Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

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Mariusz Cycoń

2015-01-01

Full Text Available The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA and ammonia-oxidizing bacteria (AOB in soil using the denaturing gradient gel electrophoresis (DGGE approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S and the Shannon-Wiener index (H values for soil treated with the field rate (FR dosage of imidacloprid (1 mg/kg soil showed no changes in measured indices for the AOA and AOB community members. In turn, the 10*FR dosage of insecticide (10 mg/kg soil negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4+, known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are linked to the bacterial ammonia oxidizer community.

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Fan, Fenliang; Yang, Qianbao; Li, Zhaojun; Wei, Dan; Cui, Xi'an; Liang, Yongchao

2011-11-01

The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.

Ammonia and nitrite oxidation in the Eastern Tropical North Pacific

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Peng, Xuefeng; Fuchsman, Clara A.; Jayakumar, Amal; Oleynik, Sergey; Martens-Habbena, Willm; Devol, Allan H.; Ward, Bess B.

2015-12-01

Nitrification plays a key role in the marine nitrogen (N) cycle, including in oceanic oxygen minimum zones (OMZs), which are hot spots for denitrification and anaerobic ammonia oxidation (anammox). Recent evidence suggests that nitrification links the source (remineralized organic matter) and sink (denitrification and anammox) of fixed N directly in the steep oxycline in the OMZs. We performed shipboard incubations with 15N tracers to characterize the depth distribution of nitrification in the Eastern Tropical North Pacific (ETNP). Additional experiments were conducted to investigate photoinhibition. Allylthiourea (ATU) was used to distinguish the contribution of archaeal and bacterial ammonia oxidation. The abundance of archaeal and β-proteobacterial ammonia monooxygenase gene subunit A (amoA) was determined by quantitative polymerase chain reaction. The rates of ammonia and nitrite oxidation showed distinct subsurface maxima, with the latter slightly deeper than the former. The ammonia oxidation maximum coincided with the primary nitrite concentration maximum, archaeal amoA gene maximum, and the subsurface nitrous oxide maximum. Negligible rates of ammonia oxidation were found at anoxic depths, where high rates of nitrite oxidation were measured. Archaeal amoA gene abundance was generally 1 to 2 orders of magnitude higher than bacterial amoA gene abundance, and inhibition of ammonia-oxidizing bacteria with 10 μM ATU did not affect ammonia oxidation rates, indicating the dominance of archaea in ammonia oxidation. These results depict highly dynamic activities of ammonia and nitrite oxidation in the oxycline of the ETNP OMZ.

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems

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Juan Ling

2018-01-01

Full Text Available Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA and bacteria (AOB, yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR assays, targeting the ammonia monooxygenase-subunit (amoA genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root at the DNA level (P < 0.05. Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle

Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

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Diallo, MD.

2015-01-01

Full Text Available Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB community composition and nitrogen (N availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. The aim of this study was to determine the influence of leaf litter decomposition on N mineralization. The specific objectives of this study were to evaluate the influence of the litter biochemistry of five plants species (Faidherbia albida A.Chev., Azadirachta indica A.Juss., Casuarina equisetifolia L., Andropogon gayanus Kunth and Eragrostis tremula Hochst. ex Steud. on N mineralization in a tropical ferrous soil (Lixisol, nitrification, and genetic diversity of ammonia-oxidizing bacteria. Denaturing gradient gel electrophoresis (DGGE of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of leaf litter in soils. Method. Community structure of AOB was determined at two time periods: day 0 and day 140. Ten strains were tested and each of these strains produced a single band. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. Plant secondary compounds such as polyphenols are purported to influence nutrient cycling by affecting organic matter degradation, mineralization rates, N availability and humus formation. In a laboratory study, we investigated the influence of six phenolic acids (ferulic, gallic, vanillic, syringic, p-coumaric and p-HBA acids commonly found in the plant residues on N mineralization and NH4+ and NO3- production in soils. Results. The results showed that litter type did affect soil nitrification. Faidherbia albida litter was associated with

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters

KAUST Repository

Bagchi, Samik; Vlaeminck, Siegfried E.; Sauder, Laura A.; Mosquera, Mariela; Neufeld, Josh D.; Boon, Nico; Poulain, Alexandre

2014-01-01

Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters

KAUST Repository

Bagchi, Samik

2014-12-05

Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium

Production of oceanic nitrous oxide by ammonia-oxidizing archaea

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C. R. Löscher

2012-07-01

Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N₂O that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N₂O.

Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the eastern tropical North Atlantic (ETNA and eastern tropical South Pacific (ETSP Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N₂O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N₂O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N₂O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N₂O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N₂O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N₂O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians.

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Erwin, Patrick M; Pineda, Mari Carmen; Webster, Nicole; Turon, Xavier; López-Legentil, Susanna

2014-03-01

Ascidians are ecologically important components of marine ecosystems yet the ascidian microbiota remains largely unexplored beyond a few model species. We used 16S rRNA gene tag pyrosequencing to provide a comprehensive characterization of microbial symbionts in the tunic of 42 Great Barrier Reef ascidian samples representing 25 species. Results revealed high bacterial biodiversity (3 217 unique operational taxonomic units (OTU0.03) from 19 described and 14 candidate phyla) and the widespread occurrence of ammonia-oxidizing Thaumarchaeota in coral reef ascidians (24 of 25 host species). The ascidian microbiota was clearly differentiated from seawater microbial communities and included symbiont lineages shared with other invertebrate hosts as well as unique, ascidian-specific phylotypes. Several rare seawater microbes were markedly enriched (200-700 fold) in the ascidian tunic, suggesting that the rare biosphere of seawater may act as a conduit for horizontal symbiont transfer. However, most OTUs (71%) were rare and specific to single hosts and a significant correlation between host relatedness and symbiont community similarity was detected, indicating a high degree of host-specificity and potential role of vertical transmission in structuring these communities. We hypothesize that the complex ascidian microbiota revealed herein is maintained by the dynamic microenvironments within the ascidian tunic, offering optimal conditions for different metabolic pathways such as ample chemical substrate (ammonia-rich host waste) and physical habitat (high oxygen, low irradiance) for nitrification. Thus, ascidian hosts provide unique and fertile niches for diverse microorganisms and may represent an important and previously unrecognized habitat for nitrite/nitrate regeneration in coral reef ecosystems.

Ammonia- and Nitrite-Oxidizing Bacterial Communities in a Pilot-Scale Chloraminated Drinking Water Distribution System

OpenAIRE

Regan, John M.; Harrington, Gregory W.; Noguera, Daniel R.

2002-01-01

Nitrification in drinking water distribution systems is a common operational problem for many utilities that use chloramines for secondary disinfection. The diversity of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the distribution systems of a pilot-scale chloraminated drinking water treatment system was characterized using terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene (ribosomal DNA [rDNA]) cloning and sequencing. For ammon...

Nitrification of archaeal ammonia oxidizers in a high- temperature hot spring

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Chen, Shun; Peng, Xiaotong; Xu, Hengchao; Ta, Kaiwen

2016-04-01

The oxidation of ammonia by microbes has been shown to occur in diverse natural environments. However, the link of in situ nitrification activity to taxonomic identities of ammonia oxidizers in high-temperature environments remains poorly understood. Here, we studied in situ ammonia oxidation rates and the diversity of ammonia-oxidizing Archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface and bottom sediments were 4.80 and 5.30 nmol N g-1 h-1, respectively. Real-time quantitative polymerase chain reaction (qPCR) indicated that the archaeal 16S rRNA genes and amoA genes were present in the range of 0.128 to 1.96 × 108 and 2.75 to 9.80 × 105 gene copies g-1 sediment, respectively, while bacterial amoA was not detected. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic Candidatus Nitrosocaldus yellowstonii, which represented the most abundant operational taxonomic units (OTU) in both surface and bottom sediments. The archaeal predominance was further supported by fluorescence in situ hybridization (FISH) visualization. The cell-specific rate of ammonia oxidation was estimated to range from 0.410 to 0.790 fmol N archaeal cell-1 h-1, higher than those in the two US Great Basin hot springs. These results suggest the importance of archaeal rather than bacterial ammonia oxidation in driving the nitrogen cycle in terrestrial geothermal environments.

Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

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Ziye eHu

2014-07-01

Full Text Available Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA are much higher than that of ammonia oxidizing bacteria (AOB. The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition.

Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification

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Laverock, B.; Kitidis, V.; Tait, K.; Gilbert, J. A.; Osborn, A. M.; Widdicombe, S.

2013-01-01

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79–97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pHT declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms. PMID:23980243

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

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Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

OpenAIRE

Diallo, M. D.; Guisse, A.; Sall, S. N.; Dick, R. P.; Assigbetsé, Komi; Dieng, A. L.; Chotte, Jean-Luc

2015-01-01

Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB) community composition and nitrogen (N) availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C) and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. T...

The history of aerobic ammonia oxidizers: from the first discoveries to today.

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Monteiro, Maria; Séneca, Joana; Magalhães, Catarina

2014-07-01

Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China.

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Liu, Junjie; Yu, Zhenhua; Yao, Qin; Sui, Yueyu; Shi, Yu; Chu, Haiyan; Tang, Caixian; Franks, Ashley E; Jin, Jian; Liu, Xiaobing; Wang, Guanghua

2018-01-01

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content ( p 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH ( p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community ( p = 0.048), whereas PNR significantly correlated positively with the richness ( p = 0.003), diversity ( p = 0.001) and abundance ( p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when

Substrate type and free ammonia determine bacterial community structure in full-scale mesophilic anaerobic digesters treating cattle or swine manure

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Jiabao eLi

2015-11-01

Full Text Available The microbial-mediated anaerobic digestion (AD process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

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Wang, Baozhan; Zhao, Jun; Guo, Zhiying; Ma, Jing; Xu, Hua; Jia, Zhongjun

2015-01-01

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO3−-N g−1 dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in 13C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of 13CO2 by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the 13C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The 13C-NOB was overwhelmingly

Spatial distribution of archaeal and bacterial ammonia oxidizers in the littoral buffer zone of a nitrogen-rich lake.

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Wang, Yu; Zhu, Guibing; Ye, Lei; Feng, Xiaojuan; Op den Camp, Huub J M; Yin, Chengqing

2012-01-01

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.

Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations.

Science.gov (United States)

Oishi, Ryu; Tada, Chika; Asano, Ryoki; Yamamoto, Nozomi; Suyama, Yoshihisa; Nakai, Yutaka

2012-05-01

A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.

Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

Science.gov (United States)

Yao, Huaiying; Huang, Sha; Qiu, Qiongfen; Li, Yaying; Wu, Lianghuan; Mi, Wenhai; Dai, Feng

2016-08-01

Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

Nitrate Reduction to Nitrite, Nitric Oxide and Ammonia by Gut Bacteria under Physiological Conditions

Science.gov (United States)

Tiso, Mauro; Schechter, Alan N.

2015-01-01

The biological nitrogen cycle involves step-wise reduction of nitrogen oxides to ammonium salts and oxidation of ammonia back to nitrites and nitrates by plants and bacteria. Neither process has been thought to have relevance to mammalian physiology; however in recent years the salivary bacterial reduction of nitrate to nitrite has been recognized as an important metabolic conversion in humans. Several enteric bacteria have also shown the ability of catalytic reduction of nitrate to ammonia via nitrite during dissimilatory respiration; however, the importance of this pathway in bacterial species colonizing the human intestine has been little studied. We measured nitrite, nitric oxide (NO) and ammonia formation in cultures of Escherichia coli, Lactobacillus and Bifidobacterium species grown at different sodium nitrate concentrations and oxygen levels. We found that the presence of 5 mM nitrate provided a growth benefit and induced both nitrite and ammonia generation in E.coli and L.plantarum bacteria grown at oxygen concentrations compatible with the content in the gastrointestinal tract. Nitrite and ammonia accumulated in the growth medium when at least 2.5 mM nitrate was present. Time-course curves suggest that nitrate is first converted to nitrite and subsequently to ammonia. Strains of L.rhamnosus, L.acidophilus and B.longum infantis grown with nitrate produced minor changes in nitrite or ammonia levels in the cultures. However, when supplied with exogenous nitrite, NO gas was readily produced independently of added nitrate. Bacterial production of lactic acid causes medium acidification that in turn generates NO by non-enzymatic nitrite reduction. In contrast, nitrite was converted to NO by E.coli cultures even at neutral pH. We suggest that the bacterial nitrate reduction to ammonia, as well as the related NO formation in the gut, could be an important aspect of the overall mammalian nitrate/nitrite/NO metabolism and is yet another way in which the microbiome

Nitrate reduction to nitrite, nitric oxide and ammonia by gut bacteria under physiological conditions.

Directory of Open Access Journals (Sweden)

Mauro Tiso

Full Text Available The biological nitrogen cycle involves step-wise reduction of nitrogen oxides to ammonium salts and oxidation of ammonia back to nitrites and nitrates by plants and bacteria. Neither process has been thought to have relevance to mammalian physiology; however in recent years the salivary bacterial reduction of nitrate to nitrite has been recognized as an important metabolic conversion in humans. Several enteric bacteria have also shown the ability of catalytic reduction of nitrate to ammonia via nitrite during dissimilatory respiration; however, the importance of this pathway in bacterial species colonizing the human intestine has been little studied. We measured nitrite, nitric oxide (NO and ammonia formation in cultures of Escherichia coli, Lactobacillus and Bifidobacterium species grown at different sodium nitrate concentrations and oxygen levels. We found that the presence of 5 mM nitrate provided a growth benefit and induced both nitrite and ammonia generation in E.coli and L.plantarum bacteria grown at oxygen concentrations compatible with the content in the gastrointestinal tract. Nitrite and ammonia accumulated in the growth medium when at least 2.5 mM nitrate was present. Time-course curves suggest that nitrate is first converted to nitrite and subsequently to ammonia. Strains of L.rhamnosus, L.acidophilus and B.longum infantis grown with nitrate produced minor changes in nitrite or ammonia levels in the cultures. However, when supplied with exogenous nitrite, NO gas was readily produced independently of added nitrate. Bacterial production of lactic acid causes medium acidification that in turn generates NO by non-enzymatic nitrite reduction. In contrast, nitrite was converted to NO by E.coli cultures even at neutral pH. We suggest that the bacterial nitrate reduction to ammonia, as well as the related NO formation in the gut, could be an important aspect of the overall mammalian nitrate/nitrite/NO metabolism and is yet another way in

Determination of Ammonia Oxidizing Bacteria and Nitrate Oxidizing Bacteria in Wastewater and Bioreactors

Science.gov (United States)

Francis, Somilez Asya

2014-01-01

The process of water purification has many different physical, chemical, and biological processes. One part of the biological process is the task of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). Both play critical roles in the treatment of wastewater by oxidizing toxic compounds. The broad term is nitrification, a naturally occurring process that is carried out by AOB and NOB by using oxidation to convert ammonia to nitrite and nitrite to nitrate. To monitor this biological activity, bacterial staining was performed on wastewater contained in inoculum tanks and biofilm samples from bioreactors. Using microscopy and qPCR, the purpose of this experiment was to determine if the population of AOB and NOB in wastewater and membrane bioreactors changed depending on temperature and hibernation conditions to determine the optimal parameters for AOB/NOB culture to effectively clean wastewater.

Diversity, abundance and niche differentiation of ammonia-oxidizing prokaryotes in mud deposits of the eastern China marginal seas

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Shaolan eYu

2016-02-01

Full Text Available The eastern China marginal seas are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA and bacteria (AOB were investigated in mud deposits of the South Yellow Sea (SYS and the East China Sea (ECS by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia and silicate (SiO32-, was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ15NTN and SiO32-, and nitrate and δ13C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO32-. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.

Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas.

Science.gov (United States)

Yu, Shaolan; Yao, Peng; Liu, Jiwen; Zhao, Bin; Zhang, Guiling; Zhao, Meixun; Yu, Zhigang; Zhang, Xiao-Hua

2016-01-01

The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO[Formula: see text]), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ(15)NTN and SiO[Formula: see text], and nitrate and δ(13)C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO[Formula: see text]. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.

Responses of Ammonia-Oxidising Bacterial Communities to Nitrogen, Lime, and Plant Species in Upland Grassland Soil

International Nuclear Information System (INIS)

Rooney, D.C.; Kennedy, N.M.; Clipson, N.J.W.; Rooney, D.C.; Kennedy, N.M.; Gleeson, D.B.

2010-01-01

Agricultural improvement of semi natural grasslands has been shown to result in changes to plant and microbial diversity, with consequences for ecosystem functioning. A microcosm approach was used to elucidate the effects of two key components of agricultural improvement (nitrogen addition and liming) on ammonia-oxidising bacterial (AOB) communities in an upland grassland soil. Plant species characteristic of unimproved and improved pastures (A. capillaries and L. perenne) were planted in microcosms, and lime, nitrogen (NH 4 NO 3 ), or lime plus nitrogen added. The AOB community was profiled using terminal restriction fragment length polymorphism (TRFLP) of the amoA gene. AOB community structure was largely altered by NH 4 NO 3 addition, rather than liming, although interactions between nitrogen addition and plant species were also evident. Results indicate that nitrogen addition drives shifts in the structure of key microbial communities in upland grassland soils, and that plant species may play a significant role in determining AOB community structure

Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil

International Nuclear Information System (INIS)

Okamura, K; Yamada, T; Hiraishi, A; Takanashi, A

2012-01-01

The purpose of this study was to determine the ammonia-oxidizing activity and the phylogentic composition of microorganisms involved in acid tea (Camellia sinensis) orchard soil. All soil samples were collected from three sites located in Tahara and Toyohashi, Aichi Prefecture, Japan. The potential nitrification rate (PNR) was measured by the chlorate inhibition method. The soil pH of tea orchards studied ranged from 2.78 to 4.84, differing significantly from sample to sample, whereas that of meadow and unplanted fields ranged from 5.78 to 6.35. The PNR ranged from 0.050 to 0.193 μg NO 2 - -Ng -1 h -1 and were positively correlated with the soil pH (r 2 0.382, p 2 - -Ng -1 h -1 ) and subjected to PCR-aided clone library analyses targeting archaeal and bacterial amoA genes. The detected archaeal clones separated from the cluster of the 'Soil clones' and tightly clustered with the clones originating from other acidic soil environments including the Chinese tea orchard soil. These results suggest that the specific archaeal populations dominate as the ammonia oxidizers in acid tea-orchard soils and possibly other acid soils, independent of geographic locations, which results from the adaptation to specific ecological niches.

Catalyst for Ammonia Oxidation

DEFF Research Database (Denmark)

2015-01-01

The present invention relates to a bimetallic catalyst for ammonia oxidation, a method for producing a bimetallic catalyst for ammonia oxidation and a method for tuning the catalytic activity of a transition metal. By depositing an overlayer of less catalytic active metal onto a more catalytic...

Do freshwater macrophytes influence the community structure of ammonia-oxidizing and denitrifying bacteria in the rhizospere?

DEFF Research Database (Denmark)

Herrmann, Martina; Schramm, Andreas

2006-01-01

to unvegetated sediment, especially with respect to the availability of oxygen, organic carbon, and inorganic nitrogen. We hypothesize that macrophyte species create specific niches for ammonia oxidizing and nitrate-reducing bacteria in their rhizosphere, leading to plant-dependant differences in abundance...... dortmanna have been shown to release oxygen from their roots and to stimulate nitrification and coupled nitrification-denitrification in the rhizosphere. Together with the excretion of root exudates, this effect leads to strongly modified microenvironments at the root surface and in the rhizosphere compared......-denitrification using the 15N isotope pairing technique. Ammonia-oxidizing and nitrate-reducing populations are analyzed based on the ammonia monooxygenase gene (amoA) and the nitrate reductase gene (narG) as functional markers. Preliminary data indicate that there in fact exist differences in the community composition...

High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.

Directory of Open Access Journals (Sweden)

Guy C J Abell

Full Text Available Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively, combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil

Science.gov (United States)

Okamura, K.; Takanashi, A.; Yamada, T.; Hiraishi, A.

2012-03-01

The purpose of this study was to determine the ammonia-oxidizing activity and the phylogentic composition of microorganisms involved in acid tea (Camellia sinensis) orchard soil. All soil samples were collected from three sites located in Tahara and Toyohashi, Aichi Prefecture, Japan. The potential nitrification rate (PNR) was measured by the chlorate inhibition method. The soil pH of tea orchards studied ranged from 2.78 to 4.84, differing significantly from sample to sample, whereas that of meadow and unplanted fields ranged from 5.78 to 6.35. The PNR ranged from 0.050 to 0.193 μg NO2--Ng-1 h-1 and were positively correlated with the soil pH (r2 = 0.382, p<0.001). Bulk DNA was extracted from a tea orchard soil (pH 4.8; PNR, 0.078 μg NO2--Ng-1 h-1) and subjected to PCR-aided clone library analyses targeting archaeal and bacterial amoA genes. The detected archaeal clones separated from the cluster of the 'Soil clones' and tightly clustered with the clones originating from other acidic soil environments including the Chinese tea orchard soil. These results suggest that the specific archaeal populations dominate as the ammonia oxidizers in acid tea-orchard soils and possibly other acid soils, independent of geographic locations, which results from the adaptation to specific ecological niches.

Adaptation of ammonia-oxidizing microorganisms to environment shift of paddy field soil.

Science.gov (United States)

Ke, Xiubin; Lu, Yahai

2012-04-01

Adaptation of microorganisms to the environment is a central theme in microbial ecology. The objective of this study was to investigate the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to a soil medium shift. We employed two rice field soils collected from Beijing and Hangzhou, China. These soils contained distinct AOB communities dominated by Nitrosomonas in Beijing rice soil and Nitrosospira in Hangzhou rice soil. Three mixtures were generated by mixing equal quantities of Beijing soil and Hangzhou soil (BH), Beijing soil with sterilized Hangzhou soil (BSH), and Hangzhou soil with sterilized Beijing soil (HSB). Pure and mixed soils were permanently flooded, and the surface-layer soil where ammonia oxidation occurred was collected to determine the response of AOB and AOA to the soil medium shift. AOB populations increased during the incubation, and the rates were initially faster in Beijing soil than in Hangzhou soil. Nitrosospira (cluster 3a) and Nitrosomonas (communis cluster) increased with time in correspondence with ammonia oxidation in the Hangzhou and Beijing soils, respectively. The 'BH' mixture exhibited a shift from Nitrosomonas at day 0 to Nitrosospira at days 21 and 60 when ammonia oxidation became most active. In 'HSB' and 'BSH' mixtures, Nitrosospira showed greater stimulation than Nitrosomonas, both with and without N amendment. These results suggest that Nitrosospira spp. were better adapted to soil environment shifts than Nitrosomonas. Analysis of the AOA community revealed that the composition of AOA community was not responsive to the soil environment shifts or to nitrogen amendment. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents

Directory of Open Access Journals (Sweden)

Julien Crovadore

2017-10-01

Full Text Available Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS. For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less costly alternative for the elimination of ammonia, resulting in a reduction of the use of chemicals and energy consumption in sewage plants. This study reached a strong sequencing depth (from 4.4 to 7.6 Gb and enlightened a yet unknown diversity of the microorganisms involved in the nitrogen pathway. Moreover, this approach revealed the abundance and expression levels of specialised enzymes involved in nitrification, denitrification, ammonification, dissimilatory nitrate reduction to ammonium (DNRA and nitrogen fixation processes in AS. Keywords: Applied sciences, Biological sciences, Environmental science, Genetics, Microbiology

Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.

