101
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Zeng W, Bai X, Zhang L, Wang A, Peng Y. Population dynamics of nitrifying bacteria for nitritation achieved in Johannesburg (JHB) process treating municipal wastewater. BIORESOURCE TECHNOLOGY 2014; 162:30-37. [PMID: 24736209 DOI: 10.1016/j.biortech.2014.03.102] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 06/03/2023]
Abstract
Population dynamic of nitrifying bacteria was investigated for nitrogen removal from municipal wastewater. Nitritation was established with nitrite accumulation ratios above 85%. Quantitative PCR indicated that Nitrospira was dominant nitrite oxidizing bacteria (NOB) and Nitrobacter was few. During nitritation achieving, Nitrobacter was firstly eliminated, along with inhibition of Nitrospira bioactivities, then Nitrospira percentage declined and was finally washed out. Nitritation establishment depended on inhibiting and eliminating of NOB rather than ammonia oxidizing bacteria (AOB) enriching. This is the first study where population dynamics of Nitrobacter and Nitrospira were investigated to reveal mechanism of nitritation in a continuous-flow process. Phylogenetic analysis of AOB indicated that Nitrosomonas-like cluster and Nitrosomonas oligotropha were dominant AOB, accounting for 81.6% of amoA gene clone library. Community structure of AOB was similar to that of complete nitrification system with long hydraulic retention time, but different from that of nitritation reactor with low DO concentration.
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Affiliation(s)
- Wei Zeng
- Key Laboratory of Beijing for Water Environment Recovery, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Xinlong Bai
- Key Laboratory of Beijing for Water Environment Recovery, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Limin Zhang
- Key Laboratory of Beijing for Water Environment Recovery, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Anqi Wang
- Key Laboratory of Beijing for Water Environment Recovery, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Environment Recovery, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
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102
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Seasonal dynamics of ammonia-oxidizing microorganisms in freshwater aquaculture ponds. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0903-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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103
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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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104
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Bollmann A, Bullerjahn GS, McKay RM. Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior. PLoS One 2014; 9:e97068. [PMID: 24819357 PMCID: PMC4018257 DOI: 10.1371/journal.pone.0097068] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/15/2014] [Indexed: 11/29/2022] Open
Abstract
Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.
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Affiliation(s)
- Annette Bollmann
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
- * E-mail: *
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Robert Michael McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
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105
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Pacchioni RG, Carvalho FM, Thompson CE, Faustino ALF, Nicolini F, Pereira TS, Silva RCB, Cantão ME, Gerber A, Vasconcelos ATR, Agnez-Lima LF. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil. Microbiologyopen 2014; 3:299-315. [PMID: 24706600 PMCID: PMC4082704 DOI: 10.1002/mbo3.169] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/23/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas.
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Affiliation(s)
- Ralfo G Pacchioni
- Department of Cellular Biology and Genetics, UFRN, Natal, Rio Grande do Norte, Brazil
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106
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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107
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Srithep P, Khinthong B, Chodanon T, Powtongsook S, Pungrasmi W, Limpiyakorn T. Communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in shrimp ponds. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0858-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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108
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Wang C, Shan B, Zhang H, Zhao Y. Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals. J Environ Sci (China) 2014; 26:502-511. [PMID: 25079261 DOI: 10.1016/s1001-0742(13)60443-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/04/2013] [Accepted: 06/08/2013] [Indexed: 06/03/2023]
Abstract
The Haihe River is characterized by high ammonia pollution. Therefore, it is necessary to determine how environmental factors, such as heavy metals in the river limit the spatial distribution of ammonia-oxidizing microorganisms. In this study, the relationships between five heavy metals and ammonia-oxidizing microorganisms were studied. The results showed that under high ammonia, low oxygen and high concentrations of suspended particles, ammonia-oxidizing bacteria (AOB) ranged from 10(1.3) to 10(4.8) gene copies/mL and ammonia-oxidizing archaea (AOA) ranged from 10(2.7) to 10(4.9) gene copies/mL. The average metal concentrations in water were 23.57 (Cr), 21.58 (Ni), 65.09 (Cu), 622.03 (Zn) and 10.16 (As) μg/L, with those of Zn, Cu and Cr being higher than the US EPA criteria. Scatter plots of microbial abundance and metals indicated that both AOA and AOB were limited by heavy metals, but in different ways. As had an inhibitory effect on AOB, while Ni and Zn promoted AOA, and the other metals investigated showed no significant correlation with microbial abundance. Overall, our results indicated that the effects of heavy metals on ammonia-oxidizing microorganisms in water are complex, and that the final effect is determined by the physiological role of each element in the microorganisms, as well as environmental conditions such as complexation of organic matter, not simply the total metal concentration.
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Affiliation(s)
- Chao Wang
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Baoqing Shan
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hong Zhang
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu Zhao
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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109
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Wells GF, Wu CH, Piceno YM, Eggleston B, Brodie EL, DeSantis TZ, Andersen GL, Hazen TC, Francis CA, Criddle CS. Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes. Appl Microbiol Biotechnol 2014; 98:4723-36. [DOI: 10.1007/s00253-014-5564-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 11/28/2022]
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110
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Almstrand R, Persson F, Daims H, Ekenberg M, Christensson M, Wilén BM, Sörensson F, Hermansson M. Three-dimensional stratification of bacterial biofilm populations in a moving bed biofilm reactor for nitritation-anammox. Int J Mol Sci 2014; 15:2191-206. [PMID: 24481066 PMCID: PMC3958845 DOI: 10.3390/ijms15022191] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/10/2014] [Accepted: 01/14/2014] [Indexed: 11/18/2022] Open
Abstract
Moving bed biofilm reactors (MBBRs) are increasingly used for nitrogen removal with nitritation-anaerobic ammonium oxidation (anammox) processes in wastewater treatment. Carriers provide protected surfaces where ammonia oxidizing bacteria (AOB) and anammox bacteria form complex biofilms. However, the knowledge about the organization of microbial communities in MBBR biofilms is sparse. We used new cryosectioning and imaging methods for fluorescence in situ hybridization (FISH) to study the structure of biofilms retrieved from carriers in a nitritation-anammox MBBR. The dimensions of the carrier compartments and the biofilm cryosections after FISH showed good correlation, indicating little disturbance of biofilm samples by the treatment. FISH showed that Nitrosomonas europaea/eutropha-related cells dominated the AOB and Candidatus Brocadia fulgida-related cells dominated the anammox guild. New carriers were initially colonized by AOB, followed by anammox bacteria proliferating in the deeper biofilm layers, probably in anaerobic microhabitats created by AOB activity. Mature biofilms showed a pronounced three-dimensional stratification where AOB dominated closer to the biofilm-water interface, whereas anammox were dominant deeper into the carrier space and towards the walls. Our results suggest that current mathematical models may be oversimplifying these three-dimensional systems and unless the multidimensionality of these systems is considered, models may result in suboptimal design of MBBR carriers.
