151
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Community shift of ammonia-oxidizing bacteria along an anthropogenic pollution gradient from the Pearl River Delta to the South China Sea. Appl Microbiol Biotechnol 2011; 94:247-59. [PMID: 22005744 PMCID: PMC3304064 DOI: 10.1007/s00253-011-3636-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/22/2011] [Accepted: 10/06/2011] [Indexed: 11/20/2022]
Abstract
The phylogenetic diversity and abundance of ammonia-oxidizing beta-proteobacteria (beta-AOB) was analyzed along an anthropogenic pollution gradient from the coastal Pearl River Delta to the South China Sea using the ammonia monooxygenase subunit A (amoA) gene. Along the gradient from coastal to the open ocean, the phylogenetic diversity of the dominant genus changed from Nitrosomonas to Nitrosospira, indicating the niche specificity by these two genera as both salinity and anthropogenic influence were major factors involved. The diversity of bacterial amoA gene was also variable along the gradient, with the highest in the deep-sea sediments, followed by the marshes sediments and the lowest in the coastal areas. Within the Nitrosomonas-related clade, four distinct lineages were identified including a putative new one (A5-16) from the different sites over the large geographical area. In the Nitrosospira-related clade, the habitat-specific lineages to the deep-sea and coastal sediments were identified. This study also provides strong support that Nitrosomonas genus, especially Nitrosomonas oligotropha lineage (6a) could be a potential bio-indicator species for pollution or freshwater/wastewater input into coastal environments. A suite of statistical analyses used showed that water depth and temperature were major factors shaping the community structure of beta-AOB in this study area.
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152
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Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil. Appl Environ Microbiol 2011; 77:8635-47. [PMID: 22003023 DOI: 10.1128/aem.05787-11] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [¹³C]bicarbonate assimilation assay showed stoichiometric incorporation of ¹³C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to "Candidatus Nitrosopumilus maritimus" revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N₂O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated "Candidatus Nitrosoarchaeum koreensis."
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153
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Active autotrophic ammonia-oxidizing bacteria in biofilm enrichments from simulated creek ecosystems at two ammonium concentrations respond to temperature manipulation. Appl Environ Microbiol 2011; 77:7329-38. [PMID: 21890674 DOI: 10.1128/aem.05864-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first step of nitrification, the oxidation of ammonia to nitrite, is important for reducing eutrophication in freshwater environments when coupled with anammox (anaerobic ammonium oxidation) or denitrification. We analyzed active formerly biofilm-associated aerobic ammonia-oxidizing communities originating from Ammerbach (AS) and Leutra South (LS) stream water (683 ± 550 [mean ± standard deviation] and 16 ± 7 μM NH(4)(+), respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using (13)CO(2), we found that members of the Bacteria and not Archaea were the functionally dominant autotrophic ammonia oxidizers at all temperatures under relatively high ammonium loads. The copy numbers of bacterial amoA genes in (13)C-labeled DNA were lower at 30°C than at 13°C in both stream enrichment cultures. However, the community composition of the ammonia-oxidizing bacteria (AOB) in the (13)C-labeled DNA responded differently to temperature manipulation at two ammonium concentrations. In LS enrichments incubated at the in situ temperature (13°C), Nitrosomonas oligotropha-like sequences were retrieved with sequences from Nitrosospira AmoA cluster 4, while the proportion of Nitrosospira sequences increased at higher temperatures. In AS enrichments incubated at 13°C and 20°C, AmoA cluster 4 sequences were dominant; Nitrosomonas nitrosa-like sequences dominated at 30°C. Biofilm-associated AOB communities were affected differentially by temperature at two relatively high ammonium concentrations, implicating them in a potential role in governing contaminated freshwater AOB distributions.
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154
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Daims H, Wagner M. In situ techniques and digital image analysis methods for quantifying spatial localization patterns of nitrifiers and other microorganisms in biofilm and flocs. Methods Enzymol 2011; 496:185-215. [PMID: 21514465 DOI: 10.1016/b978-0-12-386489-5.00008-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The spatial localization patterns of microorganisms in multispecies biofilms reflect numerous phenomena that influence sessile microbial life, such as substrate concentration gradients within the biofilm and biological interactions with other biofilm populations. Quantitative and population-specific in situ analyses of spatial patterns have a high potential to provide novel insights into the biology of biofilm organisms, including yet uncultured microbes, but such approaches have been developed and used in a few studies only. Here, we outline digital image analysis methods to quantify the coaggregation, mutual avoidance, or random distribution of microbial populations in biofilm and flocs. A protocol is provided for fluorescence in situ hybridization with rRNA-targeted probes, which preserves the three-dimensional biofilm architecture for confocal microscopy and image analysis, and the combined use of these approaches is demonstrated by spatial analyses of nitrifying bacteria in complex biofilm samples.
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Affiliation(s)
- Holger Daims
- Department of Microbial Ecology, Ecology Center, University of Vienna, Vienna, Austria
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155
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Cold temperature decreases bacterial species richness in nitrogen-removing bioreactors treating inorganic mine waters. Biotechnol Bioeng 2011; 108:2876-83. [DOI: 10.1002/bit.23267] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/29/2011] [Accepted: 07/05/2011] [Indexed: 11/07/2022]
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156
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Cherobaeva AS, Kizilova AK, Stepanov AL, Kravchenko IK. Molecular analysis of the diversity of nitrifying bacteria in the soils of the forest and steppe zones of European Russia. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711030064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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157
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Dhanasiri A, Kiron V, Fernandes J, Bergh Ø, Powell M. Novel application of nitrifying bacterial consortia to ease ammonia toxicity in ornamental fish transport units: trials with zebrafish. J Appl Microbiol 2011; 111:278-92. [DOI: 10.1111/j.1365-2672.2011.05050.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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158
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Zhang R, Jin R, Liu G, Zhou J, Li CL. Study on nitrogen removal performance of sequencing batch reactor enhanced by low intensity ultrasound. BIORESOURCE TECHNOLOGY 2011; 102:5717-5721. [PMID: 21440436 DOI: 10.1016/j.biortech.2011.02.112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/25/2011] [Accepted: 02/26/2011] [Indexed: 05/30/2023]
Abstract
Sequencing batch reactor (SBR) was widely used in the treatment of various wastewater. The effects of low intensity ultrasound on the nitrogen removal performance of SBR were studied. The optimum operation conditions were determined to be 35 kHz, 0.15 W cm(-2), and irradiation time of 10 min. Compared with those of the control reactor, the organic, NH(4)(+)-N, NO(2)(-)-N and NO(3)(-)-N loads of the ultrasound enhanced reactor (UER) were improved by 16.5%, 35.0%, 41.7% and 61.9%, respectively. Increased 2,3,5-triphenyl tetrazolium chloride-dehydrogenase and nitrification activities were observed with sludge in UER. Furthermore, negligible negative effects of ultrasound irradiation on the settle ability and sludge concentration were found, which resulted in no decrease of the nitrogen removal performance of the UER.