Science.gov (United States)

Hink, Linda; Nicol, Graeme W; Prosser, James I

2017-12-01

Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N 2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N 2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N 2 O production under conditions of high inorganic ammonia (NH 3 ) input, but result mainly from the activity of AOA when NH 3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N 2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N 2 O production. In unamended soils, ammonia oxidation and N 2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N 2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N 2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N 2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N 2 O emissions from fertilised agricultural soils. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Anodic ammonia oxidation to nitrogen gas catalyzed by mixed biofilms in bioelectrochemical systems

International Nuclear Information System (INIS)

Zhan, Guoqiang; Zhang, Lixia; Tao, Yong; Wang, Yujian; Zhu, Xiaoyu; Li, Daping

2014-01-01

In this paper we report ammonia oxidation to nitrogen gas using microbes as biocatalyst on the anode, with polarized electrode (+600 mV vs. Ag/AgCl) as electron acceptor. In batch experiments, the maximal rate of ammonia-N oxidation by the mixed culture was ∼ 60 mg L −1 d −1 , and nitrogen gas was the main products in anode compartment. Cyclic voltammetry for testing the electroactivity of the anodic biofilms revealed that an oxidation peak appeared at +600 mV (vs. Ag/AgCl), whereas the electrode without biofilms didn’t appear oxidation peak, indicating that the bioanode had good electroactivities for ammonia oxidation. Microbial community analysis of 16S rRNA genes based on high throughput sequencing indicated that the combination of the dominant genera of Nitrosomonas, Comamonas and Paracocus could be important for the electron transfer from ammonia oxidation to anode

Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream.

Science.gov (United States)

Nishizawa, Manabu; Sakai, Sanae; Konno, Uta; Nakahara, Nozomi; Takaki, Yoshihiro; Saito, Yumi; Imachi, Hiroyuki; Tasumi, Eiji; Makabe, Akiko; Koba, Keisuke; Takai, Ken

2016-08-01

the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilic Thaumarchaeota and elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

Science.gov (United States)

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

Science.gov (United States)

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

Influence of oxygen partial pressure and salinity on the community composition of ammonia-oxidizing bacteria in the Schelde estuary

NARCIS (Netherlands)

Bollmann, A.; Laanbroek, H.J.

2002-01-01

The influence of environmental factors on the community structure of ammonia-oxidizing bacteria (AOB) was investigated in the Schelde estuary. Simultaneously with the increase of oxygen and salinity, a shift of the dominant AOB was observed. Molecular analysis based on 16S rRNA genes showed that the

Bacterial domination over Archaea in ammonia oxidation in a monsoon-driven tropical estuary

Digital Repository Service at National Institute of Oceanography (India)

Vipindas, P.V.; Anas, A.; Jasmin, C.; Lallu, K.R.; Fausia, K.H.; Balachandran, K.K.; Muraleedharan, K.R.; Nair, S.

Autotrophic ammonia oxidizing microorganisms,which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon...

Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough

Science.gov (United States)

Wang, Long; Yu, Min; Liu, Yan; Liu, Jiwen; Wu, Yonghua; Li, Li; Liu, Jihua; Wang, Min; Zhang, Xiao-Hua

2018-04-01

As an ideal place to study back-arc basins and hydrothermal eco-system, Okinawa Trough has attracted the interests of scientists for decades. However, there are still no in-depth studies targeting the bacterial community of the seafloor sediments and hydrothermal deposits in Okinawa Trough. In the present study, we reported the bacterial community of the surface deposits of a newly found hydrothermal field in the southern Okinawa Trough, and the horizontal and vertical variation of bacterial communities in the sediments of the northern Okinawa Trough. The hydrothermal deposits had a relatively high 16S rRNA gene abundance but low bacterial richness and diversity. Epsilonproteobacteria and Bacteroidetes were predominant in hydrothermal deposits whereas Deltaproteobacteria, Gammaproteobacteria and Chloroflexi were abundant across all samples. The bacterial distribution in the seafloor of Okinawa Trough was significantly correlated to the content of total nitrogen, and had consistent relationship with total carbon. Gradual changes of sulfur-oxidizing bacteria were found with the distance away from hydrothermal fields, while the hydrothermal activity did not influence the distribution of the major clades of sulfate-reducing bacteria. Higher abundance of the sulfur cycle related genes (aprA and dsrB), and lower abundance of the bacterial ammonia-oxidizing related gene (amoA) were quantified in hydrothermal deposits. In addition, the present study also compared the inter-field variation of Epsilonproteobacteria among multi-types of hydrothermal vents, revealing that the proportion and diversity of this clade were quite various.

Reverse-transcriptional gene expression of anammox and ammonia-oxidizing archaea and bacteria in soybean and rice paddy soils of Northeast China.

Science.gov (United States)

Wang, Jing; Dong, Hailiang; Wang, Weidong; Gu, Ji-Dong

2014-03-01

The relative gene expression of hydrazine oxidoreductase encoding gene (hzo) for anaerobic ammonium oxidizing bacteria (anammox) and ammonia monooxygenase encoding gene (amoA) for both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in Sanjiang Plain soybean and rice paddy soils of Northeast China was investigated by using real-time reverse-transcriptional quantitative PCR. Metabolically active populations of anammox, AOA, and AOB in rice paddy soils were evident by the presence and successful quantification of hzo mRNA and amoA mRNA genes. The expression ratio of amoA gene for both AOA and AOB varied between soybean soils and different rice paddy soils while the expression of hzo gene for anammox was detectable only in rice paddy soils by showing a diverse relative expression ratio in each soil sample. Gene expression of both archaeal and bacterial amoA genes in rice paddy soils differed among the three sampling depths, but that of hzo was not. Both archaeal and bacterial amoA genes showed an increase trend of expression level with continuation of rice paddy cultivation, but the low expression ratio of hzo gene indicated a relatively small contribution of anammox in overall removal of inorganic nitrogen through N2 even under anoxic and high nitrogen input in agriculture. Bacterial amoA gene from two soybean fields and three rice paddy fields were also analyzed for community composition by denaturing gradient gel electrophoresis fingerprint. Community shift was observed between soybean and paddy fields and within each of them. The consistent occurrence of three bands 5, 6, and 7 in all samples showed their high adaptability for both arid cultivation and continuous rice paddy cultivation. Our data suggest that AOA and AOB are playing a more important role in nitrogen transformation in agricultural soils in oxic or anoxic environment and anammox bacteria may also contribute but in a less extent to N transformation in these agricultural soils

Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

Science.gov (United States)

Stahl, David A.

2013-01-01

The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2 fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon Nitrosopumilus maritimus SCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above the Km for ammonia oxidation (∼500 μM) and the other well below the Km (ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2 fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment. PMID:23995944

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

NARCIS (Netherlands)

Zhang, Qiufang; Tang, Fang-Yuan; Zhou, Yang-Jing; Xu, Jirong; Chen, Heping; Wang, Ming-Juang; Laanbroek, H.J.

2015-01-01

BACKGROUND: Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface

Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

Directory of Open Access Journals (Sweden)

Vidya eDe Gannes

2012-07-01

Full Text Available Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, coffee hulls, which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase and the finished product (mature phase. The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (groub I.1b, in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have signifcant effects on its performanc as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities with nitrification in these systems.

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.

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Ye, Fei; Ma, Mao-Hua; Op den Camp, Huub J M; Chatzinotas, Antonis; Li, Lei; Lv, Ming-Quan; Wu, Sheng-Jun; Wang, Yu

2018-04-11

Understanding how microorganisms respond to environmental disturbance is one of the key focuses in microbial ecology. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are responsible for ammonia oxidation which is a crucial step in the nitrogen cycle. Although the physiology, distribution, and activity of AOA and AOB in soil have been extensively investigated, their recovery from a natural disturbance remains largely unknown. To assess the recovery capacities, including resistance and resilience, of AOA and AOB, soil samples were taken from a reservoir riparian zone which experienced periodically water flooding. The samples were classified into three groups (flooding, recovery, and control) for a high-throughput sequencing and quantitative PCR analysis. We used a relative quantitative index of both the resistance (RS) and resilience (RL) to assess the variation of gene abundance, alpha-diversity, and community composition. The AOA generally demonstrated a better recovery capability after the flooding disturbance compared to AOB. In particular, AOA were more resilient after the flooding disturbance. Taxa within the AOA and AOB showed different RS and RL values, with the most abundant taxa showing in general the highest RS indices. Soil NH 4 + and Fe 2+ /Fe 3+ were the main variables controlling the key taxa of AOA and AOB and probably influenced the resistance and resilience properties of AOA and AOB communities. The distinct mechanisms of AOA and AOB in maintaining community stability against the flooding disturbance might be linked to the different life-history strategies: the AOA community was more likely to represent r-strategists in contrast to the AOB community following a K-life strategy. Our results indicated that the AOA may play a vital role in ammonia oxidation in a fluctuating habitat and contribute to the stability of riparian ecosystem.

Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea.

Science.gov (United States)

Dodsworth, Jeremy A; Hungate, Bruce A; Hedlund, Brian P

2011-08-01

Many thermophiles catalyse free energy-yielding redox reactions involving nitrogenous compounds; however, little is known about these processes in natural thermal environments. Rates of ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in source water and sediments of two ≈ 80°C springs in the US Great Basin. Ammonia oxidation and denitrification occurred mainly in sediments. Ammonia oxidation rates measured using (15)N-NO(3)(-) pool dilution ranged from 5.5 ± 0.8 to 8.6 ± 0.9 nmol N g(-1) h(-1) and were unaffected or only mildly stimulated by amendment with NH(4) Cl. Denitrification rates measured using acetylene block ranged from 15.8 ± 0.7 to 51 ± 12 nmol N g(-1) h(-1) and were stimulated by amendment with NO(3)(-) and complex organic compounds. The DNRA rate in one spring sediment measured using an (15)N-NO(3)(-) tracer was 315 ± 48 nmol N g(-1) h(-1). Both springs harboured distinct planktonic and sediment microbial communities. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both spring sediments by 16S rRNA gene pyrotag analysis. Quantitative PCR (qPCR) indicated that 'Ca. N. yellowstonii'amoA and 16S rRNA genes were present at 3.5-3.9 × 10(8) and 6.4-9.0 × 10(8) copies g(-1) sediment. Potential denitrifiers included members of the Aquificales and Thermales. Thermus spp. comprised <1% of 16S rRNA gene pyrotags in both sediments and qPCR for T. thermophilus narG revealed sediment populations of 1.3-1.7 × 10(6) copies g(-1) sediment. These data indicate a highly active nitrogen cycle (N-cycle) in these springs and suggest that ammonia oxidation may be a major source of energy fuelling primary production. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.

Science.gov (United States)

Niu, Jia; Kasuga, Ikuro; Kurisu, Futoshi; Furumai, Hiroaki; Shigeeda, Takaaki; Takahashi, Kazuhiko

2016-01-01

Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance.

Hydrothermal oxidation of ammonia/organic waste mixtures

International Nuclear Information System (INIS)

Luan, Li; Proesmans, P.I.; Buelow, S.J.

1997-01-01

Hydrothermal oxidation is a promising new technology for the treatment of radioactive contaminated hazardous organic wastes. Los Alamos National Laboratory is currently evaluating this technology for the U. S. Department of Energy. In this paper, we present experimental results from the study of the hydrothermal oxidation of an ammonia/alcohol/uranium waste mixture. The use of a co-oxidant system consisting of hydrogen peroxide combined with nitrate is discussed. Experiments demonstrate near complete destruction of ammonia and organic compounds at 500 degrees C, 38 MPa, and 50 seconds reaction time. The ammonia and total organic carbon (TOC) concentrations in a waste simulant is reduced from 8,500 mg/L of ammonia and 12,500 mg/L TOC to 30 mg/L ammonia and less than 10 mg/L TOC. The major reaction products are CO 2 , N 2 , and a small amount of N 2 O. Comparison experiments with nitrate and hydrogen peroxide used individually show the advantage of the co-oxidant system

Responses of soil microbial biomass and bacterial community structure to closed-off management (an ecological natural restoration measures): A case study of Dongting Lake wetland, middle China.

Science.gov (United States)

Dai, Juan; Wu, Haipeng; Zhang, Chang; Zeng, Guangming; Liang, Jie; Guo, Shenglian; Li, Xiaodong; Huang, Lu; Lu, Lunhui; Yuan, Yujie

2016-09-01

Soil microbial biomass (SMB) and bacterial community structure, which are critical to global ecosystem and fundamental ecological processes, are sensitive to anthropogenic activities and environmental conditions. In this study, we examined the possible effects of closed-off management (an ecological natural restoration measures, ban on anthropogenic activity, widely employed for many important wetlands) on SMB, soil bacterial community structure and functional marker genes of nitrogen cycling in Dongting Lake wetland. Soil samples were collected from management area (MA) and contrast area (CA: human activities, such as hunting, fishing and draining, are permitted) in November 2013 and April 2014. Soil properties, microbial biomass carbon (MBC), and bacterial community structure were investigated. Comparison of the values of MA and CA showed that SMB and bacterial community diversity of the MA had a significant increase after 7 years closed-off management. The mean value of Shannon-Weiner diversity index of MA and CA respectively were 2.85 and 2.07. The gene copy numbers of 16S rRNA and nosZ of MA were significant higher than those of CA. the gene copy numbers of ammonia-oxidizing archaea (AOA) and nirK of MA were significant lower than those of CA. However, there was no significant change in the gene copy numbers of ammonia-oxidizing bacteria (AOB) and nirS. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting.

Science.gov (United States)

Zeng, Guangming; Zhang, Jiachao; Chen, Yaoning; Yu, Zhen; Yu, Man; Li, Hui; Liu, Zhifeng; Chen, Ming; Lu, Lunhui; Hu, Chunxiao

2011-10-01

The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R²=0.554; Parchaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R²=0.503; P=0.03) especially during the mesophilic and maturation stages. Copyright © 2011 Elsevier Ltd. All rights reserved.

Impact of heavy metal contamination on oxidative stress of Eisenia andrei and bacterial community structure in Tunisian mine soil.

Science.gov (United States)

Boughattas, Iteb; Hattab, Sabrine; Boussetta, Hamadi; Banni, Mohamed; Navarro, Elisabeth

2017-08-01

The aims of this work were firstly to study the effect of heavy metal-polluted soils from Tunisian mine on earthworm biochemical biomarkers and on bacterial communities and therefore to analyze the interaction between earth worms and bacterial communities in these contaminated soils. For this purpose, we had introduced earthworm Eisenia andrei in six soils: one from mine spoils and five from agricultural soils, establishing a gradient of contamination. The response of worms to the presence of heavy metal was analyzed at the biochemical and transcriptional levels. In a second time, the impact of worm on bacterial community structure was investigated using automated ribosomal intergenic spacer analysis (ARISA) fingerprinting. An impact of heavy metal-contaminated soils on the oxidative status of E. andrei was observed, but this effect was dependent of the level of heavy metal contamination. Moreover, our results demonstrate that the introduction of earthworms E. andrei has an impact on bacterial community; however, the major change was observed in the less contaminated site. Furthermore, a significant correlation between earthworm oxidative status biomarkers and bacterial community structure was observed, mainly in the mine spoils. Therefore, we contribute to a better understanding of the relationships between epigenic earthworms and bacterial communities in heavy metal-contaminated soils.

Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

KAUST Repository

Scarascia, Giantommaso

2017-04-04

Background: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. Conclusions: Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.

Bacterial community involved in the nitrogen cycle in a down-flow sponge-based trickling filter treating UASB effluent.

Science.gov (United States)

Mac Conell, E F A; Almeida, P G S; Martins, K E L; Araújo, J C; Chernicharo, C A L

2015-01-01

The bacterial community composition of a down-flow sponge-based trickling filter treating upflow anaerobic sludge blanket (UASB) effluent was investigated by pyrosequencing. Bacterial community composition considerably changed along the reactor and over the operational period. The dominant phyla detected were Proteobacteria, Verrucomicrobia, and Planctomycetes. The abundance of denitrifiers decreased from the top to the bottom and it was consistent with the organic matter concentration gradients. At lower loadings (organic and nitrogen loading rates), the abundance of anammox bacteria was higher than that of the ammonium-oxidizing bacteria in the upper portion of the reactor, suggesting that aerobic and anaerobic ammonium oxidation occurred. Nitrification occurred in all the compartments, while anammox bacteria prominently appeared even in the presence of high organic carbon to ammonia ratios (around 1.0-2.0 gCOD gN(-1)). The results suggest that denitrifiers, nitrifiers, and anammox bacteria coexisted in the reactor; thus, different metabolic pathways were involved in ammonium removal in the post-UASB reactor sponge-based.

Ammonia oxidation driven by archaea rather than bacteria in the hot spring at Tengchong geothermal field, China.

Science.gov (United States)

Chen, Shun; Peng, Xiaotong; Xu, Hengchao; Li, Jiwei; Ta, Kaiwen

2015-04-01

The occurrence of microbial mediated ammonia oxidation and these organisms are present in large numbers in natural environments indicated a potential biogeochemical role for them in the global nitrogen cycle. However, very little is understood about their role and contribution to nitrification in the high temperature extreme environments. Here we explore the ammonia oxidation rates and abundance of potential ammonia-oxidizing archaea (AOA) in upper and bottom sediments from Gongxiaoshe hot spring, Tengchong, Yunnan, China. The 15N-incorporating AOA cells and cell aggregated were detected with Fluorescence in situ hybridization (FISH) and Nano secondary ion mass spectrometry (Nano-SIMS). Ammonia oxidation rates measured using 15N-NO3- pool dilution in upper and bottom sediments (without NH4+ stimulated) were 4.8 and 5.3 nmol N g-1h-1, respectively. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both of the two spring sediments by 16S rRNA gene analysis. Furthermore, it should be noted that no ammonia-oxidizing bacterial clones detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present at 2.75-9.80×105 and 0.128-1.96×108 gene copies g-1 sediment. Based on the reaction rates and AOA abundance, we estimated the cell-specific nitrification rates were 0.41 to 0.79 fmol N archaeal cell-1 h-1, which are comparable to those observed in estuary environment. We suggest that AOA have the responsibility in nitrification in this hot spring, and these archaea rather than bacteria may be considered as a driver in nitrogen cycling in terrestrial hot ecosystems. Key words: ammonia-oxidizing archaea (AOA); nitrification; ammonia-oxidizing rate; hot spring;

Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge.

Science.gov (United States)

Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

2013-07-01

The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes.

Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.

Science.gov (United States)

Martens-Habbena, Willm; Stahl, David A

2011-01-01

The discovery of ammonia-oxidizing mesophilic and thermophilic Group I archaea changed the century-old paradigm that aerobic ammonia oxidation is solely mediated by two small clades of Beta- and Gammaproteobacteria. Group I archaea are extremely diverse and ubiquitous in marine and terrestrial environments, accounting for 20-30% of the microbial plankton in the global oceans. Recent studies indicated that many of these organisms carry putative ammonia monooxygenase genes and are more abundant than ammonia-oxidizing bacteria in most natural environments suggesting a potentially significant role in the nitrogen cycle. The isolation of Nitrosopumilus maritimus strain SCM1 provided the first direct evidence that Group I archaea indeed gain energy from ammonia oxidation. To characterize the physiology of this archaeal nitrifier, we developed a respirometry setup particularly suited for activity measurements in dilute microbial cultures with extremely low oxygen uptake rates. Here, we describe the setup and review the kinetic experiments conducted with N. maritimus and other nitrifying microorganisms. These experiments demonstrated that N. maritimus is adapted to grow on ammonia concentrations found in oligotrophic open ocean environments, far below the survival threshold of ammonia-oxidizing bacteria. The described setup and experimental procedures should facilitate physiological studies on other nitrifying archaea and oligotrophic microorganisms in general. Copyright © 2011 Elsevier Inc. All rights reserved.

Ammonia removal in electrochemical oxidation: Mechanism and pseudo-kinetics

International Nuclear Information System (INIS)

Li Liang; Liu Yan

2009-01-01

This paper investigated the mechanism and pseudo-kinetics for removal of ammonia by electrochemical oxidation with RuO 2 /Ti anode using batch tests. The results show that the ammonia oxidation rates resulted from direct oxidation at electrode-liquid interfaces of the anode by stepwise dehydrogenation, and from indirect oxidation by hydroxyl radicals were so slow that their contribution to ammonia removal was negligible under the condition with Cl - . The oxidation rates of ammonia ranged from 1.0 to 12.3 mg N L -1 h -1 and efficiency reached nearly 100%, primarily due to the indirect oxidation of HOCl, and followed pseudo zero-order kinetics in electrochemical oxidation with Cl - . About 88% ammonia was removed from the solution. The removed one was subsequently found in the form of N 2 in the produced gas. The rate at which Cl - lost electrons at the anode was a major factor in the overall ammonia oxidation. Current density and Cl - concentration affected the constant of the pseudo zero-order kinetics, expressed by k = 0.0024[Cl - ] x j. The ammonia was reduced to less than 0.5 mg N L -1 after 2 h of electrochemical oxidation for the effluent from aerobic or anaerobic reactors which treated municipal wastewater. This result was in line with the strict discharge requirements

Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

OpenAIRE

Nakagawa, Tatsunori; Stahl, David A.

2013-01-01

The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2 fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon Nitrosopu...

Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China.

Directory of Open Access Journals (Sweden)

Yuan Liu

Full Text Available While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg-1. Copy numbers of amoA (AOA and AOB genes were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils.

Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau.

Science.gov (United States)

Zhao, Kang; Kong, Weidong; Khan, Ajmal; Liu, Jinbo; Guo, Guangxia; Muhanmmad, Said; Zhang, Xianzhou; Dong, Xiaobin

2017-09-01

Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.

Immobilization of ammonia-oxidizing bacteria by polyvinyl alcohol and sodium alginate.

Science.gov (United States)

Dong, Yuwei; Zhang, Yanqiu; Tu, Baojun

Ammonia-oxidizing bacteria were immobilized by polyvinyl alcohol (PVA) and sodium alginate. The immobilization conditions and ammonia oxidation ability of the immobilized bacteria were investigated. The following immobilization conditions were observed to be optimal: PVA, 12%; sodium alginate, 1.1%; calcium chloride, 1.0%; inoculum concentration, 1.3 immobilized balls/mL of immobilized medium; pH, 10; and temperature, 30°C. The immobilized ammonia-oxidizing bacteria exhibited strong ammonia oxidation ability even after being recycled four times. The ammonia nitrogen removal rate of the immobilized ammonia-oxidizing bacteria reached 90.30% under the optimal immobilization conditions. When compared with ammonia-oxidizing bacteria immobilized by sodium alginate alone, the bacteria immobilized by PVA and sodium alginate were superior with respect to pH resistance, the number of reuses, material cost, heat resistance, and ammonia oxidation ability. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Impacts of multiwalled carbon nanotubes on nutrient removal from wastewater and bacterial community structure in activated sludge.