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Affiliation(s)
- Robert Almstrand
- Department of Chemistry & Molecular Biology, Microbiology, University of Gothenburg, Box 462, Göteborg SE-405 30, Sweden.
| | - Frank Persson
- Water Environment Technology, Department of Civil and Environmental Engineering, Chalmers University of Technology, Göteborg SE-412 96, Sweden.
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna 1090, Austria.
| | - Maria Ekenberg
- AnoxKaldnes AB, Klosterängsvägen 11A, Lund SE-226 47, Sweden.
| | | | - Britt-Marie Wilén
- Water Environment Technology, Department of Civil and Environmental Engineering, Chalmers University of Technology, Göteborg SE-412 96, Sweden.
| | - Fred Sörensson
- Department of Chemistry & Molecular Biology, Microbiology, University of Gothenburg, Box 462, Göteborg SE-405 30, Sweden.
| | - Malte Hermansson
- Department of Chemistry & Molecular Biology, Microbiology, University of Gothenburg, Box 462, Göteborg SE-405 30, Sweden.
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111
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Gao J, Luo X, Wu G, Li T, Peng Y. Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten wastewater treatment systems. Appl Microbiol Biotechnol 2013; 98:3339-54. [DOI: 10.1007/s00253-013-5428-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/18/2013] [Accepted: 11/21/2013] [Indexed: 10/25/2022]
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112
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Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats. PLoS One 2013; 8:e80835. [PMID: 24278328 PMCID: PMC3835317 DOI: 10.1371/journal.pone.0080835] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/14/2013] [Indexed: 11/19/2022] Open
Abstract
The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called “marine” group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as “Candidatus Nitrosotenuis uzonensis”, is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, “Candidatus N. uzonensis” also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in “Ca. N. uzonensis”, which potentially include genetic determinants of ecological niche differentiation.
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113
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Wang YF, Li XY, Gu JD. Differential responses of ammonia/ammonium-oxidizing microorganisms in mangrove sediment to amendment of acetate and leaf litter. Appl Microbiol Biotechnol 2013; 98:3165-80. [PMID: 24169949 DOI: 10.1007/s00253-013-5318-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/03/2013] [Indexed: 02/07/2023]
Abstract
The effects of acetate and leaf litter powder on ammonia/ammonium-oxidizing microorganisms (AOMs) in mangrove sediment were investigated in a laboratory incubation study for a period of 60 days. The results showed that different AOMs responded differently to the addition of acetate and leaf litter. A higher diversity of anaerobic ammonium-oxidizing (anammox) bacteria was observed when acetate or leaf litter was added than the control. However, acetate and leaf litter generally inhibited the growth of anammox bacteria despite that leaf litter promoted their growth in the first 5 days. The inhibitory effects on anammox bacteria were more pronounced by acetate than by leaf litter. Neither acetate nor leaf litter affected ammonia-oxidizing archaea (AOA) community structures, but promoted their growth. For ammonia-oxidizing bacteria (AOB), the addition of acetate or leaf litter resulted in changes of community structures and promoted their growth in the early phase of the incubation. In addition, the promoting effects by leaf litter on AOB growth were more obvious than acetate. These results indicated that organic substances affect AOM community structures and abundances. The study suggests that leaf litter has an important influence on the community structures and abundances of AOMs in mangrove sediment and affects the nitrogen cycle in such ecosystem.
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Affiliation(s)
- Yong-Feng Wang
- Laboratory of Microbial Ecology, Guangdong Academy of Forestry, No. 233, Guangshan 1st Road, Guangzhou, People's Republic of China
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114
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Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia. World J Microbiol Biotechnol 2013; 30:757-66. [DOI: 10.1007/s11274-013-1506-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/21/2013] [Indexed: 01/13/2023]
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115
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Oswald R, Behrendt T, Ermel M, Wu D, Su H, Cheng Y, Breuninger C, Moravek A, Mougin E, Delon C, Loubet B, Pommerening-Röser A, Sörgel M, Pöschl U, Hoffmann T, Andreae MO, Meixner FX, Trebs I. HONO emissions from soil bacteria as a major source of atmospheric reactive nitrogen. Science 2013; 341:1233-5. [PMID: 24031015 DOI: 10.1126/science.1242266] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Abiotic release of nitrous acid (HONO) in equilibrium with soil nitrite (NO2(-)) was suggested as an important contributor to the missing source of atmospheric HONO and hydroxyl radicals (OH). The role of total soil-derived HONO in the biogeochemical and atmospheric nitrogen cycles, however, has remained unknown. In laboratory experiments, we found that for nonacidic soils from arid and arable areas, reactive nitrogen emitted as HONO is comparable with emissions of nitric oxide (NO). We show that ammonia-oxidizing bacteria can directly release HONO in quantities larger than expected from the acid-base and Henry's law equilibria of the aqueous phase in soil. This component of the nitrogen cycle constitutes an additional loss term for fixed nitrogen in soils and a source for reactive nitrogen in the atmosphere.
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Affiliation(s)
- R Oswald
- Biogeochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany.
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116
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Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada. Appl Environ Microbiol 2013; 79:7454-65. [PMID: 24056472 DOI: 10.1128/aem.02202-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3- or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.
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117
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Wu YJ, Whang LM, Chang MY, Fukushima T, Lee YC, Cheng SS, Hsu SF, Chang CH, Shen W, Yang CY, Fu R, Tsai TY. Impact of food to microorganism (F/M) ratio and colloidal chemical oxygen demand on nitrification performance of a full-scale membrane bioreactor treating thin film transistor liquid crystal display wastewater. BIORESOURCE TECHNOLOGY 2013; 141:35-40. [PMID: 23561953 DOI: 10.1016/j.biortech.2013.02.108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/22/2013] [Accepted: 02/23/2013] [Indexed: 06/02/2023]
Abstract
This study investigated impact of food to microorganism (F/M) ratio and colloidal chemical oxygen demand (COD) on nitrification performance in one full-scale membrane bioreactor (MBR) treating monoethanolamine (MEA)/dimethyl sulfoxide (DMSO)-containing thin film transistor liquid crystal display (TFT-LCD) wastewater. Poor nitrification was observed under high organic loading and high colloidal COD conditions, suggesting that high F/M ratio and colloidal COD situations should be avoided to minimize their negative impacts on nitrification. According to the nonmetric multidimensional scaling (NMS) statistical analyses on terminal restriction fragment length polymorphism (T-RFLP) results of ammonia monooxygenase (amoA) gene, the occurrence of Nitrosomonas oligotropha-like ammonia oxidizing bacteria (AOB) was positively related to successful nitrification in the MBR systems, while Nitrosomonas europaea-like AOB was positively linked to nitrification rate, which can be attributed to the high influent total nitrogen condition. Furthermore, Nitrobacter- and Nitrospira-like nitrite oxidizing bacteria (NOB) were both abundant in the MBR systems, but the continuously low nitrite environment is likely to promote the growth of Nitrospira-like NOB.
