Xavier Le Roux
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Nicholas J Bouskill
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Audrey Niboyet
- UMR 8079, AgroParisTech, Ecology Systematics and Evolution Laboratory, CNRS, Université Paris-Sud 11 Orsay, France
| | - Laure Barthes
- UMR 8079, AgroParisTech, Ecology Systematics and Evolution Laboratory, CNRS, Université Paris-Sud 11 Orsay, France
| | - Paul Dijkstra
- Ecosystem Science and Society Center, Department of Biological Sciences, Northern Arizona University, Flagstaff AZ, USA
| | - Chris B Field
- Department of Global Ecology, Carnegie Institution, Stanford University, Stanford CA, USA
| | - Bruce A Hungate
- Ecosystem Science and Society Center, Department of Biological Sciences, Northern Arizona University, Flagstaff AZ, USA
| | - Catherine Lerondelle
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Thomas Pommier
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Jinyun Tang
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Akihiko Terada
- Department of Environmental Engineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Maria Tourna
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
| | - Franck Poly
- UMR INRA 1418, UMR CNRS 5557, Microbial Ecology Centre, INRA, CNRS, Université Lyon 1, Université de Lyon Villeurbanne, France
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Stempfhuber B, Richter-Heitmann T, Regan KM, Kölbl A, Wüst PK, Marhan S, Sikorski J, Overmann J, Friedrich MW, Kandeler E, Schloter M. Spatial Interaction of Archaeal Ammonia-Oxidizers and Nitrite-Oxidizing Bacteria in an Unfertilized Grassland Soil. Front Microbiol 2016; 6:1567. [PMID: 26834718 PMCID: PMC4722141 DOI: 10.3389/fmicb.2015.01567] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/27/2015] [Indexed: 12/18/2022] Open
Abstract
Interrelated successive transformation steps of nitrification are performed by distinct microbial groups - the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m(2). Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation.
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Affiliation(s)
- Barbara Stempfhuber
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health Neuherberg, Germany
| | | | - Kathleen M Regan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Angelika Kölbl
- Lehrstuhl für Bodenkunde, Technische Universität München Freising, Germany
| | - Pia K Wüst
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | | | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Michael Schloter
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health Neuherberg, Germany
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Li Y, Lin Q, Wang S, Li X, Liu W, Luo C, Zhang Z, Zhu X, Jiang L, Li X. Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow. FEMS Microbiol Ecol 2015; 92:fiv152. [PMID: 26635411 DOI: 10.1093/femsec/fiv152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2015] [Indexed: 02/04/2023] Open
Abstract
Warming and grazing significantly affect the structure and function of an alpine meadow ecosystem. Yet, the responses of soil microbes to these disturbances are not well understood. Controlled asymmetrical warming (+1.2/1.7°C during daytime/nighttime) with grazing experiments were conducted to study microbial response to warming, grazing and their interactions. Significant interactive effects of warming and grazing were observed on soil bacterial α-diversity and composition. Warming only caused significant increase in bacterial α-diversity under no-grazing conditions. Grazing induced no substantial differences in bacterial α-diversity and composition irrespective of warming. Warming, regardless of grazing, caused a significant increase in soil bacterial community similarity across space, but grazing only induced significant increases under no-warming conditions. The positive effects of warming on bacterial α-diversity and grazing on community similarity were weakened by grazing and warming, respectively. Soil and plant variables explained well the variations in microbial communities, indicating that changes in soil and plant properties may primarily regulate soil microbial responses to warming in this alpine meadow. The results suggest that bacterial communities may become more similar across space in a future, warmed climate and moderate grazing may potentially offset, at least partially, the effects of global warming on the soil microbial diversity.