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Reti Hai

Full Text Available BACKGROUND: The increasing use of multiwalled carbon nanotubes (MWCNTs will inevitably lead to the exposure of wastewater treatment facilities. However, knowledge of the impacts of MWCNTs on wastewater nutrient removal and bacterial community structure in the activated sludge process is sparse. AIMS: To investigate the effects of MWCNTs on wastewater nutrient removal, and bacterial community structure in activated sludge. METHODS: Three triplicate sequencing batch reactors (SBR were exposed to wastewater which contained 0, 1, and 20 mg/L MWCNTs. MiSeq sequencing was used to investigate the bacterial community structures in activated sludge samples which were exposed to different concentrations of MWCNTs. RESULTS: Exposure to 1 and 20 mg/L MWCNTs had no acute (1 day impact on nutrient removal from wastewater. After long-term (180 days exposure to 1 mg/L MWCNTs, the average total nitrogen (TN removal efficiency was not significantly affected. TN removal efficiency decreased from 84.0% to 71.9% after long-term effects of 20 mg/L MWCNTs. After long-term exposure to 1 and 20 mg/L MWCNTs, the total phosphorus removal efficiencies decreased from 96.8% to 52.3% and from 98.2% to 34.0% respectively. Further study revealed that long-term exposure to 20 mg/L MWCNTs inhibited activities of ammonia monooxygenase and nitrite oxidoreductase. Long-term exposure to 1 and 20 mg/L MWCNTs both inhibited activities of exopolyphosphatase and polyphosphate kinase. MiSeq sequencing data indicated that 20 mg/L MWCNTs significantly decreased the diversity of bacterial community in activated sludge. Long-term exposure to 1 and 20 mg/L MWCNTs differentially decreased the abundance of nitrifying bacteria, especially ammonia-oxidizing bacteria. The abundance of PAOs was decreased after long-term exposure to 20 mg/L MWCNTs. The abundance of glycogen accumulating organisms (GAOs was increased after long-term exposure to 1 mg/L MWCNTs. CONCLUSION: MWCNTs have adverse effects on

Diversity and abundance of ammonia oxidizing archaea in tropical compost systems.

Science.gov (United States)

de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H; Hickey, William J

2012-01-01

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.

Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols

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Wenjie Yang

2017-11-01

Full Text Available Dicyandiamide, a routinely used commercial nitrification inhibitor (NI, inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO. Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO. The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

Science.gov (United States)

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-11-01

Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China.

Directory of Open Access Journals (Sweden)

Yaohui Bai

Full Text Available Bacteria play an important role in the decomposition and cycling of a variety of compounds in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. A unique Chinese eutrophic lake--Dianchi--was selected for study because it has two separate and distinct basins, Caohai with higher organic carbon levels and Waihai with lower organic carbon levels. Sediment bacterial communities were studied in the two basins using samples collected in each season from June 2010 to March 2011. Barcoded pyrosequencing based on the 16 S rRNA gene found that certain common phyla, Proteobacteria, Bacteroidetes, Firmicutes and Chloroflexi, were dominant in the sediments from both basins. However, from the class to genus level, the dominant bacterial groups found in the sediments were distinct between the two basins. Correlation analysis revealed that, among the environmental parameters examined, total organic carbon (TOC accounted for the greatest proportion of variability in bacterial community. Interestingly, study results suggest that increasing allochthonous organic carbon could enhance bacterial diversity and biomass in the sediment. In addition, analysis of function genes (amoA and nosZ demonstrated that ammonia-oxidizing bacteria (AOB were dominant in sediments, with 99% belonging to Nitrosomonas. Denitrifying bacteria were comparatively diverse and were associated with some cultivatable bacteria.

[Effects of transgenic Bt + CpTI cotton on rhizosphere bacteria and ammonia oxidizing bacteria population].

Science.gov (United States)

Dong, Lianhua; Meng, Ying; Wang, Jing

2014-03-04

The effect of transgenic cotton on the rhizosphere bacteria can be important to the risk assessment for the genetically modified crops. We studied the rhizosphere microbial community with cultivating genetically modified cotton. The effects of transgenic Bt + CpTI Cotton (SGK321) and its receptor cotton (SY321) on rhizosphere total bacteria and ammonia oxidizing bacteria population size were studied by using droplet digital PCR. We collected rhizosphere soil before cotton planting and along with the cotton growth stage (squaring stage, flowering stage, belling stage and boll opening stage). There was no significant change on the total bacterial population between the transgenic cotton and the receptor cotton along with the growth stage. However, the abundance of ammonia oxidizing bacteria (AOB) in both type of cottons showed significant difference between different growth stages, and the variation tendency was different. In squaring stage, the numbers of AOB in rhizosphere of SY321 and SGK321 increased 4 and 2 times, respectively. In flowering stage, AOB number in rhizosphere of SY321 significantly decreased to be 5.96 x 10(5) copies/g dry soil, however, that of SGK321 increased to be 1.25 x 10(6) copies/g dry soil. In belling stage, AOB number of SY321 greatly increased to be 1.49 x 10(6) copies/g dry soil, but no significant change was observed for AOB number of SGK321. In boll opening stage, both AOB number of SY321 and SGK321 clearly decreased and they were significantly different from each other. Compared to the non-genetically modified cotton, the change in abundance of ammonia oxidizing bacteria was slightly smooth in the transgenic cotton. Not only the cotton growth stage but also the cotton type caused this difference. The transgenic cotton can slow down the speed of ammonia transformation through impacting the number of AOB, which is advantageous for plant growth.

Interactions between ammonia and nitrite oxidizing bacteria in co-cultures: Is there evidence for mutualism, commensalism, or competition?

Energy Technology Data Exchange (ETDEWEB)

Sayavedra-Soto, Luis [Oregon State Univ., Corvallis, OR (United States); Arp, Daniel [Oregon State Univ., Corvallis, OR (United States)

2017-08-01

Nitrification is a two-step environmental microbial process in the nitrogen cycle in which ammonia is oxidized to nitrate. Ammonia-oxidizing bacteria and archaea oxidize ammonia to nitrite and nitrite is oxidized to nitrate by nitrite-oxidizing bacteria. These microorganisms, which likely act in concert in a microbial community, play critical roles in the movement of inorganic N in soils, sediments and waters and are essential to the balance of the nitrogen cycle. Anthropogenic activity has altered the balance of the nitrogen cycle through agriculture practices and organic waste byproducts. Through their influence on available N for plant growth, nitrifying microorganisms influence plant productivity for food and fiber production and the associated carbon sequestration. N Fertilizer production, primarily as ammonia, requires large inputs of natural gas and hydrogen. In croplands fertilized with ammonia-based fertilizers, nitrifiers contribute to the mobilization of this N by producing nitrate (NO3-), wasting the energy used in the production and application of ammonia-based fertilizer. The resulting nitrate is readily leached from these soils, oxidized to gaseous N oxides (greenhouse gases), and denitrified to N2 (which is no longer available as a plant N source). Still, ammonia oxidizers are beneficial in the treatment of wastewater and they also show potential to contribute to microbial bioremediation strategies for clean up of environments contaminated with chlorinated hydrocarbons. Mitigation of the negative effects and exploitation of the beneficial effects of nitrifiers will be facilitated by a systems-level understanding of the interactions of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria with the environment and with each other.

Effect of communities of ammonia-oxidizing bacteria on degradation of 17-alpha-ethynylestradiol by nitrifying activated sludge

Energy Technology Data Exchange (ETDEWEB)

Limpiyakorn, T.; Sermwaraphan, P.; Kurisu, F.

2009-07-01

An endocrine disrupting compound, 17-alpha-ethynylestradiol (EE2), is a synthetic estrogen used as a key ingredient in oral contraceptives pill. this persistent organic pollutant, no biodegradable by most microorganisms, is discharged via municipal waste streams to natural receiving waters. Recently, it was found that ammonia-oxidizing bacteria (AOB) in nitrifying activated sludge (NAS) enriched with high ammonium loads can degrade EE2 via co-metabolism during ammonia oxidation. (Author)

Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

Science.gov (United States)

Chen, S.; Peng, X.-T.; Xu, H.-C.; Ta, K.-W.

2015-10-01

The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g-1 h-1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU) in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g-1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell-1 h-1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

OpenAIRE

Vidya eDe Gannes; Gaius eEudoxie; David H Dyer; William James Hickey

2012-01-01

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

Removal of ammonia solutions used in catalytic wet oxidation processes.

Science.gov (United States)

Hung, Chang Mao; Lou, Jie Chung; Lin, Chia Hua

2003-08-01

Ammonia (NH(3)) is an important product used in the chemical industry, and is common place in industrial wastewater. Industrial wastewater containing ammonia is generally either toxic or has concentrations or temperatures such that direct biological treatment is unfeasible. This investigation used aqueous solutions containing more of ammonia for catalytic liquid-phase oxidation in a trickle-bed reactor (TBR) based on Cu/La/Ce composite catalysts, prepared by co-precipitation of Cu(NO(3))(2), La(NO(3))(2), and Ce(NO(3))(3) at 7:2:1 molar concentrations. The experimental results indicated that the ammonia conversion of the wet oxidation in the presence of the Cu/La/Ce composite catalysts was determined by the Cu/La/Ce catalyst. Minimal ammonia was removed from the solution by the wet oxidation in the absence of any catalyst, while approximately 91% ammonia removal was achieved by wet oxidation over the Cu/La/Ce catalyst at 230 degrees C with oxygen partial pressure of 2.0 MPa. Furthermore, the effluent streams were conducted at a liquid hourly space velocity of under 9 h(-1) in the wet catalytic processes, and a reaction pathway was found linking the oxidizing ammonia to nitric oxide, nitrogen and water. The solution contained by-products, including nitrates and nitrites. Nitrite selectivity was minimized and ammonia removal maximized when the feed ammonia solution had a pH of around 12.0.

Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing Crenarchaeota.

Science.gov (United States)

Weidler, Gerhard W; Dornmayr-Pfaffenhuemer, Marion; Gerbl, Friedrich W; Heinen, Wolfgang; Stan-Lotter, Helga

2007-01-01

Scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal Alpine springs, which contain radium 226 and radon 222. A culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the "Franz-Josef-Quelle" in Bad Gastein, Austria, was performed. Four hundred fifteen clones were analyzed. One hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units (OTUs) and 283 with four archaeal OTUs. Rarefaction analysis indicated a high diversity of bacterial sequences, while archaeal sequences were less diverse. The majority of the cloned archaeal 16S rRNA gene sequences belonged to the soil-freshwater-subsurface (1.1b) crenarchaeotic group; other representatives belonged to the freshwater-wastewater-soil (1.3b) group, except one clone, which was related to a group of uncultivated Euryarchaeota. These findings support recent reports that Crenarchaeota are not restricted to high-temperature environments. Most of the bacterial sequences were related to the Proteobacteria (alpha, beta, gamma, and delta), Bacteroidetes, and Planctomycetes. One OTU was allied with Nitrospina sp. (delta-Proteobacteria) and three others grouped with Nitrospira. Statistical analyses suggested high diversity based on 16S rRNA gene analyses; the rarefaction plot of archaeal clones showed a plateau. Since Crenarchaeota have been implicated recently in the nitrogen cycle, the spring environment was probed for the presence of the ammonia monooxygenase subunit A (amoA) gene. Sequences were obtained which were related to crenarchaeotic amoA genes from marine and soil habitats. The data suggested that nitrification processes are occurring in the subterranean environment and that ammonia may possibly be an energy source for the resident communities.

Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora

DEFF Research Database (Denmark)

Herrmann, Martina; Saunders, Aaron M.; Schramm, Andreas

2008-01-01

Archaeal and bacterial ammonia monooxygenase genes (amoA) had similar low relative abundances in freshwater sediment. In the rhizosphere of the submersed macrophyte Littorella uniflora, archaeal amoA was 500- to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrifi...

Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity.

Science.gov (United States)

Nacke, Heiko; Schöning, Ingo; Schindler, Malte; Schrumpf, Marion; Daniel, Rolf; Nicol, Graeme W; Prosser, James I

2017-11-01

Coastal areas worldwide are challenged by climate change-associated increases in sea level and storm surge quantities that potentially lead to more frequent flooding of soil ecosystems. Currently, little is known of the effects of inundation events on microorganisms controlling nitrification in these ecosystems. The goal of this study was to investigate the impact of seawater flooding on the abundance, community composition and salinity tolerance of soil ammonia oxidisers. Topsoil was sampled from three islands flooded at different frequencies by the Wadden Sea. Archaeal ammonia oxidiser amoA genes were more abundant than their betaproteobacterial counterparts, and the distribution of archaeal and bacterial ammonia oxidiser amoA and 16S rRNA gene sequences significantly differed between the islands. The findings indicate selection of ammonia oxidiser phylotypes with greater tolerance to high salinity and slightly alkaline pH (e.g. Nitrosopumilus representatives) in frequently flooded soils. A cluster phylogenetically related to gammaproteobacterial ammonia oxidisers was detected in all samples analysed in this survey. Nevertheless, no gammaprotebacterial amoA genes could be amplified via PCR and only betaproteobacterial ammonia oxidisers were detected in enrichment cultures. A slurry-based experiment demonstrated the tolerance of both bacterial and archaeal ammonia oxidisers to a wide range of salinities (e.g. Wadden Sea water salinity) in soil naturally exposed to seawater at a high frequency. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Nitrite as a stimulus for ammonia-starved Nitrosomonas europaea

NARCIS (Netherlands)

Laanbroek, H.J.; Bär-Gilissen, M.J.; Hoogveld, H.L.

2002-01-01

Ammonia-starved cells of Nitrosomonas europaea are able to preserve a high level of ammonia-oxidizing activity in the absence of ammonium. However, when the nitrite-oxidizing cells that form part of the natural nitrifying community do not keep pace with the ammonia-oxidizing cells, nitrite

Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

NARCIS (Netherlands)

Daebeler, A.; Abell, G.C.J.; Bodelier, P.L.E.; Bodrossy, L.; Frampton, D.M.; Hefting, M.M.; Laanbroek, H.J.

2012-01-01

The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of

Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics

DEFF Research Database (Denmark)

Tian, Hailin; Fotidis, Ioannis; Mancini, Enrico

2018-01-01

Acclimatized anaerobic communities to high ammonia levels can offer a solution to the ammonia toxicity problem in biogas reactors. In the current study, a stepwise acclimation strategy up to 10 g NH4+-N L−1, was performed in mesophilic (37 ± 1 °C) continuously stirred tank reactors. The reactors...... change throughout the ammonia acclimation process. Clostridium ultunense, a syntrophic acetate oxidizing bacteria, increased significantly alongside with hydrogenotrophic methanogen Methanoculleus spp., indicating strong hydrogenotrophic methanogenic activity at extreme ammonia levels (>7 g NH4+-N L−1...

Ammonia oxidation at high pressure and intermediate temperatures

DEFF Research Database (Denmark)

Song, Yu; Hashemi, Hamid; Christensen, Jakob Munkholt

2016-01-01

Ammonia oxidation experiments were conducted at high pressure (30 bar and 100 bar) under oxidizing and stoichiometric conditions, respectively, and temperatures ranging from 450 to 925 K. The oxidation of ammonia was slow under stoichiometric conditions in the temperature range investigated. Under...... oxidizing conditions the onset temperature for reaction was 850–875 K at 30 bar, while at 100 bar it was about 800 K, with complete consumption of NH3 at 875 K. The products of reaction were N2 and N2O, while NO and NO2 concentrations were below the detection limit even under oxidizing conditions. The data...... was satisfactory. The main oxidation path for NH3 at high pressure under oxidizing conditions is NH3⟶+OH NH2⟶+HO2,NO2 H2NO⟶+O2 HNO⟶+O2 NO ⟶+NH2 N2. The modeling predictions are most sensitive to the reactions NH2 + NO = NNH + OH and NH2 + HO2 = H2NO + OH, which promote the ammonia consumption by forming OH...

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments.

Science.gov (United States)

Wang, Linqiong; Li, Yi; Niu, Lihua; Zhang, Wenlong; Zhang, Huanjun; Wang, Longfei; Wang, Peifang

2018-01-01

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg -1 ) and copper (Cu, 50-500 mg kg -1 ) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg -1 BDE 209 with a 100 mg kg -1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments. Copyright © 2017 Elsevier Ltd. All rights reserved.

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures.

Science.gov (United States)

Cai, Wei; Li, Yi; Niu, Lihua; Zhang, Wenlong; Wang, Chao; Wang, Peifang; Meng, Fangang

2017-10-15

The composition and distribution characteristics of bacterial communities in biofilms attached to hydraulic concrete structure (HCS) surfaces were investigated for the first time in four reservoirs in the middle and lower reaches of the Yangtze River Basin using 16S rRNA Miseq sequencing. High microbial diversity was found in HCS biofilms, and notable differences were observed in different types of HCS. Proteobacteria, Cyanobacteria and Chloroflexi were the predominant phyla, with respective relative abundances of 35.3%, 25.4% and 13.0%. The three most abundant genera were Leptolyngbya, Anaerolineaceae and Polynucleobacter. The phyla Beta-proteobacteria and Firmicutes and genus Lyngbya were predominant in CGP, whereas the phyla Cyanobacteria and Chloroflexi and genera Leptolyngbya, Anaerolinea and Polynucleobacter survived better in land walls and bank slopes. Dissolved oxygen, ammonia nitrogen and temperature were characterized as the main factors driving the bacterial community composition. The most abundant groups of metabolic functions were also identified as ammonia oxidizers, sulphate reducers, and dehalogenators. Additionally, functional groups related to biocorrosion were found to account for the largest proportion (14.0% of total sequences) in gate piers, followed by those in land walls (11.5%) and bank slopes (10.2%). Concrete gate piers were at the greatest risk of biocorrosion with the most abundant negative bacterial groups, especially for sulphate reducers. Thus, it should be paid high attention to the biocorrosion prevention of concrete gate piers. Overall, this study contributed to the optimization of microbial control and the improvement of the safety management for water conservation structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

Geographic Distribution of Ammonia-Oxidizing Archaea along the Kuril Islands in the Western Subarctic Pacific

Directory of Open Access Journals (Sweden)

Hongmei Jing

2017-06-01

Full Text Available Community composition and abundance of ammonia-oxidizing archaea (AOA in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively. Quantitative PCR assays revealed that the occurrence and ammonia-oxidizing activity of ammonia-oxidizing archaea (AOA reached their maxima at the depth of 200 m, where a higher diversity and abundance of actively transcribed AOA was observed at the station located in the marginal sea exposed to more terrestrial input. Similar community composition of AOA observed at the two stations adjacent to the Kuril Islands maybe due to water exchange across the Bussol Strait. They distinct from the station located in the western subarctic gyre, where sub-cluster WCAII had a specific distribution in the surface water, and this sub-cluster seemed having a confined distribution in the western Pacific. Habitat-specific groupings of different WCB sub-clusters were observed reflecting the isolated microevolution existed in cluster WCB. The effect of the Kuril Islands on the phylogenetic composition of AOA between the Sea of Okhotsk and the western subarctic Pacific is not obvious, possibly because our sampling stations are near to the Bussol Strait, the main gateway through which water is exchanged between the Sea of Okhotsk and the Pacific. The vertical and horizontal distribution patterns of AOA communities among stations along the Kuril Islands were essentially determined by the in situ prevailing physicochemical gradients along the two dimensions.

Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

OpenAIRE

de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H.; Hickey, William J.

2012-01-01

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

SOIL NITROUS OXIDE, NITRIC OXIDE, AND AMMONIA EMISSIONS FROM A RECOVERING RIPARIAN ECOSYSTEM IN SOUTHERN APPALACHIA

Science.gov (United States)

The paper presents two years of seasonal nitric oxide, ammonia, and nitrous oxide trace gas fluxes measured in a recovering riparian zone with cattle excluded and in an adjacent riparian zone grazed by cattle. In the recovering riparian zone, average nitric oxide, ammonia, and ni...

Catalytic wet oxidation of ammonia solution: Activity of the nanoscale platinum-palladium-rhodium composite oxide catalyst

International Nuclear Information System (INIS)

Hung, C.-M.

2009-01-01

Aqueous solutions of 400-1000 mg/L of ammonia were oxidized in a trickle-bed reactor (TBR) in this study of nanoscale platinum-palladium-rhodium composite oxide catalysts, which were prepared by the co-precipitation of H 2 PtCl 6 , Pd(NO 3 ) 3 and Rh(NO 3 ) 3 . Hardly any of the dissolved ammonia was removed by wet oxidation in the absence of any catalyst, whereas about 99% of the ammonia was reduced during wet oxidation over nanoscale platinum-palladium-rhodium composite oxide catalysts at 503 K in an oxygen partial pressure of 2.0 MPa. A synergistic effect exists in the nanoscale platinum-palladium-rhodium composite structure, which is the material with the highest ammonia reduction activity. The nanometer-sized particles were characterized by TEM, XRD and FTIR. The effect of the initial concentration and reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid hourly space velocity of under 9 h -1 in the wet catalytic processes

Catalytic wet oxidation of ammonia solution: Activity of the nanoscale platinum-palladium-rhodium composite oxide catalyst

Energy Technology Data Exchange (ETDEWEB)

Hung, C.-M. [Department of Industry Engineering and Management, Yung-Ta Institute of Technology and Commerce, 316 Chung-shan Road, Linlo, Pingtung 909, Taiwan (China)], E-mail: hungcm1031@gmail.com

2009-04-15

Aqueous solutions of 400-1000 mg/L of ammonia were oxidized in a trickle-bed reactor (TBR) in this study of nanoscale platinum-palladium-rhodium composite oxide catalysts, which were prepared by the co-precipitation of H{sub 2}PtCl{sub 6}, Pd(NO{sub 3}){sub 3} and Rh(NO{sub 3}){sub 3}. Hardly any of the dissolved ammonia was removed by wet oxidation in the absence of any catalyst, whereas about 99% of the ammonia was reduced during wet oxidation over nanoscale platinum-palladium-rhodium composite oxide catalysts at 503 K in an oxygen partial pressure of 2.0 MPa. A synergistic effect exists in the nanoscale platinum-palladium-rhodium composite structure, which is the material with the highest ammonia reduction activity. The nanometer-sized particles were characterized by TEM, XRD and FTIR. The effect of the initial concentration and reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid hourly space velocity of under 9 h{sup -1} in the wet catalytic processes.

Catalytic wet oxidation of ammonia solution: activity of the nanoscale platinum-palladium-rhodium composite oxide catalyst.

Science.gov (United States)

Hung, Chang-Mao

2009-04-15

Aqueous solutions of 400-1000 mg/L of ammonia were oxidized in a trickle-bed reactor (TBR) in this study of nanoscale platinum-palladium-rhodium composite oxide catalysts, which were prepared by the co-precipitation of H(2)PtCl(6), Pd(NO(3))(3) and Rh(NO(3))(3). Hardly any of the dissolved ammonia was removed by wet oxidation in the absence of any catalyst, whereas about 99% of the ammonia was reduced during wet oxidation over nanoscale platinum-palladium-rhodium composite oxide catalysts at 503 K in an oxygen partial pressure of 2.0 MPa. A synergistic effect exists in the nanoscale platinum-palladium-rhodium composite structure, which is the material with the highest ammonia reduction activity. The nanometer-sized particles were characterized by TEM, XRD and FTIR. The effect of the initial concentration and reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid hourly space velocity of under 9 h(-1) in the wet catalytic processes.