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Affiliation(s)
- Yi-Ju Wu
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan
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118
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Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China. J Basic Microbiol 2013; 54:180-9. [DOI: 10.1002/jobm.201300217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/13/2013] [Indexed: 11/07/2022]
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119
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Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME JOURNAL 2013; 7:1962-73. [PMID: 23702516 DOI: 10.1038/ismej.2013.85] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 04/11/2013] [Accepted: 04/22/2013] [Indexed: 02/01/2023]
Abstract
The deep ocean is an important component of global biogeochemical cycles because it contains one of the largest pools of reactive carbon and nitrogen on earth. However, the microbial communities that drive deep-sea geochemistry are vastly unexplored. Metatranscriptomics offers new windows into these communities, but it has been hampered by reliance on genome databases for interpretation. We reconstructed the transcriptomes of microbial populations from Guaymas Basin, in the deep Gulf of California, through shotgun sequencing and de novo assembly of total community RNA. Many of the resulting messenger RNA (mRNA) contiguous sequences contain multiple genes, reflecting co-transcription of operons, including those from dominant members. Also prevalent were transcripts with only limited representation (2.8 times coverage) in a corresponding metagenome, including a considerable portion (1.2 Mb total assembled mRNA sequence) with similarity (96%) to a marine heterotroph, Alteromonas macleodii. This Alteromonas and euryarchaeal marine group II populations displayed abundant transcripts from amino-acid transporters, suggesting recycling of organic carbon and nitrogen from amino acids. Also among the most abundant mRNAs were catalytic subunits of the nitrite oxidoreductase complex and electron transfer components involved in nitrite oxidation. These and other novel genes are related to novel Nitrospirae and have limited representation in accompanying metagenomic data. High throughput sequencing of 16S ribosomal RNA (rRNA) genes and rRNA read counts confirmed that Nitrospirae are minor yet widespread members of deep-sea communities. These results implicate a novel bacterial group in deep-sea nitrite oxidation, the second step of nitrification. This study highlights metatranscriptomic assembly as a valuable approach to study microbial communities.
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120
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Microbial Community Structure of a Leachfield Soil: Response to Intermittent Aeration and Tetracycline Addition. WATER 2013. [DOI: 10.3390/w5020505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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121
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Mußmann M, Ribot M, von Schiller D, Merbt SN, Augspurger C, Karwautz C, Winkel M, Battin TJ, Martí E, Daims H. Colonization of freshwater biofilms by nitrifying bacteria from activated sludge. FEMS Microbiol Ecol 2013; 85:104-15. [DOI: 10.1111/1574-6941.12103] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/12/2013] [Accepted: 02/24/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Marc Mußmann
- Department of Microbial Ecology; Ecology Center; University of Vienna; Vienna; Austria
| | - Miquel Ribot
- Biogeodynamics and Biodiversity Group; Center for Advanced Studies of Blanes (CEAB-CSIC); Blanes; Spain
| | - Daniel von Schiller
- Biogeodynamics and Biodiversity Group; Center for Advanced Studies of Blanes (CEAB-CSIC); Blanes; Spain
| | - Stephanie N. Merbt
- Biogeodynamics and Biodiversity Group; Center for Advanced Studies of Blanes (CEAB-CSIC); Blanes; Spain
| | - Clemens Augspurger
- Department of Freshwater Ecology and Hydrobotany; Ecology Center; University of Vienna; Vienna; Austria
| | - Clemens Karwautz
- Institute of Groundwater Ecology; Helmholtz Center Munich; Neuherberg; Germany
| | - Matthias Winkel
- Max Planck Institute for Marine Microbiology; Bremen; Germany
| | | | - Eugènia Martí
- Biogeodynamics and Biodiversity Group; Center for Advanced Studies of Blanes (CEAB-CSIC); Blanes; Spain
| | - Holger Daims
- Department of Microbial Ecology; Ecology Center; University of Vienna; Vienna; Austria
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122
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Wu YJ, Whang LM, Fukushima T, Chang SH. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant. J Biosci Bioeng 2013; 115:424-32. [DOI: 10.1016/j.jbiosc.2012.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/06/2012] [Accepted: 11/06/2012] [Indexed: 11/17/2022]
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123
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Kim YM, Park H, Cho KH, Park JM. Long term assessment of factors affecting nitrifying bacteria communities and N-removal in a full-scale biological process treating high strength hazardous wastewater. BIORESOURCE TECHNOLOGY 2013; 134:180-189. [PMID: 23500576 DOI: 10.1016/j.biortech.2013.02.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/12/2013] [Accepted: 02/14/2013] [Indexed: 06/01/2023]
Abstract
Over a 3 year period, interactions between nitrifying bacterial communities and the operational parameters of a full-scale wastewater treatment plant were analyzed to assess their impact on nitrification performance. Throughout the study period, nitrification fluctuated while Nitrosomonas europaea and Nitrosomonas nitrosa, the two major ammonia oxidizing bacteria (AOB) communities, showed resistance to changes in operational and environmental conditions. Nitrobacter populations mostly exceeded those of Nitrospira within nitrite oxidizing bacteria (NOB). Meanwhile, principal component analysis (PCA) results revealed that a close association between Nitrobacter and nitrite concentration as well as a direct correlation between the quantity of AOB and influent SCN- concentration. The serial shifts of data points over time showed that the nitrification of a full-scale treatment plant has been gradually suppressed by the influence of influent COD and phenol concentrations.
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Affiliation(s)
- Young Mo Kim
- Department of Civil Engineering, Dong-A University, Busan 604-714, Republic of Korea.