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Affiliation(s)
- Ruina Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
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159
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Pellitteri-Hahn MC, Halligan BD, Scalf M, Smith L, Hickey WJ. Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells. J Proteomics 2011; 74:411-9. [DOI: 10.1016/j.jprot.2010.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 11/01/2010] [Accepted: 12/10/2010] [Indexed: 01/05/2023]
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160
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Auguet JC, Nomokonova N, Camarero L, Casamayor EO. Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes. Appl Environ Microbiol 2011; 77:1937-45. [PMID: 21239556 PMCID: PMC3067326 DOI: 10.1128/aem.01213-10] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 01/03/2011] [Indexed: 02/01/2023] Open
Abstract
The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ± 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.
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Affiliation(s)
- Jean-Christophe Auguet
- Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc 14, E-17300, Blanes, Spain.
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161
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Abstract
The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by (13)CO(2) after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the (13)C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the (13)C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that (13)CO(2) assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested.
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162
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Koper TE, Stark JM, Habteselassie MY, Norton JM. Nitrification exhibits Haldane kinetics in an agricultural soil treated with ammonium sulfate or dairy-waste compost. FEMS Microbiol Ecol 2011; 74:316-22. [PMID: 21039648 DOI: 10.1111/j.1574-6941.2010.00960.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
An agricultural soil was treated with dairy-waste compost, ammonium-sulfate fertilizer or no added nitrogen (control) and planted to silage corn for 6 years. The kinetics of nitrification were determined in laboratory-shaken slurry assays with a range of substrate concentrations (0-20 mM NH(4)(+)) over a 24-h period for soils from the three treatments. Determined concentrations of substrate and product were fit to Michaelis-Menten and Haldane models. For all the treatments, the Haldane model was a better fit, suggesting that significant nitrification inhibition may occur in soils under high ammonium conditions similar to those found immediately after fertilization or waste applications. The maximum rate of nitrification (V(max)) was significantly higher for the fertilized and compost-treated soils (1.74 and 1.50 mmol N kg(-1) soil day(-1)) vs. control soil (0.98 mmol kg(-1) soil day(-1)). The K(m) and K(i) values were not significantly different, with average values of 0.02 and 27 mM NH(4)(+), respectively. Our results suggest that both N sources increased nitrifier community size, but did not shift the nitrifier community structure in ways that influenced enzyme affinity or sensitivity to ammonium. The K(m) values are comparable to those determined directly in other soils, but are substantially lower than those from most pure cultures of ammonia-oxidizing bacteria.
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Affiliation(s)
- Teresa E Koper
- Department of Biology, Utah State University, Logan, UT 84322-4820, USA
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163
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Rodríguez DC, Pino N, Peñuela G. Monitoring the removal of nitrogen by applying a nitrification-denitrification process in a Sequencing Batch Reactor (SBR). BIORESOURCE TECHNOLOGY 2011; 102:2316-2321. [PMID: 21075619 DOI: 10.1016/j.biortech.2010.10.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/15/2010] [Accepted: 10/20/2010] [Indexed: 05/30/2023]
Abstract
In this study the evaluation of nitrogen removal in wastewater from a meat products processing company was performed, using a Sequencing Batch Reactor (SBR) at pilot scale. The phases of the SBR operation were: filling, reaction (aeration and intermittent anoxia), sedimentation and discharge. In each of these phases analyses of ammonium (NH(4)(+)), nitrite (NO(2)(-)), nitrate (NO(3)(-)), pH and dissolved oxygen (DO) were carried out to monitor the process of nitrification-denitrification. The results showed that stage IV had the best performance (2.49 g COD(F)/Ld and 1.02 g NH(4)(+)-N/Ld) with a NH(4)(+)-N removal of 71%. The transformation of much of the NH(4)(+)-N to gaseous nitrogen was confirmed, with the concentration of NO(2)(-)-N and NO(3)(-)-N increasing during the reaction phase but decreasing in the effluent due to its transformation to gaseous nitrogen.
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Affiliation(s)
- Diana Catalina Rodríguez
- University of Antioquia, Laboratory Diagnostics and Pollution Control (GDCON), Medellin, Colombia.
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164
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Nguyen MD, Risgaard-Petersen N, Sørensen J, Brandt KK. Rapid and sensitive Nitrosomonas europaea biosensor assay for quantification of bioavailable ammonium sensu strictu in soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:1048-1054. [PMID: 21174468 DOI: 10.1021/es1030036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Knowledge on bioavailable ammonium sensu strictu (i.e., immediately available for cellular uptake) in soil is required to understand nutrient uptake processes in microorganisms and thus of vital importance for plant production. We here present a novel ammonium biosensor approach based on the lithoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea transformed with a luxAB sensor plasmid. Bioluminescence-based ammonium detection was achieved within 10 min with a quantification limit in liquid samples of ∼20 μM and a linear response range up to 400 μM. Biosensor and conventional chemical quantification of ammonium in soil solutions agreed well across a range of sample and assay conditions. The biosensor was subsequently applied for a solid phase-contact assay allowing for direct interaction of biosensor cells with soil particle-associated (i.e., exchangeable plus fixed) ammonium. The assay successfully quantified bioavailable ammonium even in unfertilized soil and demonstrated markedly higher ratios of bioavailable ammonium to water- or 2 M KCl-exchangeable ammonium in anoxic soil than in corresponding oxic soil. Particle-associated ammonium contributed by at least 74% and 93% of the total bioavailable pool in oxic and anoxic soil, respectively. The N. europaea biosensor should have broad relevance for environmental monitoring of bioavailable ammonium and processes depending on ammonium bioavailability.
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Affiliation(s)
- Minh Dong Nguyen
- Department of Agriculture and Ecology, Faculty of Life Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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165
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Ammonium availability affects the ratio of ammonia-oxidizing bacteria to ammonia-oxidizing archaea in simulated creek ecosystems. Appl Environ Microbiol 2011; 77:1896-9. [PMID: 21239545 DOI: 10.1128/aem.02879-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ammonia-oxidizing microbial community colonizing clay tiles in flow channels changed in favor of ammonia-oxidizing bacteria during a 12-week incubation period even at originally high ratios of ammonia-oxidizing archaea to ammonia-oxidizing bacteria (AOB). AOB predominance was established more rapidly in flow channels incubated at 350 μM NH(4)(+) than in those incubated at 50 or 20 μM NH(4)(+). Biofilm-associated potential nitrification activity was first detected after 28 days and was positively correlated with bacterial but not archaeal amoA gene copy numbers.