Enrichment of Thermophilic Ammonia-Oxidizing Archaea from an Alkaline Hot Spring in the Great Basin, USA

Science.gov (United States)

Zhang, C.; Huang, Z.; Jiang, H.; Wiegel, J.; Li, W.; Dong, H.

2010-12-01

One of the major advances in the nitrogen cycle is the recent discovery of ammonia oxidation by archaea. While culture-independent studies have revealed occurrence of ammonia-oxidizing archaea (AOA) in nearly every surface niche on earth, most of these microorganisms have resisted isolation and so far only a few species have been identified. The Great Basin contains numerous hot springs, which are characterized by moderately high temperature (40-65 degree C) and circumneutral or alkaline pH. Unique thermophilic archaea have been identified based on molecular DNA and lipid biomarkers; some of which may be ammonia oxidizers. This study aims to isolate some of these archaea from a California hot spring that has pH around 9.0 and temperature around 42 degree C. Mat material was collected from the spring and transported on ice to the laboratory. A synthetic medium (SCM-5) was inoculated with the mat material and the culture was incubated under varying temperature (35-65 degree C) and pH (7.0-10.0) conditions using antibiotics to suppress bacterial growth. Growth of the culture was monitored by microscopy, decrease in ammonium and increase in nitrite, and increases in Crenarchaeota and AOA abundances over time. Clone libraries were constructed to compare archaeal community structures before and after the enrichment experiment. Temperature and pH profiles indicated that the culture grew optimally at pH 9.0 and temperature 45 degree C, which are consistent with the geochemical conditions of the natural environment. Phylogenetic analysis showed that the final OTU was distantly related to all known hyperthermophilic archaea. Analysis of the amoA genes showed two OTUs in the final culture; one of them was closely related to Candidatus Nitrososphaera gargensis. However, the enrichment culture always contained bacteria and attempts to separate them from archaea have failed. This highlights the difficulty in bringing AOA into pure culture and suggests that some of the AOA may

Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries.

Science.gov (United States)

Polymenakou, Paraskevi N; Bertilsson, Stefan; Tselepides, Anastasios; Stephanou, Euripides G

2005-10-01

The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.

Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments.

Science.gov (United States)

dos Santos, A C F; Marques, E L S; Gross, E; Souza, S S; Dias, J C T; Brendel, M; Rezende, R P

2012-01-27

Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

Amperometric detection and electrochemical oxidation of aliphatic amines and ammonia on silver-lead oxide thin-film electrodes

Energy Technology Data Exchange (ETDEWEB)

Ge, Jisheng [Iowa State Univ., Ames, IA (United States)

1996-01-08

This thesis comprises three parts: Electrocatalysis of anodic oxygen-transfer reactions: aliphatic amines at mixed Ag-Pb oxide thin-film electrodes; oxidation of ammonia at anodized Ag-Pb eutectic alloy electrodes; and temperature effects on oxidation of ethylamine, alanine, and aquated ammonia.

Ammonia concentration and bacterial evaluation of feline whole blood and packed red blood cell units stored for transfusion

Directory of Open Access Journals (Sweden)

Eva Spada

2014-10-01

Full Text Available Ammonia concentrations increase in human, canine and equine WB and PRBC units during storage. The aim of this study was to determine the effect of storage on ammonia concentration in feline WB and PRBC units stored in a veterinary blood bank and to evaluate possible correlations with bacterial contamination. Ammonia concentration was evaluated in 15 WB units and 2 PRBC units on day 1 and at the end of storage after 35 and 42 days, respectively. In an additional 5 WB units and 4 PRBC units ammonia concentrations were determined daily until the day the normal reference range was exceeded and then weekly to the end of storage. All units were evaluated for bacterial contamination. Ammonia increased markedly during storage as a linear function over time. On the 35th and 42th day of storage at 4±2°C mean±SD ammonia concentration reached 909±158 µg/dl and 1058±212 µg/dl in WB and PRBC units, respectively. Bacterial culture was negative in all units. High ammonia concentrations in stored WB and PRBC units could result in toxicity, particularly in feline recipients with liver failure, portosystemic shunts or those receiving large transfusion volumes. Clinical in vivo studies evaluating the effects on recipients should be performed.

Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

Directory of Open Access Journals (Sweden)

Zhu Wang

Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

Bacterial community structure of a full-scale biofilter treating pig house exhaust air

DEFF Research Database (Denmark)

Kristiansen, Anja; Pedersen, Kristina Hadulla; Nielsen, Per Halkjær

2011-01-01

Biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. Quantitative fluorescence in situ hybridization (FISH) and 16S rRNA gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter ...... consisting of two consecutive compartments (front and back filter). The analysis revealed a highly specialized bacterial community of limited diversity, dominated by a few groups of Betaproteobacteria (especially Comamonas) and diverse Bacteroidetes. Actinobacteria, Gammaproteobacteria......, and betaproteobacterial ammoniaoxidizers (Nitrosomonas eutropha/Nitrosococcus mobilis-lineage) were also quantitatively important. Only a few quantitative differences existed between the two filter compartments at the group level, with a lower relative abundance of Actinobacteria and a higher relative abundance...

Revisiting the electrochemical oxidation of ammonia on carbon-supported metal nanoparticle catalysts

International Nuclear Information System (INIS)

Li, Zhe-Fei; Wang, Yuxuan; Botte, Gerardine G.

2017-01-01

Highlights: • A procedure to pretreat electrocatalysts to study the ammonia oxidation is provided. • N ads and O/OH ads were identified as the major deactivation species that prevent ammonia oxidatoin. • The electrocatalytic activity, thermodynamics, and possible deactivation mechanisms for ammonia oxidation were elucidated. • The onset potential for ammonia oxidation is related to the hydrogen binding energy of the catalyst. • Ammonia electro-oxidation involves a complex decoupled electron and proton transfer process. - Abstract: The ammonia electro-oxidation reaction (AOR) has been studied due to its promising applications in ammonia electrolysis, wastewater remediation, direct ammonia fuel cells, and sensors. However, it is difficult to compare and analyze the reported electrocatalytic activity of AOR reliably, likely due to the variation in catalyst synthesis, electrode composition, electrode morphology, and testing protocol. In this paper, the electro-oxidation of ammonia on different carbon-supported precious metal nanoparticle catalysts was revisited. The effect of experimental conditions, electrochemical test parameters, electrocatalytic activity, thermodynamics, and possible deactivation mechanism of the catalysts were investigated. Pt/C catalyst possesses the highest electrocatalytic activity, while Ir/C and Rh/C show lower overpotential. The onset potential of the AOR is related to the hydrogen binding energy of the catalyst. N ads is one major cause of deactivation accompanied with the formation of surface O/OH ads at high potentials. The coulombic efficiency of N ads formation on Pt is about 1% initially and gradually decreases with reaction time. Increase in ammonia concentration leads to increase in current density, while increase in hydroxyl ions concentration can enhance the current density and reduce the overpotential simultaneously. The slopes of AOR onset potential and hydrogen adsorption/desorption potential of Pt/C as a function of p

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir.

Science.gov (United States)

Zhang, Haihan; Jia, Jingyu; Chen, Shengnan; Huang, Tinglin; Wang, Yue; Zhao, Zhenfang; Feng, Ji; Hao, Huiyan; Li, Sulin; Ma, Xinxin

2018-02-18

The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.

Controls of nitrite oxidation in ammonia-removing biological air filters

DEFF Research Database (Denmark)

Juhler, Susanne; Ottosen, Lars Ditlev Mørck; Nielsen, Lars Peter

2008-01-01

in accumulation of nitrate rather than nitrite and a significant decline in pH. As a consequence, ammonia is removed more efficiently, but heterotrophic oxidation of odorous compounds might be inhibited.  To identify the controlling mechanisms of nitrite oxidation, full-scale biological air filters were...... activity resulting in a lowered pH and thus a decreased FA concentration, promoting further growth of NOB. Yet, in some cases a situation with a nitrate-to-nitrite ratio of 1 and moderate pH remained stable even under varying air load and water supply, suggesting that additional mechanisms were involved......In biological air filters ammonia is removed due to the action of Ammonia Oxidizing Bacteria (AOB) resulting in nitrite accumulation exceeding 100 mM. Among filters treating exhaust air from pig facilities successful establishment of Nitrite Oxidizing Bacteria (NOB) sometimes occurs, resulting...

Ammonia produced by bacterial colonies promotes growth of ampicillin-sensitive Serratia sp. by means of antibiotic inactivation.

Science.gov (United States)

Cepl, Jaroslav; Blahůšková, Anna; Cvrčková, Fatima; Markoš, Anton

2014-05-01

Volatiles produced by bacterial cultures are known to induce regulatory and metabolic alterations in nearby con-specific or heterospecific bacteria, resulting in phenotypic changes including acquisition of antibiotic resistance. We observed unhindered growth of ampicillin-sensitive Serratia rubidaea and S. marcescens on ampicillin-containing media, when exposed to volatiles produced by dense bacterial growth. However, this phenomenon appeared to result from pH increase in the medium caused by bacterial volatiles rather than alterations in the properties of the bacterial cultures, as alkalization of ampicillin-containing culture media to pH 8.5 by ammonia or Tris exhibited the same effects, while pretreatment of bacterial cultures under the same conditions prior to antibiotic exposure did not increase ampicillin resistance. Ampicillin was readily inactivated at pH 8.5, suggesting that observed bacterial growth results from metabolic alteration of the medium, rather than an active change in the target bacterial population (i.e. induction of resistance or tolerance). However, even such seemingly simple mechanism may provide a biologically meaningful basis for protection against antibiotics in microbial communities growing on semi-solid media. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland.

Science.gov (United States)

He, Yuan; Hu, Wenge; Ma, Decao; Lan, Hongzhu; Yang, Yang; Gao, Yan

2017-07-01

Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 10 4 to 2.94 × 10 5 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 10 5 and 1.05 × 10 6 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH 4 + -N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.

Ammonia release method for depositing metal oxides

Energy Technology Data Exchange (ETDEWEB)

Silver, G.L.; Martin, F.S.

1993-12-31

A method of depositing metal oxides on substrates which is indifferent to the electrochemical properties of the substrates and which comprises forming ammine complexes containing metal ions and thereafter effecting removal of ammonia from the ammine complexes so as to permit slow precipitation and deposition of metal oxide on the substrates.

Physiological plasticity of the thermophilic ammonia oxidizing archaeon Nitrosocaldus yellowstonii in response to a changing environment

Science.gov (United States)

Jewell, T.; Johnson, A.; Gelsinger, D.; de la Torre, J. R.

2012-12-01

consumed NH3 from NH4Cl when both substrates were provided in equal molar concentrations. However, the urease alpha subunit ureC was expressed in both the presence and absence of urea. One consequence of urea hydrolysis is consumption of intracellular protons during the reaction. As ammonia oxidation produces H+, leading to a decrease in pH, the hydrolysis of urea prior to ammonia oxidation may help alleviate metabolism-driven pH change in HL72. A survey of archaeal ureC sequences from metagenomic data covering a range of hydrothermal features revealed that ureolytic potential is common to many Nitrosocaldus-like organisms and is geographically widespread. Measurements of urea from siliceous circumneutral springs indicate that the concentrations are generally low, below 10 μM. One possible explanation for low steady state urea concentrations is high consumption rates by ureolytic organisms. This, combined with abiotic thermal degradation, may mask high fluxes of urea in microbial hot spring communities.

Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea

Science.gov (United States)

Zarsky, Jakub D.; Stibal, Marek; Hodson, Andy; Sattler, Birgit; Schostag, Morten; Hansen, Lars H.; Jacobsen, Carsten S.; Psenner, Roland

2013-09-01

The aggregation of surface debris particles on melting glaciers into larger units (cryoconite) provides microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (of surface debris, ice and meltwater), quantitative polymerase chain reactions (targeting the 16S ribosomal ribonucleic acid and amoA genes), pyrosequencing and multivariate statistical analysis to suggest possible factors driving the ecology of prokaryotic microbes on the surface of Aldegondabreen and their potential role in nitrogen cycling. The combination of high nutrient input with subsidy from the bird colonies, supraglacial meltwater flow and the presence of fine, clay-like particles supports the formation of centimetre-scale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are well-known in supraglacial environments. Importantly, ammonia-oxidizing archaea were detected in the aggregates for the first time on an Arctic glacier.

Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea

International Nuclear Information System (INIS)

Zarsky, Jakub D; Sattler, Birgit; Psenner, Roland; Stibal, Marek; Schostag, Morten; Jacobsen, Carsten S; Hodson, Andy; Hansen, Lars H

2013-01-01

The aggregation of surface debris particles on melting glaciers into larger units (cryoconite) provides microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (of surface debris, ice and meltwater), quantitative polymerase chain reactions (targeting the 16S ribosomal ribonucleic acid and amoA genes), pyrosequencing and multivariate statistical analysis to suggest possible factors driving the ecology of prokaryotic microbes on the surface of Aldegondabreen and their potential role in nitrogen cycling. The combination of high nutrient input with subsidy from the bird colonies, supraglacial meltwater flow and the presence of fine, clay-like particles supports the formation of centimetre-scale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are well-known in supraglacial environments. Importantly, ammonia-oxidizing archaea were detected in the aggregates for the first time on an Arctic glacier. (letter)

Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea

Energy Technology Data Exchange (ETDEWEB)

Zarsky, Jakub D; Sattler, Birgit; Psenner, Roland [Institute of Ecology, University of Innsbruck, Innsbruck (Austria); Stibal, Marek; Schostag, Morten; Jacobsen, Carsten S [Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen (Denmark); Hodson, Andy [Department of Geography, University of Sheffield, Sheffield (United Kingdom); Hansen, Lars H, E-mail: j.zarsky@gmail.com [Department of Biology, University of Copenhagen, Copenhagen (Denmark)

2013-09-15

The aggregation of surface debris particles on melting glaciers into larger units (cryoconite) provides microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (of surface debris, ice and meltwater), quantitative polymerase chain reactions (targeting the 16S ribosomal ribonucleic acid and amoA genes), pyrosequencing and multivariate statistical analysis to suggest possible factors driving the ecology of prokaryotic microbes on the surface of Aldegondabreen and their potential role in nitrogen cycling. The combination of high nutrient input with subsidy from the bird colonies, supraglacial meltwater flow and the presence of fine, clay-like particles supports the formation of centimetre-scale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are well-known in supraglacial environments. Importantly, ammonia-oxidizing archaea were detected in the aggregates for the first time on an Arctic glacier. (letter)

Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil

Science.gov (United States)

J.S. Norman; J.E. Barrett

2014-01-01

Ammonia-oxidizing microbes control the rate-limiting step of nitrification, a critical ecosystem process, which affects retention and mobility of nitrogen in soil ecosystems. This study investigated substrate (NH4þ) and nutrient (K and P) limitation of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in temperate forest soils at Coweeta Hydrologic...

Spatial interaction of archaeal ammonia-oxidizers and nitrite-oxidizing bacteria in an unfertilized grassland soil

Directory of Open Access Journals (Sweden)

Barbara eStempfhuber

2016-01-01

Full Text Available Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA and bacteria (AOB, and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m². Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onwards, indicating its important role in nitrite oxidation.

Inhibition of Direct Electrolytic Ammonia Oxidation Due to a Change in Local pH

International Nuclear Information System (INIS)

Zöllig, Hanspeter; Morgenroth, Eberhard; Udert, Kai M.

2015-01-01

Electrochemical ammonia oxidation has gained a lot of attention recently as an efficient method for ammonia removal from wastewater, for the use in ammonia-based fuel cells and the production of high purity hydrogen. Thermally decomposed iridium oxide films (TDIROF) have been shown to be catalytically active for direct ammonia oxidation in aqueous solutions if NH 3 is present. However, the process was reported to be rapidly inhibited on TDIROF. Herein, we show that this fast inhibition of direct ammonia oxidation does not result from surface poisoning by adsorbed elemental nitrogen (N ads ). Instead, we propose that direct ammonia oxidation and oxygen evolution can lead to a drop of the local pH at the electrode resulting in a low availability of the actual reactant, NH 3 . The hypothesis was tested with cyclic voltammetry (CV) experiments on stagnant and rotating disk electrodes (RDE). The CV experiments on the stagnant electrode revealed that the decrease of the ammonia oxidation peaks was considerably reduced by introducing an idle phase at open circuit potential between subsequent scans. Furthermore, the polarization of the TDIROF electrode into the hydrogen evolution region (HER) resulted in increased ammonia oxidation peaks in the following anodic scans which can be explained with an increased local pH after the consumption of protons in the HER. On the RDE, the ammonia oxidation peaks did not decrease in immediately consecutive scans. These findings would not be expected if surface poisoning was responsible for the fast inhibition but they are in good agreement with the proposed mechanism of pH induced limitation by the reactant, NH 3 . The plausibility of the mechanism was also supported by our numerical simulations of the processes in the Nernstian diffusion layer. The knowledge about this inhibition mechanism of direct ammonia oxidation is especially important for the design of electrochemical cells for wastewater treatment. The mechanism is not only

[Ammonia-oxidizing archaea and their important roles in nitrogen biogeochemical cycling: a review].

Science.gov (United States)

Liu, Jing-Jing; Wu, Wei-Xiang; Ding, Ying; Shi, De-Zhi; Chen, Ying-Xu

2010-08-01

As the first step of nitrification, ammonia oxidation is the key process in global nitrogen biogeochemical cycling. So far, the autotrophic ammonia-oxidizing bacteria (AOB) in the beta- and gamma-subgroups of proteobacteria have been considered as the most important contributors to ammonia oxidation, but the recent researches indicated that ammonia-oxidizing archaea (AOA) are widely distributed in various kinds of ecosystems and quantitatively predominant, playing important roles in the global nitrogen biogeochemical cycling. This paper reviewed the morphological, physiological, and ecological characteristics and the molecular phylogenies of AOA, and compared and analyzed the differences and similarities of the ammonia monooxygenase (AMO) and its encoding genes between AOA and AOB. In addition, the potential significant roles of AOA in nitrogen biogeochemical cycling in aquatic and terrestrial ecosystems were summarized, and the future research directions of AOA in applied ecology and environmental protection were put forward.

Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.

Science.gov (United States)

Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Wen, Donghui

2015-05-01

Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.

Diversity and abundance of ammonia-oxidizing

NARCIS (Netherlands)

Cardoso, J.F.M.F.; van Bleijswijk, J.D.L.; Witte, H.; van Duyl, F.C.

2013-01-01

We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in the shallow warm-water sponge Halisarca caerulea and the deep cold-water sponges Higginsia thielei and Nodastrella nodastrella. The abundance of AOA and AOB was analysed using catalyzed reporter

Activity of Cu-activated carbon fiber catalyst in wet oxidation of ammonia solution.

Science.gov (United States)

Hung, Chang-Mao

2009-07-30

Aqueous solutions of 200-1000 mg/L of ammonia were oxidized in a trickle-bed reactor using Cu-activated carbon fiber (ACF) catalysts, which were prepared by incipient wet impregnation with aqueous solutions of copper nitrate that was deposited on ACF substrates. The results reveal that the conversion of ammonia by wet oxidation in the presence of Cu-ACF catalysts was a function of the metal loading weight ratio of the catalyst. The total conversion efficiency of ammonia was 95% during wet oxidation over the catalyst at 463 K at an oxygen partial pressure of 3.0 MPa. Moreover, the effect of the initial concentration of ammonia and the reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid space velocity of less than 3.0 h(-1).

Activity of Cu-activated carbon fiber catalyst in wet oxidation of ammonia solution

International Nuclear Information System (INIS)

Hung, Chang-Mao

2009-01-01

Aqueous solutions of 200-1000 mg/L of ammonia were oxidized in a trickle-bed reactor using Cu-activated carbon fiber (ACF) catalysts, which were prepared by incipient wet impregnation with aqueous solutions of copper nitrate that was deposited on ACF substrates. The results reveal that the conversion of ammonia by wet oxidation in the presence of Cu-ACF catalysts was a function of the metal loading weight ratio of the catalyst. The total conversion efficiency of ammonia was 95% during wet oxidation over the catalyst at 463 K at an oxygen partial pressure of 3.0 MPa. Moreover, the effect of the initial concentration of ammonia and the reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid space velocity of less than 3.0 h -1 .

The inhibitory effects of free ammonia on ammonia oxidizing bacteria and nitrite oxidizing bacteria under anaerobic condition.

Science.gov (United States)

Qian, Wenting; Peng, Yongzhen; Li, Xiyao; Zhang, Qiong; Ma, Bin

2017-11-01

The free ammonia (FA) inhibition on ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) under anaerobic condition was investigated in this study. The results indicated that NOB was more sensitive to the FA anaerobic treatment than AOB. The FA anaerobic inhibition on nitrifier gradually heightened with the increase of FA concentration. Accompanied with FA concentration increase from 0 to 16.82mgNH 3 -N·L -1 (the highest concentration adopted in this study), the activity of AOB reduced by 15.9%, while NOB decreased by 29.2%. After FA anaerobic treatment, nitrite was accumulated during nitrification. However, the nitrite accumulation disappeared on the sixth cycle of activity recovery tests with excessive aeration. Based on this result, a novel strategy for achieving nitritation is proposed, which involves recirculating a portion of the activated sludge through a side-line sludge treatment unit, where the sludge is subjected to treatment with FA under anaerobic condition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Distribution and abundance of archaeal and bacterial ammonia oxidizers in the sediments of the Dongjiang River, a drinking water supply for Hong Kong.

Science.gov (United States)

Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Wang, Aijie; Sun, Guoping

2013-01-01

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b- and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg(-1) sediment, NH4(+)-N >144 mg kg(-1) sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg(-1) sediment, NH4(+)-N <93 mg kg(-1) sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.

Activity of Cu-activated carbon fiber catalyst in wet oxidation of ammonia solution

Energy Technology Data Exchange (ETDEWEB)

Hung, Chang-Mao, E-mail: hungcm1031@gmail.com [Department of Industry Engineering and Management, Yung-Ta Institute of Technology and Commerce, 316 Chung-shan Road, Linlo, Pingtung 909, Taiwan (China)

2009-07-30

Aqueous solutions of 200-1000 mg/L of ammonia were oxidized in a trickle-bed reactor using Cu-activated carbon fiber (ACF) catalysts, which were prepared by incipient wet impregnation with aqueous solutions of copper nitrate that was deposited on ACF substrates. The results reveal that the conversion of ammonia by wet oxidation in the presence of Cu-ACF catalysts was a function of the metal loading weight ratio of the catalyst. The total conversion efficiency of ammonia was 95% during wet oxidation over the catalyst at 463 K at an oxygen partial pressure of 3.0 MPa. Moreover, the effect of the initial concentration of ammonia and the reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid space velocity of less than 3.0 h{sup -1}.

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

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Haihan Zhang

2018-02-01

Full Text Available The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP from the outbreak to the decline period (p < 0.05 while Fe concentration increased sharply during the decline period (p < 0.05. The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02. Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of

Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils.