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124
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Elawwad A, Sandner H, Kappelmeyer U, Koeser H. Long-term starvation and subsequent recovery of nitrifiers in aerated submerged fixed-bed biofilm reactors. ENVIRONMENTAL TECHNOLOGY 2013; 34:945-959. [PMID: 23837346 DOI: 10.1080/09593330.2012.722758] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The effectiveness of three operational strategies for maintaining nitrifiers in bench-scale, aerated, submerged fixed-bed biofilm reactors (SFBBRs) during long-term starvation at 20 degrees C were evaluated. The operational strategies were characterized by the resulting oxidation-reduction potential (ORP) in the SFBBRs. The activity rates of the nitrifiers were measured and the activity decay was expressed by half-life times. It was found that anoxic and alternating anoxic/aerobic conditions were the best ways to preserve ammonia-oxidizing bacteria (AOB) during long starvation periods and resulted in half-life times of up to 34 and 28 days, respectively. Extended anaerobic conditions caused the half-life for AOB to decrease to 21 days. In comparison, the activity decay of nitrite-oxidizing bacteria (NOB) tended to be slightly faster. The activity of AOB biofilms that were kept for 97 days under anoxic conditions could be completely recovered in less than one week, while over 4 weeks was needed for AOB kept under anaerobic conditions. NOB were more sensitive to starvation and required longer recovery periods than AOB. For complete recovery, NOB needed approximately 7 weeks, regardless of the starvation conditions applied. Using the fluorescence in situ hybridization (FISH) technique, Nitrospira was detected as the dominant NOB genus. Among the AOB, the terminal restriction fragment length polymorphism (TRFLP) technique showed that during starvation and recovery periods, the relative frequency of species shifted to Nitrosomonas europaea/eutropha, regardless of the starvation condition. The consequences of these findings for the operation of SFBBRs under low-load and starvation conditions are discussed.
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Affiliation(s)
- Abdelsalam Elawwad
- Department of Environmental Engineering (UST), Otto-von-Guericke University-Magdeburg, c/o Martin Luther University Halle-Wittenberg, Merseburg, Germany.
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125
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Hoefman S, Pommerening-Röser A, Samyn E, De Vos P, Heylen K. Efficient cryopreservation protocol enables accessibility of a broad range of ammonia-oxidizing bacteria for the scientific community. Res Microbiol 2013; 164:288-92. [PMID: 23376087 DOI: 10.1016/j.resmic.2013.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/08/2013] [Indexed: 10/27/2022]
Abstract
Long-term storage of the fastidious ammonia-oxidizing bacteria has proven difficult, which limits their public availability and results in a loss of cultured biodiversity. To enable their accessibility to the scientific community, an effective protocol for cryopreservation of ammonia-oxidizing cultures at -80 °C and in liquid nitrogen was developed. Long-term storage could be achieved using 5% DMSO as cryoprotectant, preferably in a cryoprotective preservation medium containing tenfold-diluted trypticase soy broth and 1% trehalose. As such, successful activity and growth recovery was observed for a diverse set of ammonia-oxidizing cultures.
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Affiliation(s)
- Sven Hoefman
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
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126
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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127
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Lu L, Jia Z. Urease gene-containing Archaea dominate autotrophic ammonia oxidation in two acid soils. Environ Microbiol 2013; 15:1795-809. [PMID: 23298189 DOI: 10.1111/1462-2920.12071] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 11/27/2022]
Abstract
The metabolic traits of ammonia-oxidizing archaea (AOA) and bacteria (AOB) interacting with their environment determine the nitrogen cycle at the global scale. Ureolytic metabolism has long been proposed as a mechanism for AOB to cope with substrate paucity in acid soil, but it remains unclear whether urea hydrolysis could afford AOA greater ecological advantages. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, here we show that autotrophic ammonia oxidation in two acid soils was predominately driven by AOA that contain ureC genes encoding the alpha subunit of a putative archaeal urease. In urea-amended SIP microcosms of forest soil (pH 5.40) and tea orchard soil (pH 3.75), nitrification activity was stimulated significantly by urea fertilization when compared with water-amended soils in which nitrification resulted solely from the oxidation of ammonia generated through mineralization of soil organic nitrogen. The stimulated activity was paralleled by changes in abundance and composition of archaeal amoA genes. Time-course incubations indicated that archaeal amoA genes were increasingly labelled by (13) CO2 in both microcosms amended with water and urea. Pyrosequencing revealed that archaeal populations were labelled to a much greater extent in soils amended with urea than water. Furthermore, archaeal ureC genes were successfully amplified in the (13) C-DNA, and acetylene inhibition suggests that autotrophic growth of urease-containing AOA depended on energy generation through ammonia oxidation. The sequences of AOB were not detected, and active AOA were affiliated with the marine Group 1.1a-associated lineage. The results suggest that ureolytic N metabolism could afford AOA greater advantages for autotrophic ammonia oxidation in acid soil, but the mechanism of how urea activates AOA cells remains unclear.
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Affiliation(s)
- Lu Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
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128
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Stimulatory effect of xenobiotics on oxidative electron transport of chemolithotrophic nitrifying bacteria used as biosensing element. PLoS One 2013; 8:e53484. [PMID: 23326438 PMCID: PMC3541135 DOI: 10.1371/journal.pone.0053484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/30/2012] [Indexed: 02/01/2023] Open
Abstract
Electron transport chain (ETCh) of ammonium (AOB) and nitrite oxidizing bacteria (NOB) participates in oxidation of ammonium to nitrate (nitrification). Operation of ETCh may be perturbed by a range of water-soluble xenobiotics. Therefore, consortia of nitrifying bacteria may be used as a biosensor to detect water contamination. A surprising feature of this system is an increase of oxygen consumption, detected in the presence of certain inhibitors of ETCh. Thus, to shed light on the mechanism of this effect (and other differences between inhibitors) we monitored separately respiration of the bacteria of the first (AOB - Nitrosomonas) and second (NOB -Nitrobacter) stages of nitrification. Furthermore, we measured plasma membrane potential and the level of reduction of NAD(P)H. We propose a novel model of ETCh in NOB to explain the role of reverse electron transport in the stimulation of oxygen consumption (previously attributed to hormesis).
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129
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Vasileiadis S, Coppolecchia D, Puglisi E, Balloi A, Mapelli F, Hamon RE, Daffonchio D, Trevisan M. Response of ammonia oxidizing bacteria and archaea to acute zinc stress and different moisture regimes in soil. MICROBIAL ECOLOGY 2012; 64:1028-1037. [PMID: 22688860 DOI: 10.1007/s00248-012-0081-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/29/2012] [Indexed: 06/01/2023]
Abstract
Ammonia oxidation has been intensively studied for its sensitivity to environmental shifts and stresses. However, acute stress effects on the occurrence and composition of ammonia oxidizing bacteria (AOB) and archaea (AOA) based on expression of related molecular markers in complex soil environments have been to an extent overlooked, particularly concerning transient but commonly occurring environmental changes like soil moisture shifts. The present study investigates the responses of AOB and AOA to moisture shifts and high Zn soil content. AmoA gene copies and transcripts of AOB and AOA along with potential nitrification activity were measured in a soil microcosm approach for investigating the referred environmental shifts. Moisture change from 87 to 50 % of the water holding capacity caused a ~99 % reduction of AOB but not of AOA amoA transcripts that did not change significantly. Increasing applied zinc concentrations resulted in a reduction of potential nitrification rates and negatively affected studied gene expressions of both AOB and AOA, with AOB being more responsive. Both 16 S rRNA and amoA transcripts of AOB had an inverse relation to the applied zinc, indicating a gradual loss in total cell activity. Our results suggest the existence of pronounced differences between AOB and AOA concerning ammonia oxidation activity.