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166
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Campbell MA, Chain PSG, Dang H, El Sheikh AF, Norton JM, Ward NL, Ward BB, Klotz MG. Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'. FEMS Microbiol Ecol 2011; 76:39-48. [PMID: 21204874 DOI: 10.1111/j.1574-6941.2010.01027.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Local associations between anammox bacteria and obligate aerobic bacteria in the genus Nitrosococcus appear to be significant for ammonia oxidation in oxygen minimum zones. The literature on the genus Nitrosococcus in the Chromatiaceae family of purple sulfur bacteria (Gammaproteobacteria, Chromatiales) contains reports on four described species, Nitrosococcus nitrosus, Nitrosococcus oceani, 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis', of which only N. nitrosus and N. oceani are validly published names and only N. oceani is omnipresent in the world's oceans. The species 'N. halophilus' with Nc4(T) as the type strain was proposed in 1990, but the species is not validly published. Phylogenetic analyses of signature genes, growth-physiological studies and an average nucleotide identity analysis between N. oceani ATCC19707(T) (C-107, Nc9), 'N. halophilus' strain Nc4(T) and Nitrosococcus sp. strain C-113 revealed that a proposal for a new species is warranted. Therefore, the provisional taxonomic assignment Nitrosococcus watsonii is proposed for Nitrosococcus sp. strain C-113(T) . Sequence analysis of Nitrosococcus haoAB signature genes detected in cultures enriched from Jiaozhou Bay sediments (China) identified only N. oceani-type sequences, suggesting that different patterns of distribution in the environment correlate with speciation in the genus Nitrosococcus.
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Affiliation(s)
- Mark A Campbell
- Evolutionary and Genomic Microbiology Laboratory, Department of Biology, University of Louisville, Louisville, KY 40292, USA
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167
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Bae H, Park JH, Jun KS, Jung JY. The community analysis of ammonia-oxidizing bacteria in wastewater treatment plants revealed by the combination of double labeled T-RFLP and sequencing. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2011; 46:345-354. [PMID: 21337248 DOI: 10.1080/10934529.2011.542384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The functional gene of amoA, which produces the α-subunit of ammonia monooxygenase (AMO), has been analyzed to reveal the microbial community structure of ammonia-oxidizing bacteria (AOB) by culture-independent methods. In this study, the distribution of the amoA gene in 10 wastewater treatment plants (WWTPs) was revealed by the fingerprinting method of terminal restriction fragment length polymorphism (T-RFLP) and comparative sequencing. T-RFLP showed diverse communities of AOB in the modified Ludzack-Ettinger process, in the anaerobic-anoxic-oxic processes, in the hanging biological contactor, and in the sequencing batch reactor. In all of these environments, long solid retention time (SRT) was expected to be the critical factor for maintaining the diverse AOB community structure. Because T-RFLP does not offer sufficient information to confirm the phylogenetic information of AOB, the microbial community structures were analyzed by comparative sequencing for seven samples that were selected by the statistical categorization using principal component analysis (PCA) among 14 samples. The phylogenetic tree of 21 operational taxonomic units (OTUs) among 88 clones obtained in this study revealed that AOB of Nitrosomonas oligotropha and europaea lineages were predominant in WWTPs. Double labeled T-RFLP produced group-specific terminal restriction fragments (T-RFs) representing several groups of AOB and offered advanced resolution comparing with the single labeled T-RFLP.
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Affiliation(s)
- Hyokwan Bae
- Environment Division, Korea Institute of Science and Technology, Sungbuk-Gu, Seoul, Republic of Korea
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168
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Wan CY, De Wever H, Diels L, Thoeye C, Liang JB, Huang LN. Biodiversity and population dynamics of microorganisms in a full-scale membrane bioreactor for municipal wastewater treatment. WATER RESEARCH 2011; 45:1129-1138. [PMID: 21112606 DOI: 10.1016/j.watres.2010.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 09/30/2010] [Accepted: 11/04/2010] [Indexed: 05/27/2023]
Abstract
The total, ammonia-oxidizing, and denitrifying Bacteria in a full-scale membrane bioreactor (MBR) were evaluated monthly for over one year. Microbial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the 16S rRNA and ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes. The community fingerprints obtained were compared to those from a conventional activated sludge (CAS) process running in parallel treating the same domestic wastewater. Distinct DGGE profiles for all three molecular markers were observed between the two treatment systems, indicating the selection of specific bacterial populations by the contrasting environmental and operational conditions. Comparative 16S rRNA sequencing indicated a diverse bacterial community in the MBR, with phylotypes from the α- and β-Proteobacteria and Bacteroidetes dominating the gene library. The vast majority of sequences retrieved were not closely related to classified organisms or displayed relatively low levels of similarity with any known 16S rRNA gene sequences and thus represent organisms that constitute new taxa. Similarly, the majority of the recovered nosZ sequences were novel and only moderately related to known denitrifiers from the α- and β-Proteobacteria. In contrast, analysis of the amoA gene showed a remarkably simple ammonia-oxidizing community with the detected members almost exclusively affiliated with the Nitrosomonas oligotropha lineage. Major shifts in total bacteria and denitrifying community were detected and these were associated with change in the external carbon added for denitrification enhancement. In spite of this, the MBR was able to maintain a stable process performance during that period. These results significantly expand our knowledge of the biodiversity and population dynamics of microorganisms in MBRs for wastewater treatment.
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Affiliation(s)
- Cai-Yun Wan
- Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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169
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Bouskill NJ, Eveillard D, O'Mullan G, Jackson GA, Ward BB. Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure. Environ Microbiol 2010; 13:872-86. [PMID: 21054735 DOI: 10.1111/j.1462-2920.2010.02362.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Microbes exhibit remarkably high genetic diversity compared with plant and animal species. Many phylogenetically diverse but apparently functionally redundant microbial taxa are detectable within a cubic centimetre of mud or a millilitre of water, and the significance of this diversity, in terms of ecosystem function, has been difficult to understand. Thus it is not known whether temporal and spatial differences in microbial community composition are linked to particular environmental factors or might modulate ecosystem response to environmental change. Fifty-three water and sediment samples from upper and lower Chesapeake Bay were analysed in triplicate arrays to determine temporal and spatial patterns and relationships between ammonia-oxidizing bacterial (AOB) communities and environmental variables. Thirty-three water samples (three depths) collected during April, August and October, 2001-2004, from the oligohaline upper region of the Bay were analysed to investigate temporal patterns in archetype distribution. Using a combination of a non-weighted discrimination analysis and principal components analysis of community composition data obtained from functional gene microarrays, it was found that co-varying AOB assemblages reoccurred seasonally in concert with specific environmental conditions, potentially revealing patterns of niche differentiation. Among the most notable patterns were correlations of AOB archetypes with temperature, DON and ammonium concentrations. Different AOB archetypes were more prevalent at certain times of the year, e.g. some were more abundant every autumn and others every spring. This data set documents the successional return to an indigenous community following massive perturbation (hurricane induced flooding) as well as the seasonal reoccurrence of specific lineages, identified by key functional genes, associated with the biogeochemically important process nitrification.
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Affiliation(s)
- Nicholas J Bouskill
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA.