Science.gov (United States)

Wu, Ruo-Nan; Meng, Han; Wang, Yong-Feng; Gu, Ji-Dong

2018-06-01

Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO 2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 10 8 copies per gram dry soil in matured forest to 5.04 (± 0.43) × 10 8 copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al 3+ and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis.

Weakened activity of starved ammonia-oxidizing bacteria by the presence of pre-activated Nitrobacter winogradskyi

NARCIS (Netherlands)

Laanbroek, H.J.; Bär-Gilissen, M.J.

2002-01-01

Ammonia-oxidizing bacteria are able to maintain a high oxidizing potential during starvation. nitrite has a short-lasting stimulatory effect on the oxidation of ammonia after starvation when supplied simultaneously with fresh ammonium. To examine whether nitrite-oxidizing bacteria as partners in

Weakened activity of starved ammonia-oxidizing bacteria by the presence of pre-activated Nitrobacter winogradskyi

NARCIS (Netherlands)

Laanbroek, H.J.; Bär-Gilissen, M.J.

2002-01-01

Ammonia-oxidizing bacteria are able to maintain a high oxidizing potential during starvation. Nitrite has a short-lasting stimulatory effect on the oxidation of ammonia after starvation when supplied simultaneously with fresh ammonium9). To examine whether nitrite-oxidizing bacteria as partners in

A Zinc Oxide Nanorod Ammonia Microsensor Integrated with a Readout Circuit on-a-Chip

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Chyan-Chyi Wu

2011-11-01

Full Text Available A zinc oxide nanorod ammonia microsensor integrated with a readout circuit on-a-chip fabricated using the commercial 0.35 mm complementary metal oxide semiconductor (CMOS process was investigated. The structure of the ammonia sensor is composed of a sensitive film and polysilicon electrodes. The ammonia sensor requires a post-process to etch the sacrificial layer, and to coat the sensitive film on the polysilicon electrodes. The sensitive film that is prepared by a hydrothermal method is made of zinc oxide. The sensor resistance changes when the sensitive film adsorbs or desorbs ammonia gas. The readout circuit is used to convert the sensor resistance into the voltage output. Experiments show that the ammonia sensor has a sensitivity of about 1.5 mV/ppm at room temperature.

Nitrous oxide production by lithotrophic ammonia-oxidizing bacteria and implications for engineered nitrogen-removal systems.

Science.gov (United States)

Chandran, Kartik; Stein, Lisa Y; Klotz, Martin G; van Loosdrecht, Mark C M

2011-12-01

Chemolithoautotrophic AOB (ammonia-oxidizing bacteria) form a crucial component in microbial nitrogen cycling in both natural and engineered systems. Under specific conditions, including transitions from anoxic to oxic conditions and/or excessive ammonia loading, and the presence of high nitrite (NO₂⁻) concentrations, these bacteria are also documented to produce nitric oxide (NO) and nitrous oxide (N₂O) gases. Essentially, ammonia oxidation in the presence of non-limiting substrate concentrations (ammonia and O₂) is associated with N₂O production. An exceptional scenario that leads to such conditions is the periodical switch between anoxic and oxic conditions, which is rather common in engineered nitrogen-removal systems. In particular, the recovery from, rather than imposition of, anoxic conditions has been demonstrated to result in N₂O production. However, applied engineering perspectives, so far, have largely ignored the contribution of nitrification to N₂O emissions in greenhouse gas inventories from wastewater-treatment plants. Recent field-scale measurements have revealed that nitrification-related N₂O emissions are generally far higher than emissions assigned to heterotrophic denitrification. In the present paper, the metabolic pathways, which could potentially contribute to NO and N₂O production by AOB have been conceptually reconstructed under conditions especially relevant to engineered nitrogen-removal systems. Taken together, the reconstructed pathways, field- and laboratory-scale results suggest that engineering designs that achieve low effluent aqueous nitrogen concentrations also minimize gaseous nitrogen emissions.

Spatial distribution of microbial communities associated with dune landform in the Gurbantunggut Desert, China.

Science.gov (United States)

Liu, Ruyin; Li, Ke; Zhang, Hongxun; Zhu, Junge; Joshi, DevRaj

2014-11-01

The microbial community compositions and potential ammonia oxidation in the topsoil at different positions of sand dune (stoss slope, crest, lee slope, and interdune) from the Gurbantunggut Desert, the largest semi-fixed desert in China, were investigated using several molecular methods. Actinobacteria and Proteobacteria (especially Alphaproteobacteria) were commonly the dominant taxa across all soil samples. Bacterial communities were similar in soils collected from the stoss slopes and interdunes (HC-BSCs, biological soil crusts with a high abundance of cyanobacteria), containing more abundant cyanobacterial populations (16.9-24.5%) than those (0.2-0.7% of Cyanobacteria) in the crests and lee slopes (LC-BSCs, biological soil crusts with a low abundance of cyanobacteria). The Cyanobacteria were mainly composed of Microcoleus spp., and quantitative PCR analysis revealed that 16S rRNA gene copy numbers of Cyanobacteria (especially genus Microcoleus) were at least two orders of magnitude higher in HC-BSCs than in LC-BSCs. Heterotrophic Geodermatophilus spp. frequently occurred in HC-BSCs (2.5-8.0%), whereas genera Arthrobacter, Bacillus, and Segetibacter were significantly abundant in LC-BSC communities. By comparison, the desert archaeal communities were less complex, and were dominated by Nitrososphaera spp. The amoA gene abundance of ammonia-oxidizing archaea (AOA) was higher than that of ammonia-oxidizing bacteria (AOB) in all soil samples, particularly in the interdunal soils (10(6)-10(8) archaeal amoA gene copies per gram dry soil), indicating that AOA possibly dominate the ammonia oxidation at the interdunes.

Application of a novel functional gene microarray to probe the functional ecology of ammonia oxidation in nitrifying activated sludge.

Directory of Open Access Journals (Sweden)

Michael D Short

Full Text Available We report on the first study trialling a newly-developed, functional gene microarray (FGA for characterising bacterial and archaeal ammonia oxidisers in activated sludge. Mixed liquor (ML and media biofilm samples from a full-scale integrated fixed-film activated sludge (IFAS plant were analysed with the FGA to profile the diversity and relative abundance of ammonia-oxidising archaea and bacteria (AOA and AOB respectively. FGA analyses of AOA and AOB communities revealed ubiquitous distribution of AOA across all samples - an important finding for these newly-discovered and poorly characterised organisms. Results also revealed striking differences in the functional ecology of attached versus suspended communities within the IFAS reactor. Quantitative assessment of AOB and AOA functional gene abundance revealed a dominance of AOB in the ML and approximately equal distribution of AOA and AOB in the media-attached biofilm. Subsequent correlations of functional gene abundance data with key water quality parameters suggested an important functional role for media-attached AOB in particular for IFAS reactor nitrification performance and indicate possible functional redundancy in some IFAS ammonia oxidiser communities. Results from this investigation demonstrate the capacity of the FGA to resolve subtle ecological shifts in key microbial communities in nitrifying activated sludge and indicate its value as a tool for better understanding the linkages between the ecology and performance of these engineered systems.

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

Science.gov (United States)

Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

2017-10-01

Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Continuous culture enrichments of ammonia-oxidizing bacteria at low ammonium concentrations

NARCIS (Netherlands)

Bollmann, A.; Laanbroek, H.J.

2001-01-01

Until now enrichments of ammonia-oxidizing bacteria from natural ammonium-limited environments have been performed mainly in the presence of much higher ammonia concentrations than those present in the natural environment and many have resulted in the enrichment and isolation of environmentally less

Continuous culture enrichments of ammonia-oxidizing bacteria at low ammonium concentrations

NARCIS (Netherlands)

Bollmann, A.; Laanbroek, H.J.

2001-01-01

Until now enrichments of ammonia-oxidizing bacteria from natural ammonium-limited environments have been performed mainly in the presence of much higher ammonia concentrations than those present in the natural environment and many have resulted in the enrichment and isolation of environmentally

Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China

Directory of Open Access Journals (Sweden)

Xu Sun

2014-03-01

Full Text Available Ammonia-oxidizingarchaea (AOA and ammonia-oxidizing bacteria (AOB play an important role innitrogen transformation in freshwater sediments. However, it is still unclear towhat extent the distribution patterns of these microorganisms are affected bythe freshwater sediment across a large geographical scale. This study wasdesigned to gain insight into the heterogeneity distribution of AOA and AOB in32 freshwater sediments from a wide range of ecologic types. Real-time quantitative polymerasechain reaction PCR(qPCR combined with the terminal restrictionfragment length polymorphism(T-RFLP were employed to characterize the abundance, diversity, and communitystructure of the AOA and AOB in 32 freshwater sediments. AOA and AOB wereubiquitous in all sediments, and archaeal amoA far outnumbered bacterial amoA inmost sediments with lower organic matters. The abundance of AOA and AOB did notvary with the freshwater ecological type (macrophyte dominated region and algaedominated region. Based on  the T-RFLP of an amoA gene, this research found that organicmatters in pore water rather than other factors affect the AOA communitystructure in sediments, while the AOB were not significantly different in thefreshwater sediments. Phylogenetic analysis showed that all archaeal amoAsequences fell within either the Crenarchaeotal Group (CG I.1b or the CGI.1asubgroup, and all AOB clustered with genus Nitrosomonas or Nitrosospira. The data obtained inthis study elucidates the role of ammonia-oxidizing archaea andammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

Thermophilic prokaryotic communities inhabiting the biofilm and well water of a thermal karst system located in Budapest (Hungary).

Science.gov (United States)

Anda, Dóra; Makk, Judit; Krett, Gergely; Jurecska, Laura; Márialigeti, Károly; Mádl-Szőnyi, Judit; Borsodi, Andrea K

2015-07-01

In this study, scanning electron microscopy (SEM) and 16S rRNA gene-based phylogenetic approach were applied to reveal the morphological structure and genetic diversity of thermophilic prokaryotic communities of a thermal karst well located in Budapest (Hungary). Bacterial and archaeal diversity of the well water (73.7 °C) and the biofilm developed on the inner surface of an outflow pipeline of the well were studied by molecular cloning method. According to the SEM images calcium carbonate minerals serve as a surface for colonization of bacterial aggregates. The vast majority of the bacterial and archaeal clones showed the highest sequence similarities to chemolithoautotrophic species. The bacterial clone libraries were dominated by sulfur oxidizer Thiobacillus (Betaproteobacteria) in the water and Sulfurihydrogenibium (Aquificae) in the biofilm. A relatively high proportion of molecular clones represented genera Thermus and Bellilinea in the biofilm library. The most abundant phylotypes both in water and biofilm archaeal clone libraries were closely related to thermophilic ammonia oxidizer Nitrosocaldus and Nitrososphaera but phylotypes belonging to methanogens were also detected. The results show that in addition to the bacterial sulfur and hydrogen oxidation, mainly archaeal ammonia oxidation may play a decisive role in the studied thermal karst system.

Bacterial and protist community changes during a phytoplankton bloom

KAUST Repository

Pearman, John K.

2015-10-01

The present study aims to characterize the change in the composition and structure of the bacterial and microzooplankton planktonic communities in relation to the phytoplankton community composition during a bloom. High-throughput amplicon sequencing of regions of the 16S and 18S rRNA gene was undertaken on samples collected during a 20 day (d) mesocosm experiment incorporating two different nutrient addition treatments [Nitrate and Phosphate (NPc) and Nitrate, Phosphate and Silicate (NPSc)] as well as a control. This approach allowed us to discriminate the changes in species composition across a broad range of phylogenetic groups using a common taxonomic level. Diatoms dominated the bloom in the NPSc treatment while dinoflagellates were the dominant phytoplankton in the control and NPc treatment. Network correlations highlighted significant interactions between OTUs within each treatment including changes in the composition of Paraphysomonas OTUs when the dominant Chaetoceros OTU switched. The microzooplankton community composition responded to changes in the phytoplankton composition while the prokaryotic community responded more to changes in ammonia concentration.

Response of archaeal communities in the rhizosphere of maize and soybean to elevated atmospheric CO2 concentrations.

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David M Nelson

Full Text Available BACKGROUND: Archaea are important to the carbon and nitrogen cycles, but it remains uncertain how rising atmospheric carbon dioxide concentrations ([CO(2] will influence the structure and function of soil archaeal communities. METHODOLOGY/PRINCIPAL FINDINGS: We measured abundances of archaeal and bacterial 16S rRNA and amoA genes, phylogenies of archaeal 16S rRNA and amoA genes, concentrations of KCl-extractable soil ammonium and nitrite, and potential ammonia oxidation rates in rhizosphere soil samples from maize and soybean exposed to ambient (∼385 ppm and elevated (550 ppm [CO(2] in a replicated and field-based study. There was no influence of elevated [CO(2] on copy numbers of archaeal or bacterial 16S rRNA or amoA genes, archaeal community composition, KCl-extractable soil ammonium or nitrite, or potential ammonia oxidation rates for samples from maize, a model C(4 plant. Phylogenetic evidence indicated decreased relative abundance of crenarchaeal sequences in the rhizosphere of soybean, a model leguminous-C(3 plant, at elevated [CO(2], whereas quantitative PCR data indicated no changes in the absolute abundance of archaea. There were no changes in potential ammonia oxidation rates at elevated [CO(2] for soybean. Ammonia oxidation rates were lower in the rhizosphere of maize than soybean, likely because of lower soil pH and/or abundance of archaea. KCl-extractable ammonium and nitrite concentrations were lower at elevated than ambient [CO(2] for soybean. CONCLUSION: Plant-driven shifts in soil biogeochemical processes in response to elevated [CO(2] affected archaeal community composition, but not copy numbers of archaeal genes, in the rhizosphere of soybean. The lack of a treatment effect for maize is consistent with the fact that the photosynthesis and productivity of maize are not stimulated by elevated [CO(2] in the absence of drought.

Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

Science.gov (United States)

Xinda Lu; Peter J. Bottomley; David D. Myrold

2015-01-01

Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA-and AOB-supported nitrifi-cation determined both in soil-water slurries and in unsaturated...

Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

Science.gov (United States)

Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

2009-09-01

Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

Oxidative destruction of ammonia for restoration of uranium solution mining sites

International Nuclear Information System (INIS)

Humenick, M.J.; Garwacka, K.

1984-01-01

A laboratory experimental research project was conducted to evaluate the use of chlorine for the oxidative destruction of residual ammonia that may remain in ground water after in-situ uranium solution mining operations. The work tested the idea of injecting high strength calcium hypochlorite solution into the mining zone to convert ammonia to nitrogen gas as a final cleanup process for ammonia removal from the ground water system. This paper details ammonia removal efficiency as a function of chlorine dose, reactant, and product material balances, and how the concept may be used as a final ground water restoration process

Oxidative destruction of ammonia for restoration of uranium solution mining sites

Energy Technology Data Exchange (ETDEWEB)

Humenick, M.J.; Garwacka, K.

1984-02-01

A laboratory experimental research project was conducted to evaluate the use of chlorine for the oxidative destruction of residual ammonia that may remain in ground water after in-situ uranium solution mining operations. The work tested the idea of injecting high strength calcium hypochlorite solution into the mining zone to convert ammonia to nitrogen gas as a final cleanup process for ammonia removal from the ground water system. This paper details ammonia removal efficiency as a function of chlorine dose, reactant, and product material balances, and how the concept may be used as a final ground water restoration process.

Oxidative destruction of ammonia for restoration of uranium solution mining sites

Energy Technology Data Exchange (ETDEWEB)

Humenick, M.J.; Garwacka, K.

1984-01-01

A laboratory experimental research project was conducted to evaluate the use of chlorine for the oxidative destruction of residual ammonia that may remain in ground water after in-situ uranium solution mining operations. The work tested the idea of injecting high strength calcium hypochlorite solution into the mining zone to convert ammonia to nitrogen gas as a final cleanup process for ammonia removal from the ground water system. This paper details ammonia removal efficiency as a function of chlorine dose, reactant, and product material balances, and how the concept may be used as a final ground water restoration process.

Direct electrochemical oxidation of ammonia on graphite as a treatment option for stored source-separated urine.

Science.gov (United States)

Zöllig, Hanspeter; Fritzsche, Cristina; Morgenroth, Eberhard; Udert, Kai M

2015-02-01

Electrolysis can be a viable technology for ammonia removal from source-separated urine. Compared to biological nitrogen removal, electrolysis is more robust and is highly amenable to automation, which makes it especially attractive for on-site reactors. In electrolytic wastewater treatment, ammonia is usually removed by indirect oxidation through active chlorine which is produced in-situ at elevated anode potentials. However, the evolution of chlorine can lead to the formation of chlorate, perchlorate, chlorinated organic by-products and chloramines that are toxic. This study focuses on using direct ammonia oxidation on graphite at low anode potentials in order to overcome the formation of toxic by-products. With the aid of cyclic voltammetry, we demonstrated that graphite is active for direct ammonia oxidation without concomitant chlorine formation if the anode potential is between 1.1 and 1.6 V vs. SHE (standard hydrogen electrode). A comparison of potentiostatic bulk electrolysis experiments in synthetic stored urine with and without chloride confirmed that ammonia was removed exclusively by continuous direct oxidation. Direct oxidation required high pH values (pH > 9) because free ammonia was the actual reactant. In real stored urine (pH = 9.0), an ammonia removal rate of 2.9 ± 0.3 gN·m(-2)·d(-1) was achieved and the specific energy demand was 42 Wh·gN(-1) at an anode potential of 1.31 V vs. SHE. The measurements of chlorate and perchlorate as well as selected chlorinated organic by-products confirmed that no chlorinated by-products were formed in real urine. Electrode corrosion through graphite exfoliation was prevented and the surface was not poisoned by intermediate oxidation products. We conclude that direct ammonia oxidation on graphite electrodes is a treatment option for source-separated urine with three major advantages: The formation of chlorinated by-products is prevented, less energy is consumed than in indirect ammonia oxidation and

Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms.

Science.gov (United States)

Sun, Fu-Lin; Fan, Lei-Lei; Xie, Guang-Jian

2016-08-01

The anaerobic-anoxic-aerobic (A2O) process is a highly efficient sewage treatment method, which uses complex bacterial communities. However, the effect of copper on this process and the bacterial communities involved remains unknown. In this study, a systematic investigation of the effect of persistent exposure of copper in the A2O wastewater treatment system was performed. An A2O device was designed to examine the effect of copper on the removal efficiency and microbial community compositions of activated sludge that was continuously treated with 10, 20, and 40 mg L(-1) copper, respectively. Surprisingly, a decrease in chemical oxygen demand (COD) and ammonia nitrogen (NH4N) removal efficiency was observed, and the toxicity of high copper concentration was significantly greater at 7d than at 1d. Proteobacteria, Bacteroidetes, Acidobacteria, Chlorobi, and Nitrospirae were the dominant bacterial taxa in the A2O system, and significant changes in microbial community were observed during the exposure period. Most of the dominant bacterial groups were easily susceptible to copper toxicity and diversely changed at different copper concentrations. However, not all the bacterial taxa were inhibited by copper treatment. At high copper concentration, many bacterial species were stimulated and their abundance increased. Cluster analysis and principal coordinate analysis (PCoA) based on operational taxonomic units (OTUs) revealed clear differences in the bacterial communities among the samples. These findings indicated that copper severely affected the performance and key microbial populations in the A2O system as well as disturbed the stability of the bacterial communities in the system, thus decreasing the removal efficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ammonia effect on hydrogenotrophic methanogens and syntrophic acetate oxidizing bacteria

DEFF Research Database (Denmark)

Wang, Han; Fotidis, Ioannis; Angelidaki, Irini

Substrates that contain high ammonia levels can cause inhibition on anaerobic digestion process and unstable biogas production. The aim of the current study was to assess the effects of different ammonia levels on pure strains of (syntrophic acetate oxidizing) SAO bacteria and hydrogenotrophic...... methanogens. Two pure strains of hydrogenotrophic methanogens (i.e: Methanoculleus bourgensis and Methanoculleus thermophiles) and two pure strains of SAO bacteria (i.e: Tepidanaerobacter acetatoxydans and Thermacetogenium phaeum) were inoculated under four different ammonia (0.26, 3, 5 and 7g NH4+-N......, the total incubation periods of hydrogenotrophic methanogens were significantly shorter compared to the SAO bacteria incubation periods. Thus, it seems that hydrogenotrophic methanogens could be equally, if not more, tolerant to high ammonia levels compared to SAO bacteria....

Bacterial Communities: Interactions to Scale

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Reed M. Stubbendieck

2016-08-01

Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

The effect of antimony-tin and indium-tin oxide supports on the catalytic activity of Pt nanoparticles for ammonia electro-oxidation

Energy Technology Data Exchange (ETDEWEB)

Silva, Júlio César M. [Department of Chemical & Biological Engineering, Centre for Catalysis Research and Innovation (CCRI), University of Ottawa, 161 Louis-Pasteur, Ottawa, ON K1N 6N5 (Canada); Instituto de Pesquisas Energéticas e Nucleares, IPEN/CNEN-SP, Av. Prof. Lineu Prestes, 2242 Cidade Universitária, CEP 05508-900, São Paulo, SP (Brazil); Piasentin, Ricardo M.; Spinacé, Estevam V.; Neto, Almir O. [Instituto de Pesquisas Energéticas e Nucleares, IPEN/CNEN-SP, Av. Prof. Lineu Prestes, 2242 Cidade Universitária, CEP 05508-900, São Paulo, SP (Brazil); Baranova, Elena A., E-mail: elena.baranova@uottawa.ca [Department of Chemical & Biological Engineering, Centre for Catalysis Research and Innovation (CCRI), University of Ottawa, 161 Louis-Pasteur, Ottawa, ON K1N 6N5 (Canada)

2016-09-01

Platinum nanoparticles supported on carbon (Pt/C) and carbon with addition of ITO (Pt/C-ITO (In{sub 2}O{sub 3}){sub 9}·(SnO{sub 2}){sub 1}) and ATO (Pt/C-ATO (SnO{sub 2}){sub 9}·(Sb{sub 2}O{sub 5}){sub 1}) oxides were prepared by sodium borohydride reduction method and used for ammonia electro-oxidation reaction (AmER) in alkaline media. The effect of the supports on the catalytic activity of Pt for AmER was investigated using electrochemical (cyclic voltammetry and chronoamperometry) and direct ammonia fuel cell (DAFC) experiments. X-ray diffraction (XRD) showed Pt peaks attributed to the face-centered cubic (fcc) structure, as well as peaks characteristic of In{sub 2}O{sub 3} in ITO support and cassiterite SnO{sub 2} phase of ATO support. According to transmission electron micrographs the mean particles sizes of Pt over carbon were 5.4, 4.9 and 4.7 nm for Pt/C, Pt/C-ATO and Pt/C-ITO, respectively. Pt/C-ITO catalysts showed the highest catalytic activity for ammonia electrooxidation in both electrochemical and fuel cell experiments. We attributed this to the presence of In{sub 2}O{sub 3} phase in ITO, which provides oxygenated or hydroxide species at lower potentials resulting in the removal of poisonous intermediate, i.e., atomic nitrogen (N{sub ads}) and promotion of ammonia electro-oxidation. - Highlights: • Oxide support effect on the catalytic activity of Pt towards ammonia electro-oxidation. • Direct ammonia fuel cell (DAFC) performance using Pt over different supports as anode. • Pt/C-ITO shows better catalytic activity for ammonia oxidation than Pt/C and Pt/C-ATO.