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Affiliation(s)
- Sotirios Vasileiadis
- Institute of Agricultural and Environmental Chemistry, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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130
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Nitrifying bacterial community structures and their nitrification performance under sufficient and limited inorganic carbon conditions. Appl Microbiol Biotechnol 2012; 97:6513-23. [DOI: 10.1007/s00253-012-4436-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 08/13/2012] [Accepted: 09/11/2012] [Indexed: 11/25/2022]
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131
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Whang LM, Wu YJ, Lee YC, Chen HW, Fukushima T, Chang MY, Cheng SS, Hsu SF, Chang CH, Shen W, Huang CK, Fu R, Chang B. Nitrification performance and microbial ecology of nitrifying bacteria in a full-scale membrane bioreactor treating TFT-LCD wastewater. BIORESOURCE TECHNOLOGY 2012; 122:70-77. [PMID: 22595093 DOI: 10.1016/j.biortech.2012.04.092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 05/31/2023]
Abstract
This study investigated nitrification performance and nitrifying community in one full-scale membrane bioreactor (MBR) treating TFT-LCD wastewater. For the A/O MBR system treating monoethanolamine (MEA) and dimethyl sulfoxide (DMSO), no nitrification was observed, due presumably to high organic loading, high colloidal COD, low DO, and low hydraulic retention time (HRT) conditions. By including additional A/O or O/A tanks, the A/O/A/O MBR and the O/A/O MBR were able to perform successful nitrification. The real-time PCR results for quantification of nitrifying populations showed a high correlation to nitrification performance, and can be a good indicator of stable nitrification. Terminal restriction fragment length polymorphism (T-RFLP) results of functional gene, amoA, suggest that Nitrosomonas oligotropha-like AOB seemed to be important to a good nitrification in the MBR system. In the MBR system, Nitrobacter- and Nitrospira-like NOB were both abundant, but the low nitrite environment is likely to promote the growth of Nitrospira-like NOB.
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Affiliation(s)
- Liang-Ming Whang
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan.
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132
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Insights into glycogen metabolism in chemolithoautotrophic bacteria from distinctive kinetic and regulatory properties of ADP-glucose pyrophosphorylase from Nitrosomonas europaea. J Bacteriol 2012; 194:6056-65. [PMID: 22961847 DOI: 10.1128/jb.00810-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO(2) via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms.
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133
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Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 2012; 20:523-31. [PMID: 22959489 DOI: 10.1016/j.tim.2012.08.001] [Citation(s) in RCA: 412] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/28/2012] [Accepted: 08/01/2012] [Indexed: 11/27/2022]
Abstract
Autotrophic archaeal and bacterial ammonia-oxidisers (AOA and AOB) drive soil nitrification. Ammonia limitation, mixotrophy, and pH have been suggested as factors providing niche specialisation and differentiation between soil AOA and AOB. However, current data from genomes, cultures, field studies, and microcosms suggest that no single factor discriminates between AOA and AOB. In addition, there appears to be sufficient physiological diversity within each group for growth and activity in all soils investigated, with the exception of acidic soils (pH <5.5), which are dominated by AOA. Future investigation of niche specialisation in ammonia-oxidisers, and other microbial communities, requires characterisation of a wider range of environmentally representative cultures, emphasis on experimental studies rather than surveys, and greater consideration of small-scale soil heterogeneity.
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134
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Brown MN, Briones A, Diana J, Raskin L. Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system. FEMS Microbiol Ecol 2012; 83:17-25. [DOI: 10.1111/j.1574-6941.2012.01448.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 07/05/2012] [Accepted: 07/05/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Monisha N. Brown
- Department of Civil and Environmental Engineering; University of Michigan; Ann Arbor; MI; USA
| | - Aurelio Briones
- Plant, Soil & Entomological Sciences Department; University of Idaho; Moscow; ID; USA
| | - James Diana
- School of Natural Resources and the Environment; University of Michigan; Ann Arbor; MI; USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering; University of Michigan; Ann Arbor; MI; USA
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135
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French E, Kozlowski JA, Mukherjee M, Bullerjahn G, Bollmann A. Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl Environ Microbiol 2012; 78:5773-80. [PMID: 22685142 PMCID: PMC3406153 DOI: 10.1128/aem.00432-12] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/30/2012] [Indexed: 11/20/2022] Open
Abstract
Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with "Candidatus Nitrosoarchaeum koreensis" and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.
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Affiliation(s)
| | | | - Maitreyee Mukherjee
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, USA
| | - George Bullerjahn
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, USA
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136
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Prosser JI. Ecosystem processes and interactions in a morass of diversity. FEMS Microbiol Ecol 2012; 81:507-19. [PMID: 22715974 DOI: 10.1111/j.1574-6941.2012.01435.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/14/2012] [Accepted: 06/15/2012] [Indexed: 11/27/2022] Open
Abstract
High diversity in natural communities is indicated by both traditional, cultivation-based methods and molecular techniques, but the latter have significantly increased richness estimates. The increased ease and reduced cost associated with molecular analysis of microbial communities have fuelled interest in the links between richness, community composition and ecosystem function, and raise questions about our ability to understand mechanisms controlling interactions in highly complex communities. High-throughput sequencing is increasing the depth of sequencing but the relevance of such studies to important ecological questions is often unclear. This article discusses, and challenges, some of the often implicit assumptions made in community studies. It suggests greater focus on ecological questions, more critical analysis of accepted concepts and consideration of the fundamental mechanisms controlling microbial processes and interactions in situ. These considerations indicate that many questions do not require deeper sequence analysis and increased phylogenetic resolution but, rather, require analysis at smaller spatial scale, determination of phenotypic diversity and temporal, rather than snapshot, studies. Increasing realisation of the high richness of microbial communities, and potentially high physiological diversity, also require new conceptual approaches.
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Affiliation(s)
- James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.