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170
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Wang X, Wen X, Yan H, Ding K, Hu M. Community dynamics of ammonia oxidizing bacteria in a full-scale wastewater treatment system with nitrification stability. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11783-010-0254-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
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171
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Park BJ, Park SJ, Yoon DN, Schouten S, Sinninghe Damsté JS, Rhee SK. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl Environ Microbiol 2010; 76:7575-87. [PMID: 20870784 PMCID: PMC2976178 DOI: 10.1128/aem.01478-10] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/17/2010] [Indexed: 11/20/2022] Open
Abstract
The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and "Candidatus Nitrosopumilus maritimus" (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [(13)C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.
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MESH Headings
- Ammonia/metabolism
- Archaea/classification
- Archaea/growth & development
- Archaea/isolation & purification
- Archaea/metabolism
- Bacteria/classification
- Bacteria/growth & development
- Bacteria/isolation & purification
- Bacteria/metabolism
- Cluster Analysis
- Coculture Techniques
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Geologic Sediments/microbiology
- Molecular Sequence Data
- Oxidation-Reduction
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sulfur/metabolism
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Affiliation(s)
- Byoung-Joon Park
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Soo-Je Park
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Dae-No Yoon
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Stefan Schouten
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju 361-763, South Korea, Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Netherlands
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172
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Vlaeminck SE, Hay AG, Maignien L, Verstraete W. In quest of the nitrogen oxidizing prokaryotes of the early Earth. Environ Microbiol 2010; 13:283-95. [PMID: 21040354 DOI: 10.1111/j.1462-2920.2010.02345.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The introduction of nitrite and nitrate to the relatively reduced environment of the early Earth provided impetus for a tremendous diversification of microbial pathways. However, little is known about the first organisms to produce these valuable resources. In this review, the latest microbial discoveries are integrated in the evolution of the nitrogen cycle according to the great 'NO-ON' time debate, as we call it. This debate hypothesizes the first oxidation of nitrogen as abiotic and anoxic ('NO') versus biological and aerobic ('ON'). Confronting ancient biogeochemical niches with extant prokaryotic phylogenetics, physiology and morphology, pointed out that the well-described ammonia and nitrite oxidizing Proteobacteria likely did not play a pioneering role in microbial nitrogen oxidation. Instead, we hypothesize ancestral and primordial roles of methanotrophic NC10 bacteria and ammonia oxidizing archaea, respectively, for early nitrite production, and of anammox performing Planctomycetes followed by Nitrospira for early nitrate production. Additional genomic and structural information on the prokaryotic protagonists but also on their phages, together with the continued search for novel key players and processes, should further elucidate nitrogen cycle evolution. Through the ramifications between the biogeochemical cycles, this will improve our understanding on the evolution of terrestrial and perhaps extraterrestrial life.
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Affiliation(s)
- Siegfried E Vlaeminck
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium.
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173
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Nielsen PH, Mielczarek AT, Kragelund C, Nielsen JL, Saunders AM, Kong Y, Hansen AA, Vollertsen J. A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. WATER RESEARCH 2010; 44:5070-5088. [PMID: 20723961 DOI: 10.1016/j.watres.2010.07.036] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 07/09/2010] [Accepted: 07/13/2010] [Indexed: 05/29/2023]
Abstract
The microbial populations in 25 full-scale activated sludge wastewater treatment plants with enhanced biological phosphorus removal (EBPR plants) have been intensively studied over several years. Most of the important bacterial groups involved in nitrification, denitrification, biological P removal, fermentation, and hydrolysis have been identified and quantified using quantitative culture-independent molecular methods. Surprisingly, a limited number of core species was present in all plants, constituting on average approx. 80% of the entire communities in the plants, showing that the microbial populations in EBPR plants are rather similar and not very diverse, as sometimes suggested. By focusing on these organisms it is possible to make a comprehensive ecosystem model, where many important aspects in relation to microbial ecosystems and wastewater treatment can be investigated. We have reviewed the current knowledge about these microorganisms with focus on key ecophysiological factors and combined this into a conceptual ecosystem model for EBPR plants. It includes the major pathways of carbon flow with specific organic substances, the dominant populations involved in the transformations, interspecies interactions, and the key factors controlling their presence and activity. We believe that the EBPR process is a perfect model system for studies of microbial ecology in water engineering systems and that this conceptual model can be used for proposing and testing theories based on microbial ecosystem theories, for the development of new and improved quantitative ecosystem models and is beneficial for future design and management of wastewater treatment systems.
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Affiliation(s)
- Per Halkjaer Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
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174
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Wu Y, Xiang Y, Wang J, Zhong J, He J, Wu QL. Heterogeneity of archaeal and bacterial ammonia-oxidizing communities in Lake Taihu, China. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:569-576. [PMID: 23766227 DOI: 10.1111/j.1758-2229.2010.00146.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities within the surface sediments of Lake Taihu, a large eutrophic freshwater lake in China, were investigated using molecular approaches targeting the ammonia monooxygenase subunit A (amoA) gene. Large intra-lake variability in the composition and the relative abundance of both groups of ammonia-oxidizing prokaryotes was observed. Archaeal amoA far outnumbered bacterial amoA at most sites except those located in the Eastern Taihu Bay. This bay, which is used for intensive pen aquaculture, harboured the most unique AOA communities but was dominated by AOB in terms of relative abundance. Accumulation of organic substances rather than presence of submersed macrophytes significantly influenced the relative abundance of AOA. In contrast, shifts in the abundance of AOB were not found to be significantly related to the investigated environmental parameters. Phylogenetic analysis showed that all archaeal amoA sequences fell within either the Crenarchaeotal Group (CG) I.1b or the CG I.1a subgroup, and all AOB clustered exclusively with the genus Nitrosomonas. These findings represent the first detailed survey of AOA in eutrophic freshwater lake sediments by demonstrating that AOA dominate the ammonia-oxidizing communities, and are negatively correlated with the accumulation of organic substances.
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Affiliation(s)
- Yucheng Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing 210008, China. Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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175
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Terada A, Lackner S, Kristensen K, Smets BF. Inoculum effects on community composition and nitritation performance of autotrophic nitrifying biofilm reactors with counter-diffusion geometry. Environ Microbiol 2010; 12:2858-72. [PMID: 20545751 DOI: 10.1111/j.1462-2920.2010.02267.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The link between nitritation success in a membrane-aerated biofilm reactor (MABR) and the composition of the initial ammonia- and nitrite-oxidizing bacterial (AOB and NOB) population was investigated. Four identically operated flat-sheet type MABRs were initiated with two different inocula: from an autotrophic nitrifying bioreactor (Inoculum A) or from a municipal wastewater treatment plant (Inoculum B). Higher nitritation efficiencies (NO(2)(-)-N/NH(4)(+)-N) were obtained in the Inoculum B- (55.2-56.4%) versus the Inoculum A- (20.2-22.1%) initiated reactors. The biofilms had similar oxygen penetration depths (100-150 µm), but the AOB profiles [based on 16S rRNA gene targeted real-time quantitative PCR (qPCR)] revealed different peak densities at or distant from the membrane surface in the Inoculum B- versus A-initiated reactors, respectively. Quantitative fluorescence in situ hybridization (FISH) revealed that the predominant AOB in the Inoculum A- and B-initiated reactors were Nitrosospira spp. (48.9-61.2%) versus halophilic and halotolerant Nitrosomonas spp. (54.8-63.7%), respectively. The latter biofilm displayed a higher specific AOB activity than the former biofilm (1.65 fmol cell(-1) h(-1) versus 0.79 fmol cell(-1) h(-1) ). These observations suggest that the AOB and NOB population compositions of the inoculum may determine dominant AOB in the MABR biofilm, which in turn affects the degree of attainable nitritation in an MABR.