Shifts in the abundance and community structure of soil ammonia oxidizers in a wet sclerophyll forest under long-term prescribed burning.

Science.gov (United States)

Long, Xi-En; Chen, Chengrong; Xu, Zhihong; He, Ji-Zheng

2014-02-01

Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles. © 2013.

An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting-Phase II) for Agaricus bisporus Cultivation.

Science.gov (United States)

Vieira, Fabricio Rocha; Pecchia, John Andrew

2018-02-01

Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the "selectivity" and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers. Bacterial diversity, based on 16S ribosomal RNA obtained by high-throughput sequencing and classified in operational taxonomic units (OTUs), was greater than previously reported using culture-dependent methods. Alpha diversity estimators show a lower diversity of OTUs under a high-temperature pasteurization condition. Bacillales order shows a relatively higher OTU abundance under a high-pasteurization temperature, which also was related to high ammonia emission measurements. On the other hand, beta diversity analysis showed no significantly changes in the bacterial community structure under different conditions. Agaricus bisporus mycelium growth during a standard spawn run period was significantly slower in the compost pasteurized at high temperature. Since the bacterial community structure was not greatly affected by different pasteurization conditions but by-products left (e.g., ammonia) at the end of compost conditioning varied, further studies need to be conducted to determine the functional role of the microbial communities found during substrate preparation for Agaricus bisporus cultivation.

Investigation of Pristine Graphite Oxide as Room-Temperature Chemiresistive Ammonia Gas Sensing Material

Directory of Open Access Journals (Sweden)

Alexander G. Bannov

2017-02-01

Full Text Available Graphite oxide has been investigated as a possible room-temperature chemiresistive sensor of ammonia in a gas phase. Graphite oxide was synthesized from high purity graphite using the modified Hummers method. The graphite oxide sample was investigated using scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray diffraction, thermogravimetry and differential scanning calorimetry. Sensing properties were tested in a wide range of ammonia concentrations in air (10–1000 ppm and under different relative humidity levels (3%–65%. It was concluded that the graphite oxide–based sensor possessed a good response to NH3 in dry synthetic air (ΔR/R0 ranged from 2.5% to 7.4% for concentrations of 100–500 ppm and 3% relative humidity with negligible cross-sensitivity towards H2 and CH4. It was determined that the sensor recovery rate was improved with ammonia concentration growth. Increasing the ambient relative humidity led to an increase of the sensor response. The highest response of 22.2% for 100 ppm of ammonia was achieved at a 65% relative humidity level.

Co-Mn-Al Mixed Oxides as Catalysts for Ammonia Oxidation to N2O.

Czech Academy of Sciences Publication Activity Database

Ludvíková, Jana; Jablońska, M.; Jirátová, Květa; Chmielarz, L.; Balabánová, Jana; Kovanda, F.; Obalová, L.

2016-01-01

Roč. 42, č. 3 (2016), s. 2669-2690 ISSN 0922-6168 R&D Projects: GA ČR GA14-13750S Institutional support: RVO:67985858 Keywords : Co-Mn-Al mixed oxide s * catalytic ammonia oxidation * N2O production * mechanochemical production Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 1.369, year: 2016

Evaluation of zinc oxide nanoparticles on lettuce (Lactuca sativa L.) growth and soil bacterial community.

Science.gov (United States)

Xu, Jiangbing; Luo, Xiaosan; Wang, Yanling; Feng, Youzhi

2018-02-01

The wide spread of nanoparticles (NPs) has caused tremendous concerns on agricultural ecosystem. Some metallic NPs, such as zinc oxide (ZnO), can be utilized as a nano-fertilizer when used at optimal doses. However, little is known about the responses of plant development and concomitant soil bacteria community to ZnO NPs. The present pot experiment studied the impacts of different doses of ZnO NPs and bulk ZnO (0, 1, 10, 100 mg ZnO/kg), on the growth of lettuce (Lactuca sativa L.) and the associated rhizospheric soil bacterial community. Results showed that at a dose of 10 mg/kg, ZnO NPs and bulk ZnO, enhanced the lettuce biomass and the net photosynthetic rate; whereas, the Zn content in plant tissue was higher in NPs treatment than in their bulk counterpart at 10 mg/kg dose or higher. For the underground observations, 10 mg/kg treatment doses (NPs or bulk) significantly changed the soil bacterial community structure, despite the non-significant variations in alpha diversity. Taxonomic distribution revealed that some lineages within Cyanobacteria and other phyla individually demonstrated similar or different responses to ZnO NPs and bulk ZnO. Moreover, some lineages associated with plant growth promotion were also influenced to different extents by ZnO NPs and bulk ZnO, suggesting the distinct microbial processes occurring in soil. Collectively, this study expanded our understanding of the influence of ZnO NPs on plant performance and the associated soil microorganisms.

Low-temperature conversion of ammonia to nitrogen in water with ozone over composite metal oxide catalyst.

Science.gov (United States)

Chen, Yunnen; Wu, Ye; Liu, Chen; Guo, Lin; Nie, Jinxia; Chen, Yu; Qiu, Tingsheng

2018-04-01

As one of the most important water pollutants, ammonia nitrogen emissions have increased year by year, which has attracted people's attention. Catalytic ozonation technology, which involves production of ·OH radical with strong oxidation ability, is widely used in the treatment of organic-containing wastewater. In this work, MgO-Co 3 O 4 composite metal oxide catalysts prepared with different fabrication conditions have been systematically evaluated and compared in the catalytic ozonation of ammonia (50mg/L) in water. In terms of high catalytic activity in ammonia decomposition and high selectivity for gaseous nitrogen, the catalyst with MgO-Co 3 O 4 molar ratio 8:2, calcined at 500°C for 3hr, was the best one among the catalysts we tested, with an ammonia nitrogen removal rate of 85.2% and gaseous nitrogen selectivity of 44.8%. In addition, the reaction mechanism of ozonation oxidative decomposition of ammonia nitrogen in water with the metal oxide catalysts was discussed. Moreover, the effect of coexisting anions on the degradation of ammonia was studied, finding that SO 4 2- and HCO 3 - could inhibit the catalytic activity while CO 3 2- and Br - could promote it. The presence of coexisting cations had very little effect on the catalytic ozonation of ammonia nitrogen. After five successive reuses, the catalyst remained stable in the catalytic ozonation of ammonia. Copyright © 2017. Published by Elsevier B.V.

Relationship of sediment-biochemistry, bacterial morphology, and activity to geotechnical properties in the central Indian Basin

Digital Repository Service at National Institute of Oceanography (India)

Naik, S.S.; Khadge, N.H.; Valsangkar, A.B.; Das, A.; Fernandes, C.E.G.; LokaBharathi, P.A.

of bacterial community to artificially simulated disturbance (Nair et al., 2000; Raghukumar et al., 2001a, b) and long-term response to the same (Raghukumar et al., 2006). Specific observations of deep-sea cultures and their role in ammonia oxidation under... et al., 1990; Trueblood, 1993; Fukushima, 1995; Tkatchenko et al., 1996; Sharma, 2005). Earlier studies on the effect of artificial disturbance on microbiology of deep-sea sediments were restricted to culturable fraction and suggested the revival...

Coupling Solid Oxide Electrolyser (SOE) and ammonia production plant

International Nuclear Information System (INIS)

Cinti, Giovanni; Frattini, Domenico; Jannelli, Elio; Desideri, Umberto; Bidini, Gianni

2017-01-01

Highlights: • An innovative NH 3 production plant was designed. • CO 2 emissions and energy consumption are studied in three different designs. • High temperature electrolysis allows to achieve high efficiency and heat recovery. • The coupling permits storage of electricity into a liquid carbon free chemical. - Abstract: Ammonia is one of the most produced chemicals worldwide and is currently synthesized using nitrogen separated from air and hydrogen from natural gas reforming with consequent high consumption of fossil fuel and high emission of CO 2 . A renewable path for ammonia production is desirable considering the potential development of ammonia as energy carrier. This study reports design and analysis of an innovative system for the production of green ammonia using electricity from renewable energy sources. This concept couples Solid Oxide Electrolysis (SOE), for the production of hydrogen, with an improved Haber Bosch Reactor (HBR), for ammonia synthesis. An air separator is also introduced to supply pure nitrogen. SOE operates with extremely high efficiency recovering high temperature heat from the Haber-Bosch reactor. Aspen was used to develop a model to study the performance of the plant. Both the SOE and the HBR operate at 650 °C. Ammonia production with zero emission of CO 2 can be obtained with a reduction of 40% of power input compared to equivalent plants.

Simultaneous Fe(III) reduction and ammonia oxidation process in Anammox sludge.

Science.gov (United States)

Li, Xiang; Huang, Yong; Liu, Heng-Wei; Wu, Chuan; Bi, Wei; Yuan, Yi; Liu, Xin

2018-02-01

In recent years, there have been a number of reports on the phenomenon in which ferric iron (Fe(III)) is reduced to ferrous iron [Fe(II)] in anaerobic environments, accompanied by simultaneous oxidation of ammonia to NO 2 - , NO 3 - , or N 2. However, studies on the relevant reaction characteristics and mechanisms are rare. Recently, in research on the effect of Fe(III) on the activity of Anammox sludge, excess ammonia oxidization has also been found. Hence, in the present study, Fe(III) was used to serve as the electron acceptor instead of NO 2 - , and the feasibility and characteristics of Anammox coupled to Fe(III) reduction (termed Feammox) were investigated. After 160days of cultivation, the conversion rate of ammonia in the reactor was above 80%, accompanied by the production of a large amount of NO 3 - and a small amount of NO 2 - . The total nitrogen removal rate was up to 71.8%. Furthermore, quantities of Fe(II) were detected in the sludge fluorescence in situ hybridization (FISH) and denaturated gradient gel electrophoresis (DGGE) analyses further revealed that in the sludge, some Anammox bacteria were retained, and some microbes were enriched during the acclimatization process. We thus deduced that in Anammox sludge, Fe(III) reduction takes place together with ammonia oxidation to NO 2 - and NO 3 - along with the Anammox process. Copyright © 2017. Published by Elsevier B.V.

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.

Science.gov (United States)

Sauder, Laura A; Albertsen, Mads; Engel, Katja; Schwarz, Jasmin; Nielsen, Per H; Wagner, Michael; Neufeld, Josh D

2017-05-01

Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1-2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown

Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

Directory of Open Access Journals (Sweden)

Elena V Lebedeva

Full Text Available 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.

Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

Science.gov (United States)

Lebedeva, Elena V; Hatzenpichler, Roland; Pelletier, Eric; Schuster, Nathalie; Hauzmayer, Sandra; Bulaev, Aleksandr; Grigor'eva, Nadezhda V; Galushko, Alexander; Schmid, Markus; Palatinszky, Marton; Le Paslier, Denis; Daims, Holger; Wagner, Michael

2013-01-01

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.

Characterization of TEMPO-oxidized bacterial cellulose

International Nuclear Information System (INIS)

Nascimento, Eligenes S.; Pereira, Andre L.S.; Lima, Helder L.; Barroso, Maria K. de A.; Barros, Matheus de O.; Morais, Joao P.S.; Borges, Maria de F.; Rosa, Morsyleide de F.

2015-01-01

The aim of this study was to characterize the TEMPO-oxidized bacterial cellulose, as a preliminary research for further application in nanocomposites. Bacterial cellulose (BC) was selectively oxidized at C-6 carbon by TEMPO radical. Oxidized bacterial cellulose (BCOX) was characterized by TGA, FTIR, XRD, and zeta potential. BCOX suspension was stable at pH 7.0, presented a crystallinity index of 83%, in spite of 92% of BC, because of decrease in the free hydroxyl number. FTIR spectra showed characteristic BC bands and, in addition, band of carboxylic group, proving the oxidation. BCOX DTG showed, in addition to characteristic BC thermal events, a maximum degradation peak at 233 °C, related to sodium anhydro-glucuronate groups formed during the cellulose oxidation. Thus, BC can be TEMPO-oxidized without great loss in its structure and properties. (author)

Ammonia-oxidizing bacteria: A model for molecular microbial ecology

NARCIS (Netherlands)

Kowalchuk, G.A.; Stephen, J.R.

2001-01-01

The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important

Ammonia-oxidizing Bacteria and Archaea in the Rhizosphere of Freshwater Macrophytes

DEFF Research Database (Denmark)

Herrmann, Martina; Schramm, Andreas

2007-01-01

AMMONIA-OXIDIZING ARCHAEA AND BACTERIA IN THE RHIZOSPHERE OF FRESHWATER MACROPHYTES Martina Herrmann and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Aquatic macrophytes such as Littorella uniflora and Lobelia dortmanna release oxygen from...... their roots and thereby stimulate nitrification and coupled nitrification-denitrification in their rhizosphere. However, oxygen release and inorganic nitrogen concentrations differ markedly between macrophyte species. We therefore propose (i) that the rhizosphere of freshwater macrophytes harbours a species......-specific microbial community distinct from that of unvegetated sediment and (ii) that aquatic macrophytes have an impact on abundance and activity of nitrifying and denitrifying bacteria in freshwater sediment. The goal of this study was to test these hypotheses for the key functional group for coupled nitrification...

Bacterial Community Succession in Pine-Wood Decomposition.

Science.gov (United States)

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Application of a Chemiluminescence Detector for the Measurement of Total Oxides of Nitrogen and Ammonia in the Atmosphere

Science.gov (United States)

Hodgeson, J. A.; Bell, J. P.; Rehme, K. A.; Krost, K. J.; Stevens, R. K.

1971-01-01

By means of the thermal conversion of nitrogen dioxide to the nitric oxide, the chemiluminescent nitric oxide monitor, based on the nitric oxide plus ozone reaction, may be used for monitoring nitrogen dioxide plus nitric oxide (NO(x)). Under conditions previously described, ammonia is also converted to nitric oxide and therefore interferes. A metal surface, gold wool or stainless steel, operated at two different temperatures has been used to convert only nitrogen dioxide or nitrogen dioxide plus ammonia. Quantitative conversion of nitrogen dioxide to nitric oxide has been obtained at temperatures as low as 200 C. Conversion of ammonia is effected at temperatures of 300 C or higher. By the addition of a converter the basic nitric oxide monitor may be used for measuring NO(x) or NO(x) plus ammonia. As an alternate mode, for a fixed high temperature, a specific scrubber is described for removing NH3 without affecting NO2 concentrations.

Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil.

Science.gov (United States)

Liu, Dongyan; Tago, Kanako; Hayatsu, Masahito; Tokida, Takeshi; Sakai, Hidemitsu; Nakamura, Hirofumi; Usui, Yasuhiro; Hasegawa, Toshihiro; Asakawa, Susumu

2016-09-29

Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions.

Spectroscopic and electrical sensing mechanism in oxidant-mediated polypyrrole nanofibers/nanoparticles for ammonia gas

International Nuclear Information System (INIS)

Ishpal; Kaur, Amarjeet

2013-01-01

Ammonia gas sensing mechanism in oxidant-mediated polypyrrole (PPy) nanofibers/nanoparticles has been studied through spectroscopic and electrical investigations. PPy nanofibers/nanoparticles have been synthesized by chemical oxidation method in the presence of various oxidizing agents such as ammonium persulfate (APS), potassium persulfate (PPS), vanadium pentoxide (V 2 O 5 ), and iron chloride (FeCl 3 ). Scanning electron microscopy study revealed that PPy nanofibers of about 63, 71 and 79 nm diameters were formed in the presence of APS, PPS, V 2 O 5 , respectively, while PPy nanoparticles of about 100–110 nm size were obtained in the presence of FeCl 3 as an oxidant. The structural investigations and confirmation of synthesis of PPy were established through Fourier transform infrared and Raman spectroscopy. The gas sensing behavior of the prepared PPy samples is investigated by measuring the electrical resistance in ammonia environment. The observed gas sensing response (ΔR/Rx100) at 100 ppm level of ammonia is ∼4.5 and 18 % for the samples prepared with oxidizing agents FeCl 3 and APS, respectively, and by changing the ammonia level from 50 to 300 ppm, the sensing response varies from ∼4.5 to 11 % and ∼10 to 39 %, respectively. Out of all four samples, the PPy nanofibers prepared in the presence of APS have shown the best sensing response. The mechanism of gas sensing response of the PPy samples has been investigated through Raman spectroscopy study. The decrease of charge carrier concentration through reduction of polymeric chains has been recognized through Raman spectroscopic measurements recorded in ammonia environment.

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

NARCIS (Netherlands)

Bollmann, A.; Sedlacek, C.J.; Norton, J.; Laanbroek, H.J.; Suwa, Y.; Stein, L.Y.; Klotz, M.G.; Arp, D.; Sayavedra-Soto, L.; Lu, M.; Bruce, D.; Detter, C.; Tapia, R.; Han, J.; Woyke, T.; Lucas, S.; Pitluck, S.; Pennacchio, L.; Nolan, M.; Land, M.L.; Huntemann, M.; Deshpande, S.; Han, C.; Chen, A.; Kyrpides, N.; Mavromatis, K.; Markowitz, V.; Szeto, E.; Ivanova, N.; Mikhailova, N.; Pagani, I.; Pati, A.; Peters, L.; Ovchinnikova, G.; Goodwin, L.

2013-01-01

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

Directory of Open Access Journals (Sweden)

Késia S. Lourenço

2018-04-01

Full Text Available Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O emissions when applied with inorganic nitrogen (N fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.

Bacterial community succession in pine-wood decomposition

Directory of Open Access Journals (Sweden)

Anna eKielak

2016-03-01

Full Text Available Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Comparison among amoA Primers Suited for Quantification and Diversity Analyses of Ammonia-Oxidizing Bacteria in Soil

Science.gov (United States)

Shimomura, Yumi; Morimoto, Sho; Hoshino, Yuko Takada; Uchida, Yoshitaka; Akiyama, Hiroko; Hayatsu, Masahito

2012-01-01

Ammonia monooxygenase subunit A gene (amoA) is frequently used as a functional gene marker for diversity analysis of ammonia-oxidizing bacteria (AOB). To select a suitable amoA primer for real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE), three reverse primers (degenerate primer amoA-2R; non-degenerate primers amoA-2R-GG and amoA-2IR) were examined. No significant differences were observed among the three primers in terms of quantitative values of amoA from environmental samples using real-time PCR. We found that PCR-DGGE analysis with the amoA-2IR primer gave the best results in this studied soil. These results indicate that amoA-2IR is a suitable primer for community analysis of AOB in the environment. PMID:22075625

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

Energy Technology Data Exchange (ETDEWEB)

Bollmann, Annette [Miami University, Oxford, OH; Sedlacek, Christopher J [Miami University, Oxford, OH; Laanbroek, Hendrikus J [Netherlands Institute of Ecology (NIOO-KNAW); Suwa, Yuichi [Chuo University, Tokyo, Japan; Stein, Lisa Y [University of California, Riverside; Klotz, Martin G [University of Louisville, Louisville; Arp, D J [Oregon State University; Sayavedra-Soto, LA [Oregon State University; Lu, Megan [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL)

2013-01-01

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

Method for Bacterial Growth and Ammonia Production and Effect of Inhibitory Substances in Disposable Absorbent Hygiene Products.

Science.gov (United States)

Forsgren-Brusk, Ulla; Yhlen, Birgitta; Blomqvist, Marie; Larsson, Peter

The purpose of this study was to evaluate a pragmatic laboratory method to provide a technique for developing incontinence products better able to reduce malodor when used in the clinical setting. Bacterial growth and bacterially formed ammonia in disposable absorbent incontinence products was measured by adding synthetic urine inoculated with bacteria to test samples cut from the crotch area of the product. The inhibitory effect's of low pH (4.5 and 4.9) and 3 antimicrobial substances-chlorhexidine, polyhexamethylene biguanide (PHMB), and thymol-at 2 concentrations each, were studied. From the initial inocula of 3.3 log colony-forming units per milliliter (cfu/mL) at baseline, the bacterial growth of the references increased to 5.0 to 6.0 log cfu/mL at 6 hours for Escherichia coli, Proteus mirabilis, and Enterococcus faecalis. At 12 hours there was a further increase to 7.0 to 8.9 log cfu/mL. Adjusting the pH of the superabsorbent in the incontinence product from 6.0 to pH 4.5 and pH 4.9 significantly (P disposable absorbent products to inhibit bacterial growth and ammonia production. This technique, we describe, provides a pragmatic method for assessing the odor-inhibiting capacity of specific incontinence products.

RESULTS OF INITIAL AMMONIA OXIDATION TESTING

Energy Technology Data Exchange (ETDEWEB)

Nash, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Fowley, M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2016-12-30

This memo presents an experimental survey of aqueous phase chemical processes to remove aqueous ammonia from waste process streams. Ammonia is generated in both the current Hanford waste flowsheet and in future waste processing. Much ammonia will be generated in the Low Activity Waste (LAW) melters.i Testing with simulants in glass melters at Catholic University has demonstrated the significant ammonia production.ii The primary reaction there is the reducing action of sugar on nitrate in the melter cold cap. Ammonia has been found to be a problem in secondary waste stabilization. Ammonia vapors are noxious and destruction of ammonia could reduce hazards to waste treatment process personnel. It is easily evolved especially when ammonia-bearing solutions are adjusted to high pH.

Molecular Analysis of Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in Compost and Composted Materials

Science.gov (United States)

Kowalchuk, George A.; Naoumenko, Zinaida S.; Derikx, Piet J. L.; Felske, Andreas; Stephen, John R.; Arkhipchenko, Irina A.

1999-01-01

Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous compound in composting material, and the conversion of this compound to nitrite in the environment by chemolithotrophic ammonia-oxidizing bacteria is an essential step in nitrogen cycling. Therefore, the distribution of ammonia-oxidizing members of the β subdivision of the class Proteobacteria in a variety of composting materials was assessed by amplifying 16S ribosomal DNA (rDNA) and 16S rRNA by PCR and reverse transcriptase PCR (RT-PCR), respectively. The PCR and RT-PCR products were separated by denaturing gradient gel electrophoresis (DGGE) and were identified by hybridization with a hierarchical set of oligonucleotide probes designed to detect ammonia oxidizer-like sequence clusters in the genera Nitrosospira and Nitrosomonas. Ammonia oxidizer-like 16S rDNA was detected in almost all of the materials tested, including industrial and experimental composts, manure, and commercial biofertilizers. A comparison of the DGGE and hybridization results after specific PCR and RT-PCR suggested that not all of the different ammonia oxidizer groups detected in compost are equally active. amoA, the gene encoding the active-site-containing subunit of ammonia monooxygenase, was also targeted by PCR, and template concentrations were estimated by competitive PCR. Detection of ammonia-oxidizing bacteria in the composts tested suggested that such materials may not be biologically inert with respect to nitrification and that the fate of nitrogen during composting and compost storage may be affected by the presence of these organisms. PMID:9925559

Biokinetics and bacterial communities of propionate oxidizing bacteria in phased anaerobic sludge digestion systems.