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137
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Xu XY, Feng LJ, Zhu L, Xu J, Ding W, Qi HY. Biofilm formation and microbial community analysis of the simulated river bioreactor for contaminated source water remediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2012; 19:1584-1593. [PMID: 22120124 DOI: 10.1007/s11356-011-0649-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 10/18/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND, AIM, AND SCOPE The start-up pattern of biofilm remediation system affects the biofilm characteristics and operating performances. The objective of this study was to evaluate the performances of the contaminated source water remediation systems with different start-up patterns in view of the pollutants removal performances and microbial community succession. METHODS The operating performances of four lab-scale simulated river biofilm reactors were examined which employed different start-up methods (natural enrichment and artificial enhancement via discharging sediment with influent velocity gradient increase) and different bio-fillers (Elastic filler and AquaMats® ecobase). At the same time, the microbial communities of the bioreactors in different phases were analyzed by polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing. RESULTS AND DISCUSSION The pollutants removal performances became stable in the four reactors after 2 months' operation, with ammonia nitrogen and permanganate index (COD(Mn)) removal efficiencies of 84.41-94.21% and 69.66-76.60%, respectively. The biomass of mature biofilm was higher in the bioreactors by artificial enhancement than that by natural enrichment. Microbial community analysis indicated that elastic filler could enrich mature biofilm faster than AquaMats®. The heterotrophic bacteria diversity of biofilm decreased by artificial enhancement, which favored the ammonia-oxidizing bacteria (AOB) developing on the bio-fillers. Furthermore, Nitrosomonas- and Nitrosospira-like AOB coexisted in the biofilm, and Pseudomonas sp., Sphaerotilus sp., Janthinobacterium sp., Corynebacterium aurimucosum were dominant in the oligotrophic niche. CONCLUSION Artificial enhancement via the combination of sediment discharging and influent velocity gradient increasing could enhance the biofilm formation and autotrophic AOB enrichment in oligotrophic niche.
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Affiliation(s)
- Xiang-Yang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, People's Republic of China
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138
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Amand L, Carlsson B. Optimal aeration control in a nitrifying activated sludge process. WATER RESEARCH 2012; 46:2101-10. [PMID: 22341831 DOI: 10.1016/j.watres.2012.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 01/18/2012] [Accepted: 01/20/2012] [Indexed: 05/08/2023]
Abstract
An important tool to minimise energy consumption in activated sludge processes is to control the aeration system. Aeration is a costly process and the dissolved oxygen level will determine the efficiency of the operation as well as the treatment results. What aeration control should achieve is closely linked to how the effluent criteria are defined. This paper explores how the aeration process should be controlled to meet the effluent discharge limits in an energy efficient manner in countries where the effluent nitrogen criterion is defined as average values over long time frames, such as months or years. Simulations have been performed using a simplified Benchmark Simulation Model No. 1 to investigate the effect of different levels of suppressing the variations of the effluent ammonium concentration. Optimisation is performed where the manipulated variable for aeration (the oxygen transfer coefficient, K(L)a) is minimised with the constraint that the average daily flow-proportional ammonium concentration in the effluent should reach a desired level. The optimisation results are compared with constant dissolved oxygen concentrations and supervisory ammonium control with different controller settings. The results demonstrate and explain how and why energy consumption can be optimised by tolerating the ammonium concentration to vary around a given average value. In these simulations, the optimal oxygen peak-to-peak amplitude range between 0.7 and 1.8 mg/l depending on the influent variation and ammonium level in the effluent. These variations can be achieved with a slow ammonium feedback controller. The air flow requirements can be reduced by 1-4% compared to constant dissolved oxygen set-points. Optimal control of aeration requires up to 14% less energy than needed for fast feedback control of effluent ammonium.
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Affiliation(s)
- L Amand
- IVL Swedish Environmental Research Institute, P.O. Box 210 60, 100 31 Stockholm, Sweden.
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139
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Almstrand R, Lydmark P, Lindgren PE, Sörensson F, Hermansson M. Dynamics of specific ammonia-oxidizing bacterial populations and nitrification in response to controlled shifts of ammonium concentrations in wastewater. Appl Microbiol Biotechnol 2012; 97:2183-91. [DOI: 10.1007/s00253-012-4047-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/16/2012] [Accepted: 03/19/2012] [Indexed: 12/01/2022]
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140
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Kim JG, Jung MY, Park SJ, Rijpstra WIC, Sinninghe Damsté JS, Madsen EL, Min D, Kim JS, Kim GJ, Rhee SK. Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environ Microbiol 2012; 14:1528-43. [PMID: 22515152 DOI: 10.1111/j.1462-2920.2012.02740.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrification of excess ammonia in soil causes eutrophication of water resources and emission of atmospheric N(2) O gas. The first step of nitrification, ammonia oxidation, is mediated by Archaea as well as Bacteria. The physiological reactions mediated by ammonia-oxidizing archaea (AOA) and their contribution to soil nitrification are still unclear. Results of non-culture-based studies have shown the thaumarchaeotal group I.1b lineage of AOA to be dominant over both AOA of group I.1a and ammonia-oxidizing bacteria in various soils. We obtained from an agricultural soil a highly enriched ammonia-oxidizing culture dominated by a single archaeal population [c. 90% of total cells, as determined microscopically (by fluorescence in situ hybridization) and by quantitative PCR of its 16S rRNA gene]. The archaeon (termed 'strain JG1') fell within thaumarchaeotal group I.1b and was related to the moderately thermophilic archaeon, Candidatus Nitrososphaera gargensis, and the mesophilic archaeon, Ca. Nitrososphaera viennensis with 97.0% and 99.1% 16S rRNA gene sequence similarity respectively. Strain JG1 was neutrophilic (growth range pH 6.0-8.0) and mesophilic (growth range temperature 25-40°C). The optimum temperature of strain JG1 (35-40°C) is > 10°C higher than that of ammonia-oxidizing bacteria (AOB). Membrane analysis showed that strain JG1 contained a glycerol dialkyl glycerol tetraether, GDGT-4, and its regioisomer as major core lipids; this crenarchaeol regioisomer was previously detected in similar abundance in the thermophile, Ca. N. gargensis and has been frequently observed in tropical soils. Substrate uptake assays showed that the affinity of strain JG1 for ammonia and oxygen was much higher than those of AOB. These traits may give a competitive advantage to AOA related to strain JG1 in oligotrophic environments. (13) C-bicarbonate incorporation into archaeal lipids of strain JG1 established its ability to grow autotrophically. Strain JG1 produced a significant amount of N(2) O gas - implicating AOA as a possible source of N(2) O emission from soils. Sequences of archaeal amoA and 16S rRNA genes closely related to those of strain JG1 have been retrieved from various terrestrial environments in which lineage of strain JG1 is likely engaged in autotrophic nitrification.