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Affiliation(s)
- Akihiko Terada
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
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176
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Chávez-Crooker P, Obreque-Contreras J. Bioremediation of aquaculture wastes. Curr Opin Biotechnol 2010; 21:313-7. [DOI: 10.1016/j.copbio.2010.04.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/31/2010] [Accepted: 04/01/2010] [Indexed: 11/29/2022]
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177
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Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China. Appl Environ Microbiol 2010; 76:4691-702. [PMID: 20511433 DOI: 10.1128/aem.02563-09] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments.
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178
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Transcription levels (amoA mRNA-based) and population dominance (amoA gene-based) of ammonia-oxidizing bacteria. J Ind Microbiol Biotechnol 2010; 37:751-7. [DOI: 10.1007/s10295-010-0728-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 04/16/2010] [Indexed: 10/19/2022]
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179
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Tourna M, Freitag TE, Prosser JI. Stable isotope probing analysis of interactions between ammonia oxidizers. Appl Environ Microbiol 2010; 76:2468-77. [PMID: 20154116 PMCID: PMC2849185 DOI: 10.1128/aem.01964-09] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 02/03/2010] [Indexed: 11/20/2022] Open
Abstract
The response of natural microbial communities to environmental change can be assessed by determining DNA- or RNA-targeted changes in relative abundance of 16S rRNA gene sequences by using fingerprinting techniques such as denaturing gradient gel electrophoresis (DNA-DGGE and RNA-DGGE, respectively) or by stable isotope probing (SIP) of 16S rRNA genes following incubation with a (13)C-labeled substrate (DNA-SIP-DGGE). The sensitivities of these three approaches were compared during batch growth of communities containing two or three Nitrosospira pure or enriched cultures with different tolerances to a high ammonia concentration. Cultures were supplied with low, intermediate, or high initial ammonia concentrations and with (13)C-labeled carbon dioxide. DNA-SIP-DGGE provided the most direct evidence for growth and was the most sensitive, with changes in DGGE profiles evident before changes in DNA- and RNA-DGGE profiles and before detectable increases in nitrite and nitrate production. RNA-DGGE provided intermediate sensitivity. In addition, the three molecular methods were used to follow growth of individual strains within communities. In general, changes in relative activities of individual strains within communities could be predicted from monoculture growth characteristics. Ammonia-tolerant Nitrosospira cluster 3b strains dominated mixed communities at all ammonia concentrations, and ammonia-sensitive strains were outcompeted at an intermediate ammonia concentration. However, coexistence of ammonia-tolerant and ammonia-sensitive strains occurred at the lowest ammonia concentration, and, under some conditions, strains inhibited at high ammonia in monoculture were active at high ammonia in mixed cultures, where they coexisted with ammonia-tolerant strains. The results therefore demonstrate the sensitivity of SIP for detection of activity of organisms with relatively low yield and low activity and its ability to follow changes in the structure of interacting microbial communities.
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Affiliation(s)
- Maria Tourna
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, United Kingdom
| | - Thomas E. Freitag
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, United Kingdom
| | - James I. Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, United Kingdom
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180
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Barlett MA, Leff LG. The effects of N:P ratio and nitrogen form on four major freshwater bacterial taxa in biofilms. Can J Microbiol 2010; 56:32-43. [PMID: 20130692 DOI: 10.1139/w09-099] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteria in freshwater systems play an important role in nutrient cycling through both assimilatory and dissimilatory processes. Biotic and abiotic components of the environment affect these transformations as does the stoichiometry of the nutrients. We examined responses of four major taxa of bacteria in biofilms subjected to various N:P molar ratios using either nitrate or ammonium as a nitrogen source. Fluorescent in situ hybridization was used to enumerate the Domain bacteria as well as the alpha-, beta-, and gamma-proteobacteria, and the Cytophaga-Flavobacteria cluster. Generally, bacterial responses to the treatments were limited. However, the Cytophaga-Flavobacteria and beta-proteobacteria both responded more to the ammonium additions than nitrate, whereas, the alpha-proteobacteria responded more to nitrate additions. The beta-proteobacteria also exhibited peak relative abundance at the highest N:P ratio. Nutrient concentrations were significantly different after the incubation period, and there were distinct changes in the stoichiometry of the microcosms with ammonium. We demonstrated that bacteria may play an important role in nutrient uptake, and transformation, and can have a dramatic effect on the nutrient stoichiometry of the surrounding water. However, although some taxa exhibited differences in response to ammonium and nitrate, the impact of nutrient stoichiometry on the abundance of the taxa examined was limited.
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Affiliation(s)
- Melissa A Barlett
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.
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181
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Lage MD, Reed HE, Weihe C, Crain CM, Martiny JBH. Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments. ISME JOURNAL 2010; 4:933-44. [DOI: 10.1038/ismej.2010.10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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182
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Zhu G, Jetten MSM, Kuschk P, Ettwig KF, Yin C. Potential roles of anaerobic ammonium and methane oxidation in the nitrogen cycle of wetland ecosystems. Appl Microbiol Biotechnol 2010; 86:1043-55. [PMID: 20195861 DOI: 10.1007/s00253-010-2451-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/13/2010] [Accepted: 01/13/2010] [Indexed: 11/26/2022]
Abstract
Anaerobic ammonium oxidation (anammox) and anaerobic methane oxidation (ANME coupled to denitrification) with nitrite as electron acceptor are two of the most recent discoveries in the microbial nitrogen cycle. Currently the anammox process has been relatively well investigated in a number of natural and man-made ecosystems, while ANME coupled to denitrification has only been observed in a limited number of freshwater ecosystems. The ubiquitous presence of anammox bacteria in marine ecosystems has changed our knowledge of the global nitrogen cycle. Up to 50% of N(2) production in marine sediments and oxygen-depleted zones may be attributed to anammox bacteria. However, there are only few indications of anammox in natural and constructed freshwater wetlands. In this paper, the potential role of anammox and denitrifying methanotrophic bacteria in natural and artificial wetlands is discussed in relation to global warming. The focus of the review is to explore and analyze if suitable environmental conditions exist for anammox and denitrifying methanotrophic bacteria in nitrogen-rich freshwater wetlands.