Science.gov (United States)

Zamanzadeh, Mirzaman; Parker, Wayne J; Verastegui, Yris; Neufeld, Josh D

2013-03-15

Phased anaerobic digestion is a promising technology and may be a potential source of bio-energy production. Anaerobic digesters are widely used for sewage sludge stabilization and thus a better understanding of the microbial process and kinetics may allow increased volatile solids reduction and methane production through robust process operation. In this study, we analyzed the impact of phase separation and operational conditions on the bio-kinetic characteristics and communities of bacteria associated with four phased anaerobic digestion systems. In addition to significant differences between bacterial communities associated with different digester operating temperatures, our results also revealed that bacterial communities in the phased anaerobic digestion systems differed between the 1st and 2nd phase digesters and we identified strong community composition correlations with several measured physicochemical parameters. The maximum specific growth rates of propionate oxidizing bacteria (POB) in the mesophilic and thermophilic 1st phases were 11 and 23.7 mgCOD mgCOD(-1) d(-1), respectively, while those of the mesophilic and thermophilic 2nd-phase digesters were 6.7 and 18.6 mgCOD mgCOD(-1) d(-1), respectively. Hence, the biokinetic characteristics of the POB population were dependent on the digester loading. In addition, we observed that the temperature dependency factor (θ) values were higher for the less heavily loaded digesters as compared to the values obtained for the 1st-phase digesters. Our results suggested the appropriate application of two sets of POB bio-kinetic that reflect the differing growth responses as a function of propionate concentration (and/or organic loading rates). Also, modeling acetogenesis in phased anaerobic sludge digestion systems will be improved considering a population shift in separate phases. On the basis of the bio-kinetic values estimated in various digesters, high levels of propionate in the thermophilic digesters may be

Changes in the ammonia-oxidizing bacteria community in response to operational parameters during the treatment of anaerobic sludge digester supernatant.

Science.gov (United States)

Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena; Bernat, Katarzyna; Kulikowska, Dorota; Wojnowska-Baryła, Irena

2012-07-01

The understanding of the relationship between ammoniaoxidizing bacteria (AOB) communities in activated sludge and the operational treatment parameters supports the control of the treatment of ammonia-rich wastewater. The modifications of treatment parameters by alteration of the number and length of aerobic and anaerobic stages in the sequencing batch reactor (SBR) working cycle may influence the efficiency of ammonium oxidation and induce changes in the AOB community. Therefore, in the research, the impact of an SBR cycle mode with alternating aeration/ mixing conditions (7 h/1 h vs. 4 h/5.5 h) and volumetric exchange rate (n) on AOB abundance and diversity in activated sludge during the treatment of anaerobic sludge digester supernatant at limited oxygen concentration in the aeration stage (0.7 mg O2/l) was assessed. AOB diversity expressed by the Shannon-Wiener index (H') was determined by the cycle mode. At aeration/mixing stage lengths of 7 h/1 h, H' averaged 2.48 +/- 0.17, while at 4 h/ 5.5 h it was 2.35 +/- 0.16. At the given mode, AOB diversity decreased with increasing n. The cycle mode did not affect AOB abundance; however, a higher AOB abundance in activated sludge was promoted by decreasing the volumetric exchange rate. The sequences clustering with Nitrosospira sp. NpAV revealed the uniqueness of the AOB community and the simultaneously lower ability of adaptation of Nitrosospira sp. to the operational parameters applied in comparison with Nitrosomonas sp.

Effect of metal oxide nanoparticles on microbial community structure and function in two different soil types.

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Sammy Frenk

Full Text Available Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO and magnetite (Fe3O4 nanosized (<50 nm particles. Two different soil types were examined: a sandy loam (Bet-Dagan and a sandy clay loam (Yatir, under two ENP concentrations (1%, 0.1%. Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe3O4 changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls

Science.gov (United States)

Bienhold, Christina; Wenzhöfer, Frank; Rossel, Pamela E.; Boetius, Antje

2017-01-01

Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100–1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls.

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Petra Pop Ristova

Full Text Available Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100-1700 m, but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were

Denaturing Gradient Gel Electrophoretic Analysis of Ammonia-Oxidizing Bacterial Community Structure in the Lower Seine River: Impact of Paris Wastewater Effluents

NARCIS (Netherlands)

Cébron, A.; Coci, M.; Garnier, J.; Laanbroek, H.J.

2004-01-01

The Seine River is strongly affected by the effluents from the Achères wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study

Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: Impact of Paris wastewater effluents

NARCIS (Netherlands)

Cebron, A.; Coci, M.; Garnier, J.; Laanbroek, H.J.

2004-01-01

The Seine River is strongly affected by the effluents from the Acheres wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study was

Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH

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Michele C ePereira e Silva

2012-03-01

Full Text Available The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively, and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 µgN.h-1.gdw-1 and 1.68 ± 0.11 µgN.h-1.gdw-1, being higher in soils with higher clay content (1.09 ± 0.12 µgN.h-1.gdw-1 and lower in soils with lower clay percentages (0.27 ± 0.04 µgN.h-1.gdw-1. Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10% the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%. Similar trends were observed for the sizes of these communities. The present work represents a first step towards defining a NOR for soil nitrification. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil-type-specific manner.

Cultivation and genomic analysis of Candidatus Nitrosocaldus islandicus, a novel obligately thermophilic ammonia-oxidizing Thaumarchaeon

OpenAIRE

De La Torre, Jose; Kirkegaard, Rasmus; Daebeler, Anne; Sedlacek, Christopher; Wagner, Michael; Daims, Holger; Pjevac, Petra; Albersten, Mads; Vierheilig, Julia; Herbold, Craig

2017-01-01

Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaea are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaea in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50 C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a nov...

Microbial community structure of relict niter-beds previously used for saltpeter production.

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Takashi Narihiro

Full Text Available From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA. The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA, respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

Denaturing Gradient Gel Electrophoretic Analysis of Ammonia-Oxidizing Bacterial Community Structure in the Lower Seine River: Impact of Paris Wastewater Effluents

NARCIS (Netherlands)

Cébron, A.; Coci, M.; Garnier, J.; Laanbroek, H.J.

2004-01-01

The Seine River is strongly affected by the effluents from the Achères wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study was

Treatment of ammonia by catalytic wet oxidation process over platinum-rhodium bimetallic catalyst in a trickle-bed reactor: effect of pH.

Science.gov (United States)

Hung, Chang-Mao; Lin, Wei-Bang; Ho, Ching-Lin; Shen, Yun-Hwei; Hsia, Shao-Yi

2010-08-01

This work adopted aqueous solutions of ammonia for use in catalytic liquid-phase reduction in a trickle-bed reactor with a platinum-rhodium bimetallic catalyst, prepared by the co-precipitation of chloroplatinic acid (H2PtCl6) and rhodium nitrate [Rh(NO3)3]. The experimental results demonstrated that a minimal amount of ammonia was removed from the solution by wet oxidation in the absence of any catalyst, while approximately 97.0% of the ammonia was removed by wet oxidation over the platinum-rhodium bimetallic catalyst at 230 degrees C with an oxygen partial pressure of 2.0 MPa. The oxidation of ammonia has been studied as a function of pH, and the main reaction products were determined. A synergistic effect is manifest in the platinum-rhodium bimetallic structure, in which the material has the greatest capacity to reduce ammonia. The reaction pathway linked the oxidizing ammonia to nitric oxide, nitrogen, and water.

Potential nitrous oxide yield of AOA vs. AOB and utilization of carbon and nitrogen in the ammonia oxidizing process in the Pearl River Estuary

Science.gov (United States)

Ma, L.; Dai, M.; Tan, S.; Xia, X.; Liu, H.

2016-12-01

Nitrous oxide (N2O), a greenhouse gas, is a by-product during ammonia oxidation process, the production of which is often stimulated under low dissolved oxygen (DO) in the estuarine environment. The potential yield of N2O has been considered to be driven by ammonia-oxidizing bacteria (AOB) of Betaproteobacteria & Gammaproteobacteria and/or ammonia-oxidizing archaea (AOA) of Thaumarchaeota. In order to examine the relative importance of AOA and AOB in producing N2O and in modulating the potential N2O yield, arch-amoA, beta-amoA, gamma-amoA encoding for the alpha subunit of the ammonia monooxygenase (AMO) are used as biomarkers to identify the distributions and bioactivities of AOA and AOB in the Pearl River Estuary (PRE). Size fractionation experiments were conducted to distinguish AOA and AOB on particles in different size-fractions of > 3 μm, 0.45-3 μm, and 0.22-0.45 μm. Pure culture of N. maritimusSCM1 was studied as a model organism to identify the organic carbon production during ammonia oxidation by SCM1 strains. Our results show that AOA distributes largely in the free-living state and could adapt to very limited ammonia substrate and low saturation of DO; AOB mainly distributes at the particle-attached state under relative richer ammonia and high DO conditions; however, the RNA/DNA ratio of AOB was higher than that of AOA under the same conditions suggesting AOB is relatively more actively expressed. In the upper reach of PRE, the dominant microorganism in the water column was AOB and the in situ N2O/NH3 therein ranged 0.73-3.74 ‰. In the lower PRE, AOA was dominated, and the in situ N2O/NH3 was of 1.17- 7.32‰. At selected sites, we estimated isotope effect (e) of AOA (eDIC/bulk) as -23.94‰ and AOB (eDIC/bulk) as -56.6‰ to -44.8‰, which is consistent with the studies of pure cultures. The coefficient of C sequestration "k", defined as (C biomass / DIC in situ) / (N biomass / ammonia in situ) to differ the utilization of carbon and nitrogen, of

Diazotrophic Bacterial Community of Degraded Pastures

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João Tiago Correia Oliveira

2017-01-01

Full Text Available Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN of bacteria per gram of sample, in order to determine population density and calculate the Shannon-Weaver diversity index. The diversity of total diazotrophic bacterial community was determined by the technique of Denaturing Gradient Gel Electrophoresis (DGGE of the nifH gene, while the diversity of the culturable diazotrophic bacteria was determined by the Polymerase Chain Reaction (BOX-PCR technique. The increase in the degradation stage of the B. decumbens Stapf. pasture did not reduce the population density of the cultivated diazotrophic bacterial community, suggesting that the degradation at any degree of severity was highly harmful to the bacteria. The structure of the total diazotrophic bacterial community associated with B. decumbens Stapf. was altered by the pasture degradation stage, suggesting a high adaptive capacity of the bacteria to altered environments.

Antibiotics promote aggregation within aquatic bacterial communities

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Gianluca eCorno

2014-07-01

Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

Performance evaluation and microbial community analysis of the function and fate of ammonia in a sulfate-reducing EGSB reactor.

Science.gov (United States)

Wang, Depeng; Liu, Bo; Ding, Xinchun; Sun, Xinbo; Liang, Zi; Sheng, Shixiong; Du, Lingfeng

2017-10-01

Ammonia is widely distributed in sulfate-reducing bioreactor dealing with sulfate wastewater, which shows potential effect on the metabolic pathway of sulfate and ammonia. This study investigates the sulfate-reducing efficiency and microbial community composition in the sulfate-reducing EGSB reactor with the increasing ammonia loading. Results indicated that, compared with low ammonia loading (166-666 mg/L), the sulfate and organic matter removal efficiencies were improved gradually with the appropriate ammonia loading (1000-2000 mg/L), which increased from 63.58 ± 3.81 to 71.08 ± 1.36% and from 66.24 ± 1.32 to 81.88 ± 1.83%, respectively. Meanwhile, with the appropriate ratio of ammonia and sulfate (1.5-3.0) and hydraulic retention time (21 h), the sulfate-reducing anaerobic ammonia oxidation (SRAO) process was occurred efficiently, inducing the accumulation of S 0 (270 mg/L) and the simultaneous ammonia removal (70.83%) in EGSB reactor. Moreover, the key sulfate-reducing bacteria (SRB) (Desulfovibrio) and denitrification bacteria (Pseudomonas and Alcaligenes) were responsible for the sulfate and nitrogen removal in these phases, which accounted for 3.66-5.54 and 3.85-9.13%, respectively. However, as the ammonia loading higher than 3000 mg/L (phases 9 and 10), the sulfate-reducing efficiency was decreased to only 28.3 ± 1.26% with the ammonia removal rate of 18.4 ± 3.37% in the EGSB reactor. Meanwhile, the predominant SRB in phases 9 and 10 were Desulfomicrobium (1.22-1.99%) and Desulfocurvus (4.0-5.46%), and the denitrification bacteria accounted for only 0.88% (phase 10), indicating the low nitrogen removal rate.

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

OpenAIRE

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bact...

Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem.

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Zhu Chen

Full Text Available The Grain to Green Project (GGP is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L. or shrubs (Caragana korshinskii Kom.. In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.. A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems.

Stable isotope probing of acetate fed anaerobic batch incubations shows a partial resistance of acetoclastic methanogenesis catalyzed by Methanosarcina to sudden increase of ammonia level.

Science.gov (United States)

Hao, Liping; Lü, Fan; Mazéas, Laurent; Desmond-Le Quéméner, Elie; Madigou, Céline; Guenne, Angéline; Shao, Liming; Bouchez, Théodore; He, Pinjing

2015-02-01

Ammonia inhibition represents a major operational issue for anaerobic digestion. In order to refine our understanding of the terminal catabolic steps in thermophilic anaerobic digestion under ammonia stress, we studied batch thermophilic acetate fed experiments at low (0.26 g L(-1)) and high (7.00 g L(-1)) Total Ammonia Nitrogen concentrations (TAN). Although methane production started immediately for all incubations and resulted in methane yields close to stoichiometric expectations, a 62-72% decrease of methanogenic rate was observed throughout the incubation at 7.00 g L(-1) of TAN compared to 0.26 g L(-1). Stable Isotope Probing analysis of active microbial communities in (13)C-acetate fed experiments coupled to automated ribosomal intergenic spacer analysis and 16S rDNA pyrotag sequencing confirmed that microbial communities were similar for both TAN conditions. At both TAN levels, the (13)C-labeled bacterial community was mainly affiliated to Clostridia-relatives, with OPB54 bacteria being the most abundant sequence in the heavy DNA 16S rDNA pyrotag library. Sequences closely related to Methanosarcina thermophila were also abundantly retrieved in the heavy DNA fractions, showing that this methanogen was still actively assimilating labeled carbon from acetate at free ammonia nitrogen concentrations up to 916 mg L(-1). Stable isotopic signature analysis of biogas, measured in unlabeled acetate fed experiments that were conducted in parallel, confirmed that acetoclastic methanogenic pathway was dominant at both ammonia concentrations. Our work demonstrates that, besides the syntrophic acetate oxidation pathway, acetoclastic methanogenesis catalyzed by Methanosarcina can also play a major role in methane production at high ammonia levels. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

NARCIS (Netherlands)

Jung, M.Y.; Park, S.J.; Min, D.; Kim, J.S.; Rijpstra, W.I.C.; Sinninghe Damsté, J.S.; Kim, G.J.; Madsen, E.L.; Rhee, S.K.

2011-01-01

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

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem.

Science.gov (United States)

Hao, Yi; Ma, Chuanxin; Zhang, Zetian; Song, Youhong; Cao, Weidong; Guo, Jing; Zhou, Guopeng; Rui, Yukui; Liu, Liming; Xing, Baoshan

2018-01-01

The aim of this study was to compare the toxicity effects of carbon nanomaterials (CNMs), namely fullerene (C 60 ), reduced graphene oxide (rGO) and multi-walled carbon nanotubes (MWCNTs), on a mini-ecosystem of rice grown in a loamy potted soil. We measured plant physiological and biochemical parameters and examined bacterial community composition in the CNMs-treated plant-soil system. After 30 days of exposure, all the three CNMs negatively affected the shoot height and root length of rice, significantly decreased root cortical cells diameter and resulted in shrinkage and deformation of cells, regardless of exposure doses (50 or 500 mg/kg). Additionally, at the high exposure dose of CNM, the concentrations of four phytohormones, including auxin, indoleacetic acid, brassinosteroid and gibberellin acid 4 in rice roots significantly increased as compared to the control. At the high exposure dose of MWCNTs and C 60 , activities of the antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) in roots increased significantly. High-throughput sequencing showed that three typical CNMs had little effect on shifting the predominant soil bacterial species, but the presence of CNMs significantly altered the composition of the bacterial community. Our results indicate that different CNMs indeed resulted in environmental toxicity to rice and soil bacterial community in the rhizosphere and suggest that CNMs themselves and their incorporated products should be reasonably used to control their release/discharge into the environment to prevent their toxic effects on living organisms and the potential risks to food safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

Community-acquired bacterial meningitis

NARCIS (Netherlands)

van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G.; Wijdicks, Eelco

2016-01-01

Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma

Optimization of Pt-Ir on carbon fiber paper for the electro-oxidation of ammonia in alkaline media

International Nuclear Information System (INIS)

Boggs, Bryan K.; Botte, Gerardine G.

2010-01-01

Plating bath concentrations of Pt(IV) and Ir(III) have been optimized as well as the total catalytic loading of bimetallic Pt-Ir alloy for the electro-oxidation of ammonia in alkaline media at standard conditions. This was accomplished using cyclic voltammetry, scanning electron microscopy (SEM), energy dispersive X-ray (EDX), and statistical optimization tools. Concentrations of Pt(IV) and Ir(III) of the plating bath strongly influence electrode surface atomic compositions of the Pt-Ir alloy directly affecting the electro-oxidation behavior of ammonia. Several anode materials were studied using cyclic voltammetry, which demonstrated that Pt-Ir was the most active catalyst for the electro-oxidation of ammonia. Criteria for optimization were minimizing the climatic oxidation overpotential for ammonia and maximizing the exchange current density. Optimized bath composition was found to be 8.844 ± 0.001 g L -1 Pt(IV) and 4.112 ± 0.001 g L -1 Ir(III) based on electrochemical techniques. Physical characterization of the electrodes by SEM indicates that the plating bath concentrations of Pt and Ir influence the growth and deposition behavior of the alloy.

Continuous measurements of ammonia, nitrous oxide and methane from air scrubbers at pig housing facilities.

Science.gov (United States)

Van der Heyden, C; Brusselman, E; Volcke, E I P; Demeyer, P

2016-10-01

Ammonia, largely emitted by agriculture, involves a great risk for eutrophication and acidification leading to biodiversity loss. Air scrubbers are widely applied to reduce ammonia emission from pig and poultry housing facilities, but it is not always clear whether their performance meets the requirements. Besides, there is a growing international concern for the livestock related greenhouse gases methane and nitrous oxide but hardly any data concerning their fate in air scrubbers are available. This contribution presents the results from measurement campaigns conducted at a chemical, a biological and a two-stage biological air scrubber installed at pig housing facilities in Flanders. Ammonia, nitrous oxide and methane at the inlet and outlet of the air scrubbers were monitored on-line during one week using a photoacoustic gas monitor, which allowed to investigate diurnal fluctuations in the removal performance of air scrubbers. Additionally, the homogeneity of the air scrubbers, normally checked by gas detection tubes, was investigated in more detail using the continuous data. The biological air scrubber with extra nitrification tank performed well in terms of ammonia removal (86 ± 6%), while the two-stage air scrubber suffered from nitrifying bacteria inhibition. In the chemical air scrubber the pH was not kept constant, lowering the ammonia removal efficiency. A lower ammonia removal efficiency was found during the day, when the ventilation rate was the highest. Nitrous oxide was produced inside the biological and two-stage scrubber, resulting in an increased outlet concentration of more than 200%. Methane could not be removed in the different air scrubbers because of its low water solubility. Copyright © 2016 Elsevier Ltd. All rights reserved.

Indium oxide thin film based ammonia gas and ethanol vapour sensor

Indian Academy of Sciences (India)

Unknown

acetone and dried under an electric lamp (100 W). Thin films of indium oxide ... A λ-19, UV–VIS Spectrophotometer (Perkin Elmer, USA) was used for measuring .... tion of ammonia is observed through glowing of LED. LM3914, LED driver is ...

Bacterial community affects toxin production by Gymnodinium catenatum.

Directory of Open Access Journals (Sweden)

Maria E Albinsson

Full Text Available The paralytic shellfish toxin (PST-producing dinoflagellate Gymnodinium catenatum grows in association with a complex marine bacterial community that is both essential for growth and can alter culture growth dynamics. Using a bacterial community replacement approach, we examined the intracellular PST content, production rate, and profile of G. catenatum cultures grown with bacterial communities of differing complexity and composition. Clonal offspring were established from surface-sterilized resting cysts (produced by sexual crosses of strain GCDE06 and strain GCLV01 and grown with: 1 complex bacterial communities derived from each of the two parent cultures; 2 simplified bacterial communities composed of the G. catenatum-associated bacteria Marinobacter sp. strain DG879 or Alcanivorax sp. strain DG881; 3 a complex bacterial community associated with an untreated, unsterilized sexual cross of the parents. Toxin content (STX-equivalent per cell of clonal offspring (134-197 fmol STX cell(-1 was similar to the parent cultures (169-206 fmol STX cell(-1, however cultures grown with single bacterial types contained less toxin (134-146 fmol STX cell(-1 than offspring or parent cultures grown with more complex mixed bacterial communities (152-176 fmol STX cell(-1. Specific toxin production rate (fmol STX day(-1 was strongly correlated with culture growth rate. Net toxin production rate (fmol STX cell(-1 day(-1 did not differ among treatments, however, mean net toxin production rate of offspring was 8-fold lower than the parent cultures, suggesting that completion of the sexual lifecycle in laboratory cultures leads to reduced toxin production. The PST profiles of offspring cultures were most similar to parent GCDE06 with the exception of cultures grown with Marinobacter sp. DG879 which produced higher proportions of dcGTX2+3 and GC1+2, and lower proportions of C1+2 and C3+4. Our data demonstrate that the bacterial community can alter intracellular STX

Bacterial community affects toxin production by Gymnodinium catenatum.

Science.gov (United States)

Albinsson, Maria E; Negri, Andrew P; Blackburn, Susan I; Bolch, Christopher J S

2014-01-01

The paralytic shellfish toxin (PST)-producing dinoflagellate Gymnodinium catenatum grows in association with a complex marine bacterial community that is both essential for growth and can alter culture growth dynamics. Using a bacterial community replacement approach, we examined the intracellular PST content, production rate, and profile of G. catenatum cultures grown with bacterial communities of differing complexity and composition. Clonal offspring were established from surface-sterilized resting cysts (produced by sexual crosses of strain GCDE06 and strain GCLV01) and grown with: 1) complex bacterial communities derived from each of the two parent cultures; 2) simplified bacterial communities composed of the G. catenatum-associated bacteria Marinobacter sp. strain DG879 or Alcanivorax sp. strain DG881; 3) a complex bacterial community associated with an untreated, unsterilized sexual cross of the parents. Toxin content (STX-equivalent per cell) of clonal offspring (134-197 fmol STX cell(-1)) was similar to the parent cultures (169-206 fmol STX cell(-1)), however cultures grown with single bacterial types contained less toxin (134-146 fmol STX cell(-1)) than offspring or parent cultures grown with more complex mixed bacterial communities (152-176 fmol STX cell(-1)). Specific toxin production rate (fmol STX day(-1)) was strongly correlated with culture growth rate. Net toxin production rate (fmol STX cell(-1) day(-1)) did not differ among treatments, however, mean net toxin production rate of offspring was 8-fold lower than the parent cultures, suggesting that completion of the sexual lifecycle in laboratory cultures leads to reduced toxin production. The PST profiles of offspring cultures were most similar to parent GCDE06 with the exception of cultures grown with Marinobacter sp. DG879 which produced higher proportions of dcGTX2+3 and GC1+2, and lower proportions of C1+2 and C3+4. Our data demonstrate that the bacterial community can alter intracellular STX

Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the western Pacific.