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Affiliation(s)
- Yaoming Li
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiaoyan Lin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Shiping Wang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, China
| | - Wentso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Caiyun Luo
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Zhenhua Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xiaoxue Zhu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Lili Jiang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Xine Li
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Fujitani H, Kumagai A, Ushiki N, Momiuchi K, Tsuneda S. Selective isolation of ammonia-oxidizing bacteria from autotrophic nitrifying granules by applying cell-sorting and sub-culturing of microcolonies. Front Microbiol 2015; 6:1159. [PMID: 26528282 PMCID: PMC4607866 DOI: 10.3389/fmicb.2015.01159] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/05/2015] [Indexed: 11/13/2022] Open
Abstract
Nitrification is a key process in the biogeochemical nitrogen cycle and biological wastewater treatment that consists of two stepwise reactions, ammonia oxidation by ammonia-oxidizing bacteria (AOB) or archaea followed by nitrite oxidation by nitrite-oxidizing bacteria. One of the representatives of the AOB group is Nitrosomonas mobilis species. Although a few pure strains of this species have been isolated so far, approaches to their preservation in pure culture have not been established. Here, we report isolation of novel members of the N. mobilis species from autotrophic nitrifying granules used for ammonia-rich wastewater treatment. We developed an isolation method focusing on microcolonies formation of nitrifying bacteria. Two kinds of distinctive light scattering signatures in a cell-sorting system enabled to separate microcolonies from single cells and heterogeneous aggregates within granule samples. Inoculation of a pure microcolony into 96-well microtiter plates led to successful sub-culturing and increased probability of isolation. Obtained strain Ms1 is cultivated in the liquid culture with relatively high ammonia or nitrite concentration, not extremely slow growing. Considering environmental clones that were closely related to N. mobilis and detected in various environments, the availability of this novel strain would facilitate to reveal this member’s ecophysiology in a variety of habitats.
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Affiliation(s)
- Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Asami Kumagai
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Kengo Momiuchi
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
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Simonin M, Le Roux X, Poly F, Lerondelle C, Hungate BA, Nunan N, Niboyet A. Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply. MICROBIAL ECOLOGY 2015; 70:809-18. [PMID: 25877793 DOI: 10.1007/s00248-015-0604-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 03/23/2015] [Indexed: 05/25/2023]
Abstract
Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira. AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements.
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Affiliation(s)
- Marie Simonin
- Institute of Ecology and Environmental Sciences - Paris, UMR 7618 Université Pierre et Marie Curie/CNRS/AgroParisTech, 78850, Thiverval Grignon, France
- Microbial Ecology Center, Université de Lyon/Université Lyon 1/CNRS/INRA, UMR CNRS 5557, USC INRA 1364, 69622, Villeurbanne, France
| | - Xavier Le Roux
- Microbial Ecology Center, Université de Lyon/Université Lyon 1/CNRS/INRA, UMR CNRS 5557, USC INRA 1364, 69622, Villeurbanne, France
| | - Franck Poly
- Microbial Ecology Center, Université de Lyon/Université Lyon 1/CNRS/INRA, UMR CNRS 5557, USC INRA 1364, 69622, Villeurbanne, France
| | - Catherine Lerondelle
- Microbial Ecology Center, Université de Lyon/Université Lyon 1/CNRS/INRA, UMR CNRS 5557, USC INRA 1364, 69622, Villeurbanne, France
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences - Paris, UMR 7618 Université Pierre et Marie Curie/CNRS/AgroParisTech, 78850, Thiverval Grignon, France
| | - Audrey Niboyet
- Institute of Ecology and Environmental Sciences - Paris, UMR 7618 Université Pierre et Marie Curie/CNRS/AgroParisTech, 78850, Thiverval Grignon, France.
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Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc Natl Acad Sci U S A 2015; 112:11371-6. [PMID: 26305944 DOI: 10.1073/pnas.1506533112] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.
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Herrmann M, Rusznyák A, Akob DM, Schulze I, Opitz S, Totsche KU, Küsel K. Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl Environ Microbiol 2015; 81:2384-94. [PMID: 25616797 PMCID: PMC4357952 DOI: 10.1128/aem.03269-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/17/2015] [Indexed: 11/20/2022] Open
Abstract
The traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed-upper and lower-limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO2 via the Calvin cycle, with abundances of cbbM and cbbL genes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 10(3) to 6 × 10(6) genes liter(-1) over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO2-assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO2 fixation in environments with strong oxygen and CO2 fluctuations. The genera Sulfuricella and Nitrosomonas were represented by read fractions of up to 78 and 33%, respectively, within the cbbM and cbbL transcript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO2 fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds.