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Affiliation(s)
- Guibing Zhu
- State Key Laboratory of Environmental Aquatic Quality, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China.
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183
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Attard E, Poly F, Commeaux C, Laurent F, Terada A, Smets BF, Recous S, Roux XL. Shifts betweenNitrospira- andNitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices. Environ Microbiol 2010; 12:315-26. [DOI: 10.1111/j.1462-2920.2009.02070.x] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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184
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Woznica A, Nowak A, Beimfohr C, Karczewski J, Bernas T. Monitoring structure and activity of nitrifying bacterial biofilm in an automatic biodetector of water toxicity. CHEMOSPHERE 2010; 78:1121-1128. [PMID: 20096440 DOI: 10.1016/j.chemosphere.2009.12.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 12/11/2009] [Accepted: 12/14/2009] [Indexed: 05/28/2023]
Abstract
Automatic biodetector of water toxicity is a biosensor based on monitoring of catalytic activity of the nitrifying bacteria. To create a standardized biosensing system, development of the biofilm must be characterized to determine the prerequisites for its biological (biocatalytic) stability. In this paper, growth of biofilm comprising ammonium-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the open cellular polyurethane material polyurethane sponge bioreactor has been investigated. Dynamics of the biofilm formation was estimated using AOB and NOB metabolic activity and the volume occupied by these two types of bacteria in the biofilm. Spectrophotometry liquid ion chromatography and image cytometry were used, respectively, for these measurements. A mathematical model of the dynamics of biofilm formation was established. These data indicate that open cellular polyurethane material is a good basis for the immobilization of nitrifying bacteria. Moreover, growth of the biofilm leads to its stable structural form, whose biocatalytic activity (12.29 for AOB and 6.84 micromol min(-1) for NOB) is constant in the long term.
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Affiliation(s)
- Andrzej Woznica
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland.
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185
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Yasuda T, Kuroda K, Hanajima D, Fukumoto Y, Waki M, Suzuki K. Characteristics of the Microbial Community Associated with Ammonia Oxidation in a Full-Scale Rockwool Biofilter Treating Malodors from Livestock Manure Composting. Microbes Environ 2010; 25:111-9. [DOI: 10.1264/jsme2.me09175] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tomoko Yasuda
- National Institute of Livestock and Grassland Science, Pollution Control Research Team
| | - Kazutaka Kuroda
- National Institute of Livestock and Grassland Science, Pollution Control Research Team
| | - Dai Hanajima
- National Institute of Livestock and Grassland Science, Pollution Control Research Team
| | - Yasuyuki Fukumoto
- National Institute of Livestock and Grassland Science, Pollution Control Research Team
| | - Miyoko Waki
- National Institute of Livestock and Grassland Science, Pollution Control Research Team
| | - Kazuyoshi Suzuki
- National Institute of Livestock and Grassland Science, Pollution Control Research Team
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186
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Lay WCL, Liu Y, Fane AG. Impacts of salinity on the performance of high retention membrane bioreactors for water reclamation: A review. WATER RESEARCH 2010; 44:21-40. [PMID: 19815249 DOI: 10.1016/j.watres.2009.09.026] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 07/02/2009] [Accepted: 09/10/2009] [Indexed: 05/28/2023]
Abstract
Recent efforts in the field of used water treatment and water reclamation have led to the development of a number of innovative high retention membrane bioreactor (HRMBR) systems. These systems invariably combine a high rejection membrane separation with a biological treatment. A common positive outcome of these systems is that smaller size organic contaminants are effectively retained, which facilitates their biodegradation and thus produces high quality product water. This provides the desired high level of separation, but also leads to salt accumulation with potentially adverse effects on the operations. The effects of elevated salt condition are complex, and impact on aspects covering physicochemical parameters, microbiology and membrane performance. The salt concentration factor is an important operating parameter to be optimised in the HRMBR systems. This paper aims to elucidate the important issues associated with the use of HRMBR systems under elevated salt conditions up to 50gL(-1).
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Affiliation(s)
- Winson C L Lay
- Singapore Membrane Technology Centre, Nanyang Technological University, Singapore 637723, Singapore
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187
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Matsumoto S, Ishikawa D, Saeki G, Aoi Y, Tsuneda S. Microbial Population Dynamics and Community Structure during the Formation of Nitrifying Granules to Treat Ammonia-Rich Inorganic Wastewater. Microbes Environ 2010; 25:164-70. [DOI: 10.1264/jsme2.me10107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shinya Matsumoto
- Department of Life Science and Medical Bioscience, Waseda University
| | - Daisuke Ishikawa
- Department of Life Science and Medical Bioscience, Waseda University
| | - Goro Saeki
- Department of Life Science and Medical Bioscience, Waseda University
| | - Yoshiteru Aoi
- Waseda Institute for Advanced Study, Waseda University
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University
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188
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Wang X, Wen X, Criddle C, Wells G, Zhang J, Zhao Y. Community analysis of ammonia-oxidizing bacteria in activated sludge of eight wastewater treatment systems. J Environ Sci (China) 2010; 22:627-634. [PMID: 20617742 DOI: 10.1016/s1001-0742(09)60155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We investigated the communities of ammonia-oxidizing bacteria (AOB) in activated sludge collected from eight wastewater treatment systems using polymerase chain reaction (PCR) followed by terminal restriction fragment length polymorphism (T-RFLP), cloning, and sequencing of the alpha-subunit of the ammonia monooxygenase gene (amoA). The T-RFLP fingerprint analyses showed that different wastewater treatment systems harbored distinct AOB communities. However, there was no remarkable difference among the AOB T-RFLP profiles from different parts of the same system. The T-RFLP fingerprints showed that a full-scale wastewater treatment plant (WWTP) contained a larger number of dominant AOB species than a pilot-scale reactor. The source of influent affected the AOB community, and the WWTPs treating domestic wastewater contained a higher AOB diversity than those receiving mixed domestic and industrial wastewater. However, the AOB community structure was little affected by the treatment process in this study. Phylogenetic analysis of the cloned amoA genes clearly indicated that all the dominant AOB in the systems was closely related to Nitrosomonas spp. not to Nitrosospira spp. Members of the Nitrosomonas oligotropha and Nitrosomonas communis clusters were found in all samples, while members of Nitrosomonas europaea cluster occurred in some systems.
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Affiliation(s)
- Xiaohui Wang
- Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, China.