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Affiliation(s)
- Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju, Korea
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141
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Wang F, Liu Y, Wang J, Zhang Y, Yang H. Influence of growth manner on nitrifying bacterial communities and nitrification kinetics in three lab-scale bioreactors. ACTA ACUST UNITED AC 2012; 39:595-604. [DOI: 10.1007/s10295-011-1065-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 11/18/2011] [Indexed: 11/28/2022]
Abstract
Abstract
The effects of growth type, including attached growth, suspended growth, and combined growth, on the characteristics of communities of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were studied in three lab-scale Anaerobic/Anoxicm-Oxicn (AmOn) systems. These systems amplified activated sludge, biofilms, and a mixture of activated sludge and biofilm (AS-BF). Identical inocula were adopted to analyze the selective effects of mixed growth patterns on nitrifying bacteria. Fluctuations in the concentration of nitrifying bacteria over the 120 days of system operation were analyzed, as was the composition of nitrifying bacterial community in the stabilized stage. Analysis was conducted using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR. According to the DGGE patterns, the primary AOB lineages were Nitrosomonas europaea (six sequences), Nitrosomonas oligotropha (two sequences), and Nitrosospira (one sequence). The primary subclass of NOB community was Nitrospira, in which all identified sequences belonged to Nitrospira moscoviensis (14 sequences). Nitrobacter consisted of two lineages, namely Nitrobacter vulgaris (three sequences) and Nitrobacter alkalicus (two sequences). Under identical operating conditions, the composition of nitrifying bacterial communities in the AS-BF system demonstrated significant differences from those in the activated sludge system and those in the biofilm system. Major varieties included several new, dominant bacterial sequences in the AS-BF system, such as N. europaea and Nitrosospira and a higher concentration of AOB relative to the activated sludge system. However, no similar differences were discovered for the concentration of the NOB population. A kinetic study of nitrification demonstrated a higher maximum specific growth rate of mixed sludge and a lower half-saturation constant of mixed biofilm, indicating that the AS-BF system maintained relatively good nitrifying ability.
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Affiliation(s)
- Feng Wang
- grid.24516.34 0000000123704535 Key Laboratory of Yangtze River Water Environment, Ministry of Education Tongji University 200092 Shanghai China
| | - Yi Liu
- grid.419074.f 0000000417612345 Shanghai Environmental Protection Limited Company Shanghai Academy of Environmental Sciences 200233 Shanghai China
| | - Jinghan Wang
- grid.24516.34 0000000123704535 Key Laboratory of Yangtze River Water Environment, Ministry of Education Tongji University 200092 Shanghai China
| | - Yalei Zhang
- grid.24516.34 0000000123704535 Key Laboratory of Yangtze River Water Environment, Ministry of Education Tongji University 200092 Shanghai China
| | - Haizhen Yang
- grid.24516.34 0000000123704535 Key Laboratory of Yangtze River Water Environment, Ministry of Education Tongji University 200092 Shanghai China
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142
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Okabe S, Nakamura Y, Satoh H. Community structure and in situ activity of nitrifying bacteria in Phragmites root-associated biofilms. Microbes Environ 2012; 27:242-9. [PMID: 22446303 PMCID: PMC4036055 DOI: 10.1264/jsme2.me11314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The amount of oxygen released by Phragmites roots and the community structure and in situ activity of nitrifying bacteria in the root biofilms were analyzed by the combined use of 16S rRNA gene-cloning analysis, quantitative PCR (qPCR) assay and microelectrodes. Axial and radial O₂ microprofiles were obtained for individual roots of Phragmites in a horizontal flow reactor fed with artificial medium continuously. Axial O₂ profiles revealed that O₂ was released at a rate of 0.21 μmol O₂ cm⁻² (root surface area) h⁻¹ only in the apical region (up to ca. 40 mm from the root apex), where there was a high abundance (10⁷ to 10⁸ copies g⁻¹ biomass) of Nitrosomonas-like AOB and Nitrospira-like NOB. This abundance, however, sharply declined to the detection limit at positions more basal than 80 mm. Phylogenetic analysis based on 16S rRNA gene identified strains related to Nitrosomonas oligotropha and Nitrosomonas cryotolerans as the predominant AOB and strains related to Nitrospira marina and Nitrospira moscoviensis as the predominant NOB in the root biofilms. Based on radial O₂ microprofiles, the oxic region only extended about 0.5 mm into the surrounding sediment due to a high rate of O₂ consumption in the rhizosphere. The net NH₄⁺ and O₂ consumption rates in the apical region were higher than those determined at the oxic sediment surface in which the abundance of AOB and NOB was one order of magnitude lower than in the rhizosphere. These results clearly indicated that Phragmites root biofilms played an important role in nitrification in the waterlogged anoxic sediment.
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Affiliation(s)
- Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo Hokkaido 060-8628, Japan.
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143
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Ke X, Lu Y. Adaptation of ammonia-oxidizing microorganisms to environment shift of paddy field soil. FEMS Microbiol Ecol 2012; 80:87-97. [DOI: 10.1111/j.1574-6941.2011.01271.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/10/2011] [Accepted: 11/25/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Xiubin Ke
- College of Resources and Environment Sciences; China Agricultural University; Beijing; China
| | - Yahai Lu
- College of Resources and Environment Sciences; China Agricultural University; Beijing; China
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144
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Fortuna AM, Honeycutt CW, Vandemark G, Griffin TS, Larkin RP, He Z, Wienhold BJ, Sistani KR, Albrecht SL, Woodbury BL, Torbert HA, Powell JM, Hubbard RK, Eigenberg RA, Wright RJ, Alldredge JR, Harsh JB. Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry. JOURNAL OF ENVIRONMENTAL QUALITY 2012; 41:262-272. [PMID: 22218194 DOI: 10.2134/jeq2011.0202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties.
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Affiliation(s)
- Ann-Marie Fortuna
- Dep. of Crop & Soil Sci., Washington State Univ., Pullman, WA 99164-6420, USA.