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Affiliation(s)
- Martina Herrmann
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Anna Rusznyák
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Denise M Akob
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany U.S. Geological Survey, Reston, Virginia, USA
| | - Isabel Schulze
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Sebastian Opitz
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Uwe Totsche
- Department of Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Liang Y, Li D, Zhang X, Zeng H, Yang Z, Cui S, Zhang J. Stability and nitrite-oxidizing bacteria community structure in different high-rate CANON reactors. BIORESOURCE TECHNOLOGY 2015; 175:189-194. [PMID: 25459821 DOI: 10.1016/j.biortech.2014.10.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/10/2014] [Accepted: 10/17/2014] [Indexed: 06/04/2023]
Abstract
In completely autotrophic nitrogen removal over nitrite (CANON) process, the bioactivity of nitrite-oxidizing bacteria (NOB) should be effectively inhibited. In this study, the stability of four high-rate CANON reactors and the effect of free ammonia (FA) and organic material on NOB community structure were investigated using DGGE. Results suggested that with the increasing of FA, the ratio of total nitrogen removal to nitrate production went up gradually, while the biodiversity of Nitrobacter-like NOB and Nitrospira-like NOB both decreased. When the CANON reactor was transformed to simultaneous partial nitrification, anammox and denitrification (SNAD) reactor by introducing organic material, the denitrifiers and aerobic heterotrophic bacteria would compete nitrite or oxygen with NOB, which then led to the biodiversity decreasing of both Nitrobacter-like NOB and Nitrospira-like NOB. The distribution of Nitrobacter-like NOB and Nitrospira-like NOB were evaluated, and finally effective strategies for suppressing NOB in CANON reactors were proposed.
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Affiliation(s)
- Yuhai Liang
- Key Laboratory of Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Dong Li
- Key Laboratory of Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Xiaojing Zhang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Huiping Zeng
- Key Laboratory of Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Zhuo Yang
- Key Laboratory of Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Shaoming Cui
- Key Laboratory of Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jie Zhang
- Key Laboratory of Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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Nowka B, Off S, Daims H, Spieck E. Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages. FEMS Microbiol Ecol 2014; 91:fiu031. [DOI: 10.1093/femsec/fiu031] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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47
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Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation. Appl Environ Microbiol 2014; 81:745-53. [PMID: 25398863 DOI: 10.1128/aem.02734-14] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrification has an immense impact on nitrogen cycling in natural ecosystems and in wastewater treatment plants. Mathematical models function as tools to capture the complexity of these biological systems, but kinetic parameters especially of nitrite-oxidizing bacteria (NOB) are lacking because of a limited number of pure cultures until recently. In this study, we compared the nitrite oxidation kinetics of six pure cultures and one enrichment culture representing three genera of NOB (Nitrobacter, Nitrospira, Nitrotoga). With half-saturation constants (Km) between 9 and 27 μM nitrite, Nitrospira bacteria are adapted to live under significant substrate limitation. Nitrobacter showed a wide range of lower substrate affinities, with Km values between 49 and 544 μM nitrite. However, the advantage of Nitrobacter emerged under excess nitrite supply, sustaining high maximum specific activities (Vmax) of 64 to 164 μmol nitrite/mg protein/h, contrary to the lower activities of Nitrospira of 18 to 48 μmol nitrite/mg protein/h. The Vmax (26 μmol nitrite/mg protein/h) and Km (58 μM nitrite) of "Candidatus Nitrotoga arctica" measured at a low temperature of 17°C suggest that Nitrotoga can advantageously compete with other NOB, especially in cold habitats. The kinetic parameters determined represent improved basis values for nitrifying models and will support predictions of community structure and nitrification rates in natural and engineered ecosystems.