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189
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Angel R, Asaf L, Ronen Z, Nejidat A. Nitrogen transformations and diversity of ammonia-oxidizing bacteria in a desert ephemeral stream receiving untreated wastewater. MICROBIAL ECOLOGY 2010; 59:46-58. [PMID: 19593555 DOI: 10.1007/s00248-009-9555-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2009] [Accepted: 06/16/2009] [Indexed: 05/28/2023]
Abstract
Levels of inorganic nitrogen species (ammonia, nitrite, and nitrate), ammonia oxidation potential (AOP), and diversity of ammonia-oxidizing bacteria (AOB) were studied in the sediments of a 50-km-long segment of an ephemeral stream in the Negev desert, receiving untreated wastewater. Water analysis in downstream sampling points showed reductions of 91.7% in biological oxygen demand, 87.7% in chemical oxygen demand, 73.9% in total nitrogen, and 72.8% in total ammonia nitrogen. Significant AOP levels in the sediment were detected mainly in the fall and spring seasons. Denaturing gradient gel electrophoresis of AOB 16S rRNA gene fragments showed that in most sampling points, the streambed was dominated by Nitrosospira cluster 3 strains similar to those dominating the stream bank's soils and sediments in nearby springs. Nitrosomonas strains introduced by discharged wastewater and others dominated some sections of the stream characterized by high organic carbon levels. The results suggest that climatic conditions in the Negev desert select for AOB belonging to Nitrosospira cluster 3, and these conditions dominate the aquatic environment effect along most of the stream sections. In addition, the nitrification-denitrification processes were not sufficient to reduce nitrogen levels in the sediment and prevent the eutrophication of some sections of the stream ecosystem. Thus, the discharge of high nitrogen wastewater into desert streams should be done carefully as it may endanger the already fragile ecosystem.
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Affiliation(s)
- Roey Angel
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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190
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Nicolaisen MH, Risgaard-Petersen N, Revsbech NP, Reichardt W, Ramsing NB. Nitrification-denitrification dynamics and community structure of ammonia oxidizing bacteria in a high yield irrigated Philippine rice field. FEMS Microbiol Ecol 2009; 49:359-69. [PMID: 19712286 DOI: 10.1016/j.femsec.2004.04.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is the single most limiting factor for rice production. Detailed knowledge on nitrogen dynamics in rice fields is therefore of major importance for developing sustainable rice production. A combination of state-of-the-art microsensor, stable isotope tracer, and molecular techniques was used to evaluate coupled nitrification-denitrification potentials and community structure of ammonia-oxidizing bacteria in a high yield irrigated rice cropping system in the Philippines, without the use of microcosm incubations. The multiple approaches showed a high degree of concordance among methods and thereby clarified the investigated processes. Numbers and potential activity of ammonia-oxidizing bacteria in the system reflected the availability of substrate in three defined soil factions with a ranking of: surface soil > rhizosphere > bulk soil. No nitrification activity was measured between spit applications of N fertilizer. However, nitrification was induced upon nitrogen amendment in intact soil cores. Despite induction by nitrogen amendment, the loss of nitrogen through coupled nitrification-denitrification was less than 10% of the plant nitrogen uptake. Denaturant gradient gel electrophoresis of amoA fragments revealed no differences in diversity profiles between the soil fractions, and phylogenetic analysis, based on amoA genes retrieved from the rice paddy soil, identified a set of mutually very similar sequences related to Nitrosomonas nitrosa.
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Affiliation(s)
- Mette Haubjerg Nicolaisen
- Department of Microbial Ecology, Institute of Biological Sciences, University of Aarhus, DK-8000 Aarhus C, Denmark.
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191
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Wittebolle L, Verstraete W, Boon N. The inoculum effect on the ammonia-oxidizing bacterial communities in parallel sequential batch reactors. WATER RESEARCH 2009; 43:4149-4158. [PMID: 19596129 DOI: 10.1016/j.watres.2009.06.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 05/14/2009] [Accepted: 06/16/2009] [Indexed: 05/28/2023]
Abstract
Three identical sequential batch reactors (SBRs) were each inoculated with sludge from a full-scale wastewater treatment plant (WWTP) treating a waste stream of different origin, i.e. a hospital, a meat processing company, and a municipal WWTP. The SBRs were run in parallel for 84 consecutive days to investigate whether the reactors would become more phylogenetically similar or stay separated concerning their functionality and microbial communities. Overall, the nitrification functionality was high throughout the experiment, and the size and structure of the sludge flocs were very similar. The total bacterial and ammonia-oxidizing bacterial (AOB) communities were analyzed by PCR-DGGE. Cluster analysis demonstrated very distinct bacterial communities in the three SBRs, not showing any trend becoming more similar. The carrying capacity, dynamics and functional organization of the communities were assessed by DGGE analysis and based on these patterns the range-weighted richness, moving window analysis, and constructing Pareto-Lorenz evenness distribution curves were calculated. Between the SBRs, highly comparable internal structure and dynamics of the AOB communities were observed, although they had only one AOB DGGE band in common. These observations indicate that community characteristics such as the extent of biodiversity and dynamics are more important indicators of good microbial functionality than the presence of certain specific species.
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Affiliation(s)
- Lieven Wittebolle
- Laboratory of Microbial Ecology & Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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192
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Wells GF, Park HD, Yeung CH, Eggleston B, Francis CA, Criddle CS. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ Microbiol 2009; 11:2310-28. [DOI: 10.1111/j.1462-2920.2009.01958.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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193
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Ye W, Liu X, Lin S, Tan J, Pan J, Li D, Yang H. The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiol Ecol 2009; 70:107-20. [PMID: 19744240 DOI: 10.1111/j.1574-6941.2009.00761.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
This study was conducted to characterize the vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu, which underwent a change in trophic status from oligotrophic to hypertrophic in last half of the 20th century. The results revealed that the bacterial communities in different layers of sediment sample were very similar, and were related to Alpha-, Beta-, Gamma- and Deltaproteobacteria, Nitrospira, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chlorobi, Actinobacteria and Acidobacteria. In contrast, the archaeal communities varied greatly with depth. The archaeal communities were primarily related to Euryarchaeota and Crenarchaeota, with methanogenic Archaea accounting for approximately 2-35% of the total Archaea. Additionally, sequences related to putative ammonia-oxidizing Archaea and ammonia-oxidizing Bacteria were detected in different layers of sediment samples. The abundance of Archaea, Bacteria, methanogenic Archaea and Nitrospira was further characterized by real-time PCR.
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Affiliation(s)
- Wenjin Ye
- MOE Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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194
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Diversity and abundance of ammonia-oxidizing bacteria in eutrophic and oligotrophic basins of a shallow Chinese lake (Lake Donghu). Res Microbiol 2009; 160:173-8. [PMID: 19530312 DOI: 10.1016/j.resmic.2009.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Classical cultivation and molecular methods based on the ammonia monooxygenase gene (amoA) were used to study the abundance and diversity of beta-proteobacterial ammonia-oxidizing bacteria (AOB) in lake sediments. The eutrophic and oligotrophic basins of a Chinese shallow lake (Lake Donghu), in terms of ammonium (NH(+)(4)) concentrations, were sampled. The AOB number was significantly lower in the oligotrophic basin, but significantly higher in the eutrophic basin. In addition, using restriction fragment length polymorphism targeting the amoA, ten restriction patterns including six unique ones were found in the eutrophic basin, while five patterns were observed in the oligotrophic basin with only one unique restriction group. Phylogenetic analysis for AOB revealed that Nitrosomonas oligotropha- and Nitrosomonas ureae-related AOB and Nitrosospira-affiliated AOB were ubiquitous; the former dominated in the eutrophic basin (87.2%), while the latter dominated in the oligotrophic basin (65.5%). Furthermore, Nitrosomonas communis-related AOB was only detected in the eutrophic basin, at a small proportion (3.2%). These results indicate significant selection and adaptation of sediment AOB in lakes with differing trophic status.