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145
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Wang Y, Zhu G, Ye L, Feng X, Op den Camp HJM, Yin C. Spatial distribution of archaeal and bacterial ammonia oxidizers in the littoral buffer zone of a nitrogen-rich lake. J Environ Sci (China) 2012; 24:790-799. [PMID: 22893953 DOI: 10.1016/s1001-0742(11)60861-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The spatial distribution and diversity of archaeal and bacterial ammonia oxidizers (AOA and AOB) were evaluated targeting amoA genes in the gradient of a littoral buffer zone which has been identified as a hot spot for N cycling. Here we found high spatial heterogeneity in the nitrification rate and abundance of ammonia oxidizers in the five sampling sites. The bacterial amoA gene was numerically dominant in most of the surface soil but decreased dramatically in deep layers. Higher nitrification potentials were detected in two sites near the land/water interface at 4.4-6.1 microg NO(2-)-N/(g dry weight soil x hr), while only 1.0-1.7 microg NO(2-)-N/(g dry weight soil x hr) was measured at other sites. The potential nitrification rates were proportional to the amoA gene abundance for AOB, but with no significant correlation with AOA. The NH4+ concentration was the most determinative parameter for the abundance of AOB and potential nitrification rates in this study. Higher richness in the surface layer was found in the analysis of biodiversity. Phylogenetic analysis revealed that most of the bacterial amoA sequences in surface soil were affiliated with the genus of Nitrosopira while the archaeal sequences were almost equally affiliated with Candidatus 'Nitrososphaera gargensis' and Candidatus 'Nitrosocaldus yellowstonii'. The spatial distribution of AOA and AOB indicated that bacteria may play a more important role in nitrification in the littoral buffer zone of a N-rich lake.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Environmental Aquatic Quality, Research Center for Eco-Environmental Sciences, the Chinese Academy of Sciences, Beijing 100085, China.
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146
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Wang B, Wang W, Han H, Hu H, Zhuang H. Nitrogen removal and simultaneous nitrification and denitrification in a fluidized bed step-feed process. J Environ Sci (China) 2012; 24:303-308. [PMID: 22655392 DOI: 10.1016/s1001-0742(11)60767-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
For urban wastewater treatment, we conducted a novel four-stage step-feed wastewater treatment system combined with a fluidized bed laboratory experiment to investigate chemical oxygen demand (COD), NH(4+)-N, and total nitrogen (TN) removal performance. The removal rates of COD, NH(4+)-N and TN were 88.2%, 95.7%, and 86.4% with effluent concentrations of COD, NH(4+)-N and TN less than 50, 8, and 10 mg/L, respectively. Biomass and bacterial activities were also measured, with results showing more nitrobacteria in the activated sludge than in the biofilm; however, bacterial activity of the biofilm biomass and the activated sludge were similar. Nitrogen concentrations during the process were also detected, with simultaneous nitrification and denitrification found to be obvious.
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Affiliation(s)
- Bing Wang
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090, China.
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147
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Abstract
Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in (15)N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (≤372 nM NO(2)(-) d(-1)) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ~9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO(3)(-) was re-oxidized back to NO(3)(-) via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.
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148
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Merbt SN, Stahl DA, Casamayor EO, Martí E, Nicol GW, Prosser JI. Differential photoinhibition of bacterial and archaeal ammonia oxidation. FEMS Microbiol Lett 2011; 327:41-6. [PMID: 22093004 DOI: 10.1111/j.1574-6968.2011.02457.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/14/2011] [Accepted: 11/06/2011] [Indexed: 11/30/2022] Open
Abstract
Inhibition by light potentially influences the distribution of ammonia oxidizers in aquatic environments and is one explanation for nitrite maxima near the base of the euphotic zone of oceanic waters. Previous studies of photoinhibition have been restricted to bacterial ammonia oxidizers, rather than archaeal ammonia oxidizers, which dominate in marine environments. To compare the photoinhibition of bacterial and archaeal ammonia oxidizers, specific growth rates of two ammonia-oxidizing archaea (Nitrosopumilus maritimus and Nitrosotalea devanaterra) and bacteria (Nitrosomonas europaea and Nitrosospira multiformis) were determined at different light intensities under continuous illumination and light/dark cycles. All strains were inhibited by continuous illumination at the highest intensity (500 μE m(-2) s(-1)). At lower light intensities, archaeal growth was much more photosensitive than bacterial growth, with greater inhibition at 60 μE m(-2) s(-1) than at 15 μE m(-2) s(-1), where bacteria were unaffected. Archaeal ammonia oxidizers were also more sensitive to cycles of 8-h light/16-h darkness at two light intensities (60 and 15 μE m(-2) s(-1)) and, unlike bacterial strains, showed no evidence of recovery during dark phases. The findings provide evidence for niche differentiation in aquatic environments and reduce support for photoinhibition as an explanation of nitrite maxima in the ocean.
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Affiliation(s)
- Stephanie N Merbt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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149
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Bin Z, Zhe C, Zhigang Q, Min J, Zhiqiang C, Zhaoli C, Junwen L, Xuan W, Jingfeng W. Dynamic and distribution of ammonia-oxidizing bacteria communities during sludge granulation in an anaerobic-aerobic sequencing batch reactor. WATER RESEARCH 2011; 45:6207-6216. [PMID: 21955984 DOI: 10.1016/j.watres.2011.09.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/10/2011] [Accepted: 09/10/2011] [Indexed: 05/27/2023]
Abstract
The structure dynamic of ammonia-oxidizing bacteria (AOB) community and the distribution of AOB and nitrite-oxidizing bacteria (NOB) in granular sludge from an anaerobic-aerobic sequencing batch reactor (SBR) were investigated. A combination of process studies, molecular biotechniques and microscale techniques were employed to identify and characterize these organisms. The AOB community structure in granules was substantially different from that of the initial pattern of the inoculants sludge. Along with granules formation, the AOB diversity declined due to the selection pressure imposed by process conditions. Denaturing gradient gel electrophoresis (DGGE) and sequencing results demonstrated that most of Nitrosomonas in the inoculating sludge were remained because of their ability to rapidly adapt to the settling-washing out action. Furthermore, DGGE analysis revealed that larger granules benefit more AOB species surviving in the reactor. In the SBR were various size granules coexisted, granule diameter affected the distribution range of AOB and NOB. Small and medium granules (d<0.6 mm) cannot restrict oxygen mass transfer in all spaces of the sludge. Larger granules (d>0.9 mm) can result in smaller aerobic volume fraction and inhibition of NOB growth. All these observations provide support to future studies on the mechanisms responsible for the AOB in granules systems.
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Affiliation(s)
- Zhang Bin
- Institute of Hygiene and Environmental Medicine, Academy of Military Medical Sciences, Tianjin 300050, PR China
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150
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Bouskill NJ, Eveillard D, Chien D, Jayakumar A, Ward BB. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments. Environ Microbiol 2011; 14:714-29. [PMID: 22050634 DOI: 10.1111/j.1462-2920.2011.02623.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution.
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Affiliation(s)
- Nicholas J Bouskill
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA.
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