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48
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Functionally relevant diversity of closely related Nitrospira in activated sludge. ISME JOURNAL 2014; 9:643-55. [PMID: 25148481 DOI: 10.1038/ismej.2014.156] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/28/2014] [Accepted: 07/18/2014] [Indexed: 11/08/2022]
Abstract
Nitrospira are chemolithoautotrophic nitrite-oxidizing bacteria that catalyze the second step of nitrification in most oxic habitats and are important for excess nitrogen removal from sewage in wastewater treatment plants (WWTPs). To date, little is known about their diversity and ecological niche partitioning within complex communities. In this study, the fine-scale community structure and function of Nitrospira was analyzed in two full-scale WWTPs as model ecosystems. In Nitrospira-specific 16S rRNA clone libraries retrieved from each plant, closely related phylogenetic clusters (16S rRNA identities between clusters ranged from 95.8% to 99.6%) within Nitrospira lineages I and II were found. Newly designed probes for fluorescence in situ hybridization (FISH) allowed the specific detection of several of these clusters, whose coexistence in the WWTPs was shown for prolonged periods of several years. In situ ecophysiological analyses based on FISH, relative abundance and spatial arrangement quantification, as well as microautoradiography revealed functional differences of these Nitrospira clusters regarding the preferred nitrite concentration, the utilization of formate as substrate and the spatial coaggregation with ammonia-oxidizing bacteria as symbiotic partners. Amplicon pyrosequencing of the nxrB gene, which encodes subunit beta of nitrite oxidoreductase of Nitrospira, revealed in one of the WWTPs as many as 121 species-level nxrB operational taxonomic units with highly uneven relative abundances in the amplicon library. These results show a previously unrecognized high diversity of Nitrospira in engineered systems, which is at least partially linked to niche differentiation and may have important implications for process stability.
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49
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Lee MC, Lin YH, Yu HW. Kinetics of nitrification in a fixed biofilm reactor using dewatered sludge-fly ash composite ceramic particle as a supporting medium. Biodegradation 2014; 25:849-65. [DOI: 10.1007/s10532-014-9705-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 08/05/2014] [Indexed: 11/30/2022]
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50
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Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil. ISME JOURNAL 2014; 8:2397-410. [PMID: 24858784 DOI: 10.1038/ismej.2014.81] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/10/2014] [Accepted: 04/15/2014] [Indexed: 11/09/2022]
Abstract
Ammonium/ammonia is the sole energy substrate of ammonia oxidizers, and is also an essential nitrogen source for other microorganisms. Ammonia oxidizers therefore must compete with other soil microorganisms such as methane-oxidizing bacteria (MOB) in terrestrial ecosystems when ammonium concentrations are limiting. Here we report on the interactions between nitrifying communities dominated by ammonia-oxidizing archaea (AOA) and Nitrospira-like nitrite-oxidizing bacteria (NOB), and communities of MOB in controlled microcosm experiments with two levels of ammonium and methane availability. We observed strong stimulatory effects of elevated ammonium concentration on the processes of nitrification and methane oxidation as well as on the abundances of autotrophically growing nitrifiers. However, the key players in nitrification and methane oxidation, identified by stable-isotope labeling using (13)CO2 and (13)CH4, were the same under both ammonium levels, namely type 1.1a AOA, sublineage I and II Nitrospira-like NOB and Methylomicrobium-/Methylosarcina-like MOB, respectively. Ammonia-oxidizing bacteria were nearly absent, and ammonia oxidation could almost exclusively be attributed to AOA. Interestingly, although AOA functional gene abundance increased 10-fold during incubation, there was very limited evidence of autotrophic growth, suggesting a partly mixotrophic lifestyle. Furthermore, autotrophic growth of AOA and NOB was inhibited by active MOB at both ammonium levels. Our results suggest the existence of a previously overlooked competition for nitrogen between nitrifiers and methane oxidizers in soil, thus linking two of the most important biogeochemical cycles in nature.
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