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195
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Fierer N, Carney KM, Horner-Devine MC, Megonigal JP. The biogeography of ammonia-oxidizing bacterial communities in soil. MICROBIAL ECOLOGY 2009; 58:435-45. [PMID: 19352770 DOI: 10.1007/s00248-009-9517-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 03/21/2009] [Indexed: 05/10/2023]
Abstract
Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.
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Affiliation(s)
- Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
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196
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Fortunato CS, Carlini DB, Ewers E, Bushaw-Newton KL. Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay. Can J Microbiol 2009; 55:333-46. [PMID: 19370077 DOI: 10.1139/w08-124] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Temporal and spatial changes in the molecular operational taxonomic unit (OTU) compositions of bacteria harboring genes for nitrification and denitrification were assessed using denaturing gradient gel electrophoresis (DGGE), clone-based DNA sequencing of selected PCR products, and analyses of ammonium and organic matter concentrations. Sediment, overlying water, and pore-water samples were taken from different vegetated sites of Jug Bay National Estuarine Research Reserve, Maryland, during spring, summer, and fall 2006. OTU richness and the diversities of nitrifiers and denitrifiers were assessed by the presence of bands on DGGE gels, both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were seasonally dependent. AOB OTU richness was highest in the summer when NOB richness was decreased, whereas NOB richness was highest in the spring when AOB richness was decreased. The OTU diversities of nitrifiers did not correlate with ammonium concentrations, organic matter concentrations, or the presence of vegetation. The OTU diversities of denitrifiers possessing either the nirK or nosZ genes were not seasonally dependent but were positively correlated with organic matter content (p = 0.0015, r2 = 0.27; p < 0.0001, r2 = 0.39, respectively). Additionally, the presence of vegetation significantly enhanced nosZ species richness (Wilcoxon/Kruskal-Wallis test, p < 0.008), but this trend was not seen for nirK OTU richness. Banding patterns for nirK OTUs were more similar within sites for each season compared with any of the other genes. Over all seasons, nirK OTU richness was highest and AOB and nosZ OTU richness were lowest (Wilcoxon/Kruskal-Wallis test, p < 0.0001). High levels of sequence divergence among cloned nirK PCR products indicate a broad diversity of nirK homologs in this freshwater estuary.
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Affiliation(s)
- Caroline S Fortunato
- Department of Biology, American University, 4400 Massachusetts Avenue NW, Washington, D.C. 20016, USA
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197
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Cabezas A, Draper P, Etchebehere C. Fluctuation of microbial activities after influent load variations in a full-scale SBR: recovery of the biomass after starvation. Appl Microbiol Biotechnol 2009; 84:1191-202. [DOI: 10.1007/s00253-009-2138-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
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198
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Offre P, Prosser JI, Nicol GW. Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene. FEMS Microbiol Ecol 2009; 70:99-108. [PMID: 19656195 DOI: 10.1111/j.1574-6941.2009.00725.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.
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Affiliation(s)
- Pierre Offre
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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199
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Distribution and rate of microbial processes in an ammonia-loaded air filter biofilm. Appl Environ Microbiol 2009; 75:3705-13. [PMID: 19363071 DOI: 10.1128/aem.02612-08] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The in situ activity and distribution of heterotrophic and nitrifying bacteria and their potential interactions were investigated in a full-scale, two-section, trickling filter designed for biological degradation of volatile organics and NH(3) in ventilation air from pig farms. The filter biofilm was investigated by microsensor analysis, fluorescence in situ hybridization, quantitative PCR, and batch incubation activity measurements. In situ aerobic activity showed a significant decrease through the filter, while the distribution of ammonia-oxidizing bacteria (AOB) was highly skewed toward the filter outlet. Nitrite oxidation was not detected during most of the experimental period, and the AOB activity therefore resulted in NO(2)(-), accumulation, with concentrations often exceeding 100 mM at the filter inlet. The restriction of AOB to the outlet section of the filter was explained by both competition with heterotrophic bacteria for O(2) and inhibition by the protonated form of NO(2)(-), HNO(2). Product inhibition of AOB growth could explain why this type of filter tends to emit air with a rather constant NH(3) concentration irrespective of variations in inlet concentration and airflow.
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200
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Whang LM, Chien IC, Yuan SL, Wu YJ. Nitrifying community structures and nitrification performance of full-scale municipal and swine wastewater treatment plants. CHEMOSPHERE 2009; 75:234-242. [PMID: 19246073 DOI: 10.1016/j.chemosphere.2008.11.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 11/21/2008] [Accepted: 11/24/2008] [Indexed: 05/27/2023]
Abstract
This study evaluated nitrification performance and microbial ecology of nitrifying sludge in two full-scale wastewater treatment plants (WWTPs) including a municipal WWTP treating 20mgNL(-1) of ammonium and a swine WWTP treating 220mgNL(-1) of ammonium. These two plants differed in both wastewater characteristics and operating parameters, such as influent COD, TKN, ammonium, hydraulic retention time, and solids retention time, even though both plants achieve >85% nitrification efficiency. By employing molecular techniques, including terminal restriction fragment length polymorphism, cloning-sequencing and phylogenetic analyses targeting the 16S ribosomal RNA and group specific ammonia-monooxygenase functional gene (amoA), microbial community structures of nitrifying sludge and their significance to nitrification performance were evaluated. The results reveal that for the municipal WWTP Nitrosomonas marina-like AOB (ammonia-oxidizing bacteria) and Nitrospira-like NOB (nitrite-oxidizing bacteria) were the ubiquitously dominant nitrifiers, while Nitrosomonas europaea-, Nitrosomonas oligotropha-, and Nitrosospira-like AOB and Nitrobacter- and Nitrospira-like NOB were the major nitrifying populations found in the swine WWTP. The observed dissimilar nitrifying populations prevailing in these two plants may be related to niche differentiation concerning ammonium concentrations, system operation, and salinity. Moreover, our results suggest that the swine nitrifying sludge, involving relatively diverse AOB and NOB populations that perform the same task but with distinct growth and survival characters, may allow communities to maintain nitrifying capabilities when conditions change such as sudden increases in ammonium concentrations as examined with nitrification kinetic batch tests.
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Affiliation(s)
- Liang-Ming Whang
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC.
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