Science.gov (United States)

Cao, Huiluo; Hong, Yiguo; Li, Meng; Gu, Ji-Dong

2011-11-01

The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean.

Spatiotemporal Dynamics of Ammonia-Oxidizing Thaumarchaeota in Distinct Arctic Water Masses

Directory of Open Access Journals (Sweden)

Oliver Müller

2018-01-01

Full Text Available One of the most abundant archaeal groups on Earth is the Thaumarchaeota. They are recognized as major contributors to marine ammonia oxidation, a crucial step in the biogeochemical cycling of nitrogen. Their universal success is attributed to a high genomic flexibility and niche adaptability. Based on differences in the gene coding for ammonia monooxygenase subunit A (amoA, two different ecotypes with distinct distribution patterns in the water column have been identified. We used high-throughput sequencing of 16S rRNA genes combined with archaeal amoA functional gene clone libraries to investigate which environmental factors are driving the distribution of Thaumarchaeota ecotypes in the Atlantic gateway to the Arctic Ocean through an annual cycle in 2014. We observed the characteristic vertical pattern of Thaumarchaeota abundance with high values in the mesopelagic (>200 m water throughout the entire year, but also in the epipelagic (<200 m water during the dark winter months (January, March and November. The Thaumarchaeota community was dominated by three OTUs which on average comprised 76% ± 11 and varied in relative abundance according to water mass characteristics and not to depth or ammonium concentration, as suggested in previous studies. The ratios of the abundance of the different OTU types were similar to that of the functional amoA water cluster types. Together, this suggests a strong selection of ecotypes within different water masses, supporting the general idea of water mass characteristics as an important factor in defining microbial community structure. If indeed, as suggested in this study, Thaumarchaeota population dynamics are controlled by a set of factors, described here as water mass characteristics and not just depth alone, then changes in water mass flow will inevitably affect the distribution of the different ecotypes.

High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA.

Directory of Open Access Journals (Sweden)

Curtis J Hayden

Full Text Available Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems--and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA and bacteria (AOB in 9 high-altitude lakes (2289-3160 m in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r(2 = 0.32, p<0.1, whereas AOA abundance was inversely correlated with lake elevation (r(2 = 0.43, p<0.05. We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome.

Science.gov (United States)

De Vrieze, Jo; Saunders, Aaron Marc; He, Ying; Fang, Jing; Nielsen, Per Halkjaer; Verstraete, Willy; Boon, Nico

2015-05-15

Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub

Ammonia modification of activated carbon to enhance carbon dioxide adsorption: Effect of pre-oxidation

Science.gov (United States)

Shafeeyan, Mohammad Saleh; Daud, Wan Mohd Ashri Wan; Houshmand, Amirhossein; Arami-Niya, Arash

2011-02-01

A commercial granular activated carbon (GAC) was subjected to thermal treatment with ammonia for obtaining an efficient carbon dioxide (CO2) adsorbent. In general, CO2 adsorption capacity of activated carbon can be increased by introduction of basic nitrogen functionalities onto the carbon surface. In this work, the effect of oxygen surface groups before introduction of basic nitrogen functionalities to the carbon surface on CO2 adsorption capacity was investigated. For this purpose two different approaches of ammonia treatment without preliminary oxidation and amination of oxidized samples were studied. Modified carbons were characterized by elemental analysis and Fourier Transform Infrared spectroscopy (FT-IR) to study the impact of changes in surface chemistry and formation of specific surface groups on adsorption properties. The texture of the samples was characterized by conducting N2 adsorption/desorption at -196 °C. CO2 capture performance of the samples was investigated using a thermogravimetric analysis (TGA). It was found that in both modification techniques, the presence of nitrogen functionalities on carbon surface generally increased the CO2 adsorption capacity. The results indicated that oxidation followed by high temperature ammonia treatment (800 °C) considerably enhanced the CO2 uptake at higher temperatures.

3,4-Dimethylpyrazole phosphate (DMPP) reduces activity of ammonia oxidizers without adverse effects on non-target soil microorganisms and functions

DEFF Research Database (Denmark)

Kong, Xianwang; Duan, Yun-Feng (Kevin); Schramm, Andreas

2016-01-01

, dehydrogenase activity, phospholipid fatty acid composition and potential ammonia oxidation. DMPP showed no significant nontarget effects (p > 0.05), but a possible stress response in HD was indicated by a factor analysis of phospholipid fatty acid composition. There was a strong DMPP inhibition on potential...... of ammonia oxidation. We investigated effects of DMPP amendment equivalent to 0 (Control), 1 (regular dose, RD) or 10 (high dose, HD) kg ha1 in a sandy loam grassland soil at 50% water-filled pore space. Following incubation for 1, 7 or 14 d, soil was analyzed for fluorescein diacetate hydrolysis...... ammonia oxidation which was still significant (p HD after 14 d. In separate treatments receiving 50 mg NH4 +-N kg1 dry soil in addition to DMPP, the inhibition of nitrate accumulation was similar in RD and HD at around 75%. Abundances of the gene amoA from ammonia oxidizing bacteria (AOB...

Minerals in soil select distinct bacterial communities in their microhabitats.

Science.gov (United States)

Carson, Jennifer K; Campbell, Louise; Rooney, Deirdre; Clipson, Nicholas; Gleeson, Deirdre B

2009-03-01

We tested the hypothesis that different minerals in soil select distinct bacterial communities in their microhabitats. Mica (M), basalt (B) and rock phosphate (RP) were incubated separately in soil planted with Trifolium subterraneum, Lolium rigidum or left unplanted. After 70 days, the mineral and soil fractions were separated by sieving. Automated ribosomal intergenic spacer analysis was used to determine whether the bacterial community structure was affected by the mineral, fraction and plant treatments. Principal coordinate plots showed clustering of bacterial communities from different fraction and mineral treatments, but not from different plant treatments. Permutational multivariate anova (permanova) showed that the microhabitats of M, B and RP selected bacterial communities different from each other in unplanted and L. rigidum, and in T. subterraneum, bacterial communities from M and B differed (Ppermanova also showed that each mineral fraction selected bacterial communities different from the surrounding soil fraction (P<0.05). This study shows that the structure of bacterial communities in soil is influenced by the mineral substrates in their microhabitat and that minerals in soil play a greater role in bacterial ecology than simply providing an inert matrix for bacterial growth. This study suggests that mineral heterogeneity in soil contributes to the spatial variation in bacterial communities.

[Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities].

Science.gov (United States)

Pivovarova, T A; Bulaev, A G; Roshchupko, P V; Belyĭ, A V; Kondrat'eva, T F

2012-01-01

Aboriginal and experimental (constructed of pure microbial cultures) communities of acidophilic chemolithotrophs have been studied. The oxidation of elemental sulfur, sodium thiosulfate, and potassium tetrathionate as sole sources of energy has been monitored. The oxidation rate of the experimental community is higher as compared to the aboriginal community isolated from a flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore. The degree of oxidation of the mentioned S substrates amounts to 17.91, 68.30, and 93.94% for the experimental microbial community and to 10.71, 56.03, and 79.50% for the aboriginal community, respectively. The degree of oxidation of sulfur sulfide forms in the ore flotation concentrate is 59.15% by the aboriginal microbial community and 49.40% by the experimental microbial community. Despite a higher rate of oxidation of S substrates as a sole source of energy by the experimental microbial community, the aboriginal community oxidizes S substrates at a higher rate in the flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore, from which it was isolated. Bacterial-chemical oxidation of the flotation concentrate by the aboriginal microbial community allows for the extraction of an additional 32.3% of gold from sulfide minerals, which is by 5.7% larger compared to the yield obtained by the experimental microbial community.

Time-scales of hydrological forcing on the geochemistry and bacterial community structure of temperate peat soils

Science.gov (United States)

Nunes, Flavia L. D.; Aquilina, Luc; De Ridder, Jo; Francez, André-Jean; Quaiser, Achim; Caudal, Jean-Pierre; Vandenkoornhuyse, Philippe; Dufresne, Alexis

2015-10-01

Peatlands are an important global carbon reservoir. The continued accumulation of carbon in peatlands depends on the persistence of anoxic conditions, in part induced by water saturation, which prevents oxidation of organic matter, and slows down decomposition. Here we investigate how and over what time scales the hydrological regime impacts the geochemistry and the bacterial community structure of temperate peat soils. Peat cores from two sites having contrasting groundwater budgets were subjected to four controlled drought-rewetting cycles. Pore water geochemistry and metagenomic profiling of bacterial communities showed that frequent water table drawdown induced lower concentrations of dissolved carbon, higher concentrations of sulfate and iron and reduced bacterial richness and diversity in the peat soil and water. Short-term drought cycles (3-9 day frequency) resulted in different communities from continuously saturated environments. Furthermore, the site that has more frequently experienced water table drawdown during the last two decades presented the most striking shifts in bacterial community structure, altering biogeochemical functioning of peat soils. Our results suggest that the increase in frequency and duration of drought conditions under changing climatic conditions or water resource use can induce profound changes in bacterial communities, with potentially severe consequences for carbon storage in temperate peatlands.

Temporally invariable bacterial community structure in the Arabian Sea oxygen minimum zone.

Digital Repository Service at National Institute of Oceanography (India)

Jain, A.; Bandekar, M.; Gomes, J.; Shenoy, D.M.; Meena, R.M.; Naik, H.; Khandeparkar, R.; Ramaiah, N.

determining ammonia-oxidizing organism distribution and diversity in marine environments. Environ Microbiol 14: 714-729 Bulow SE, Rich JJ, Naik HS, Pratihary AK, Ward BB (2010) Denitrification exceeds anammox as a nitrogen loss pathway in the Arabian Sea... losses of fixed nitrogen to the atmosphere through denitrification (Naqvi 1994) and anaerobic oxidation of ammonia (anammox, Dalsgaard et al 2012). Although OMZ regions represent only a small fraction (~1%) of the global ocean volume (as per World...

Determinants of bacterial communities in Canadian agroforestry systems.

Science.gov (United States)

Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

2016-06-01

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.

Science.gov (United States)

Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Zhang, Zhaojing; Wang, Jingwei; Liu, Ziyan; Li, Duanxing; Li, Huijie; Zhou, Jiti

2015-03-01

In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Influence of Uranium on Bacterial Communities: A Comparison of Natural Uranium-Rich Soils with Controls

Science.gov (United States)

Mondani, Laure; Benzerara, Karim; Carrière, Marie; Christen, Richard; Mamindy-Pajany, Yannick; Février, Laureline; Marmier, Nicolas; Achouak, Wafa; Nardoux, Pascal; Berthomieu, Catherine; Chapon, Virginie

2011-01-01

This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil. PMID:21998695

Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.

Science.gov (United States)

Daebeler, Anne; Herbold, Craig W; Vierheilig, Julia; Sedlacek, Christopher J; Pjevac, Petra; Albertsen, Mads; Kirkegaard, Rasmus H; de la Torre, José R; Daims, Holger; Wagner, Michael

2018-01-01

Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as " Candidatus Nitrosocaldus islandicus," is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. " Ca. N. islandicus" encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as " Ca. N. islandicus" is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that " Ca. N. islandicus" has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase ( iorAB ) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.

Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades.

Science.gov (United States)

Chauhan, Ashvini; Pathak, Ashish; Ogram, Andrew

2012-10-01

Agricultural runoff of phosphorus (P) in the northern Florida Everglades has resulted in several ecosystem level changes, including shifts in the microbial ecology of carbon cycling, with significantly higher methane being produced in the nutrient-enriched soils. Little is, however, known of the structure and activities of methane-oxidizing bacteria (MOB) in these environments. To address this, 0 to 10 cm plant-associated soil cores were collected from nutrient-impacted (F1), transition (F4), and unimpacted (U3) areas, sectioned in 2-cm increments, and methane oxidation rates were measured. F1 soils consumed approximately two-fold higher methane than U3 soils; additionally, most probable numbers of methanotrophs were 4-log higher in F1 than U3 soils. Metabolically active MOB containing pmoA sequences were characterized by stable-isotope probing using 10 % (v/v) (13)CH(4). pmoA sequences, encoding the alpha subunit of methane monooxygenase and related to type I methanotrophs, were identified from both impacted and unimpacted soils. Additionally, impacted soils also harbored type II methanotrophs, which have been shown to exhibit preferences for high methane concentrations. Additionally, across all soils, novel pmoA-type sequences were also detected, indicating presence of MOB specific to the Everglades. Multivariate statistical analyses confirmed that eutrophic soils consisted of metabolically distinct MOB community that is likely driven by nutrient enrichment. This study enhances our understanding on the biological fate of methane being produced in productive wetland soils of the Florida Everglades and how nutrient-enrichment affects the composition of methanotroph bacterial communities.

Metamorphosis of a butterfly-associated bacterial community.

Science.gov (United States)

Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Metamorphosis of a butterfly-associated bacterial community.

Directory of Open Access Journals (Sweden)

Tobin J Hammer

Full Text Available Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Intensive Ammonia and Methane Oxidation in Organic Liquid Manure Crusts

DEFF Research Database (Denmark)

Nielsen, Daniel Aagren; Nielsen, Lars Peter; Schramm, Andreas

methane oxidizing bacteria (MOB) and are known to accumulate nitrite and nitrate, indicating the presence of ammonia oxidizers (AOB). We have surveyed six manure tanks with organic covers to investigate the prevalence of MOB and AOB and to link the potential activity with physical and chemical aspects...... characterized with respect to O2 availability by in situ profiling with electrochemical microsensors. Results show that oxygen penetration increased from few micrometers up to several centimetres with crust age. AOB and ammonium oxidation are ubiquitously present in well-developed manure crusts whereas MOB were...... also CH4 emission mitigation, an organic surface crust can be effective if populations of MOB and AOB are allowed to build up....

AMMONIA REMOVAL AND NITROUS OXIDE PRODUCTION IN GAS-PHASE COMPOST BIOFILTERS

Science.gov (United States)

Biofiltration technology is widely utilized for treating ammonia gas (NH3), with one of its potential detrimental by-products being nitrous oxide (N2O), a greenhouse gas approximately 300 times more reactive to infrared than CO2. The present work intends to provide the relation between NH3 removal d...

Insights into high-temperature nitrogen cycling from studies of the thermophilic ammonia-oxidizing archaeon Nitrosocaldus yellowstonii. (Invited)

Science.gov (United States)

de la Torre, J. R.

2010-12-01

Our understanding of the nitrogen cycle has advanced significantly in recent years with the discovery of new metabolic processes and the recognition that key processes such as aerobic ammonia oxidation are more broadly distributed among extant organisms and habitat ranges. Nitrification, the oxidation of ammonia to nitrite and nitrate, is a key component of the nitrogen cycle and, until recently, was thought to be mediated exclusively by the ammonia-oxidizing bacteria (AOB). The discovery that mesophilic marine archaea, some of the most abundant microorganisms on the planet, are capable of oxidizing ammonia to nitrite fundamentally changed our perception of the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) are now thought to be significant drivers of nitrification in many marine and terrestrial environments. Most studies, however, have focused on the contribution of AOA to nitrogen cycling in mesophilic environments. Our recent discovery of a thermophilic AOA, Nitrosocaldus yellowstonii, has expanded the role and habitat range of AOA to include high temperature environments. Numerous studies have shown that AOA are widely distributed in geothermal habitats with a wide range of temperature and pH. The availability of multiple AOA genome sequences, combined with metagenomic studies from mesophilic and thermophilic environments gives us a better understanding of the physiology, ecology and evolution of these organisms. Recent studies have proposed that the AOA represent the most deeply branching lineage within the Archaea, the Thaumarchaeota. Furthermore, genomic comparisons between AOA and AOB reveal significant differences in the proposed pathways for ammonia oxidation. These genetic differences likely explain fundamental physiological differences such as the resistance of N. yellowstonii and other AOA to the classical nitrification inhibitors allylthiourea and acetylene. Physiological studies suggest that the marine AOA are adapted to oligotrophic

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

Science.gov (United States)

Angell, John H; Peng, Xuefeng; Ji, Qixing; Craick, Ian; Jayakumar, Amal; Kearns, Patrick J; Ward, Bess B; Bowen, Jennifer L

2018-01-01

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes ( amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

Microbial community response reveals underlying mechanism of industrial-scale manganese sand biofilters used for the simultaneous removal of iron, manganese and ammonia from groundwater.

Science.gov (United States)

Zhang, Yu; Sun, Rui; Zhou, Aijuan; Zhang, Jiaguang; Luan, Yunbo; Jia, Jianna; Yue, Xiuping; Zhang, Jie

2018-01-08

Most studies have employed aeration-biofiltration process for the simultaneous removal of iron, manganese and ammonia in groundwater. However, what's inside the "black box", i.e., the potential contribution of functional microorganisms behavior and interactions have seldom been investigated. Moreover, little attention has been paid to the correlations between environmental variables and functional microorganisms. In this study, the performance of industrial-scale biofilters for the contaminated groundwater treatment was studied. The effluent were all far below the permitted concentration level in the current drinking water standard. Pyrosequencing illustrated that shifts in microbial community structure were observed in the microbial samples from different depths of filter. Microbial networks showed that the microbial community structure in the middle- and deep-layer samples was similar, in which a wide range of manganese-oxidizing bacteria was identified. By contrast, canonical correlation analysis showed that the bacteria capable of ammonia-oxidizing and nitrification was enriched in the upper-layer, i.e., Propionibacterium, Nitrosomonas, Nitrosomonas and Candidatus Nitrotoga. The stable biofilm on the biofilter media, created by certain microorganisms from the groundwater microflora, played a crucial role in the simultaneous removal of the three pollutants.

Diazotrophic Bacterial Community of Degraded Pastures

OpenAIRE

João Tiago Correia Oliveira; Everthon Fernandes Figueredo; Williane Patrícia da Silva Diniz; Lucianne Ferreira Paes de Oliveira; Pedro Avelino Maia de Andrade; Fernando Dini Andreote; Júlia Kuklinsky-Sobral; Danúbia Ramos de Lima; Fernando José Freire

2017-01-01

Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN) of bacteria per gram ...

Effect of ozonation on microbial fish pathogens, ammonia, nitrate, nitrite, and bod in simulated reuse hatchery water

Energy Technology Data Exchange (ETDEWEB)

Colberg, P.J.; Lingg, A.J.

1978-10-01

The effectiveness of ozone for eliminating fish pathogens and reducing nitrite, ammonia, and BOD associated with reuse hatchery systems was evaluated. Comparative survival rates of four bacterial fish pathogens and a bacterium-protozoan population during batch and continuous flow ozonation indicated a specific microbial ozone demand during batch treatment and 99% mortality of pathogens during continuous flow treatment. Oxidation of carbon and nitrite by ozone was rapid at low ozone concentrations; carbon and ammonia oxidation rates were pH dependent. The oxidation capacity of ozone in water was greatest at elevated pH even though lower ozone concentrations were used. Ozone treatment appears to be successful for disinfecting hatchery makeup water for recycling. However, the economics of such treatment are yet to be determined. (10 graphs, 28 references, 1 table)

Bacterial community changes in an industrial algae production system.

Science.gov (United States)

Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T

2018-04-01

While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.

Effects of aluminium oxide nanoparticles on bacterial growth

Directory of Open Access Journals (Sweden)

Doskocz Nina

2017-01-01

Full Text Available Production and wide application of nanomaterials have led to nanotechnology development but their release to environment and the induction of toxic reactions, affects the natural microbial communities. Therefore, studies on the impact of nanoparticles on microorganisms and environment are required and needed. The aim of this study was to assess the impact of aluminium oxide nanoparticles on the growth of Pseudomonas putida. To compare the harmfulness of different forms of aluminium oxide, the ecotoxicity of its macro-forms was also evaluated in the study. Research showed that the exposure to nanoparticles can negatively influence microorganisms. The EC50-16h determined in this study was 0.5 mg/l, and NOEC equaled 0.19 mg/l. Nano-Al2O3 proved to be more toxic to P. putida than aluminium oxide. This indicates that the nano-form of a given substance demonstrates different properties and may constitute a far greater danger for the environment than the same substance in the large form. According to EU and US EPA criteria, nano-Al2O3 proved to be very toxic and highly toxic, respectively. Changes in bacterial communities caused by nanoparticles may affect the normal biological, chemical and nutrient cycle in the ecosystem and the effect triggered by nanomaterials in relation to other organisms is unpredictable.

amoA Gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not Archaea dominate N cycling in the Colne Estuary, United Kingdom.

Science.gov (United States)

Li, Jialin; Nedwell, David B; Beddow, Jessica; Dumbrell, Alex J; McKew, Boyd A; Thorpe, Emma L; Whitby, Corinne

2015-01-01

Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw](-1) day(-1) in June, increasing to 37.4 μmol N gdw(-1) day(-1) in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw(-1) day(-1) in June, increasing to 11.7 μmol N gdw(-1) day(-1) in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Influence of additives on selective noncatalytic reduction of nitric oxide with ammonia in circulating fluidized bed boilers

DEFF Research Database (Denmark)

Leckner, Bo; Karlsson, Maria; Dam-Johansen, Kim

1991-01-01

The application of selective noncatalytic reduction of nitric oxide with ammonia in circulating fluidized bed boilers is investigated. Special attention is directed to the use of additives to the ammonia so that the efficiency of the NO reduction at lower temperatures can be increased. Tests under...

Bioaugmentation of Syntrophic Acetate-Oxidizing Culture in Biogas Reactors Exposed to Increasing Levels of Ammonia

Science.gov (United States)

Westerholm, Maria; Levén, Lotta

2012-01-01

The importance of syntrophic acetate oxidation for process stability in methanogenic systems operating at high ammonia concentrations has previously been emphasized. In this study we investigated bioaugmentation of syntrophic acetate-oxidizing (SAO) cultures as a possible method for decreasing the adaptation period of biogas reactors operating at gradually increased ammonia concentrations (1.5 to 11 g NH4+-N/liter). Whole stillage and cattle manure were codigested semicontinuously for about 460 days in four mesophilic anaerobic laboratory-scale reactors, and a fixed volume of SAO culture was added daily to two of the reactors. Reactor performance was evaluated in terms of biogas productivity, methane content, pH, alkalinity, and volatile fatty acid (VFA) content. The decomposition pathway of acetate was analyzed by isotopic tracer experiments, and population dynamics were monitored by quantitative PCR analyses. A shift in dominance from aceticlastic methanogenesis to SAO occurred simultaneously in all reactors, indicating no influence by bioaugmentation on the prevailing pathway. Higher abundances of Clostridium ultunense and Tepidanaerobacter acetatoxydans were associated with bioaugmentation, but no influence on Syntrophaceticus schinkii or the methanogenic population was distinguished. Overloading or accumulation of VFA did not cause notable dynamic effects on the population. Instead, the ammonia concentration had a substantial impact on the abundance level of the microorganisms surveyed. The addition of SAO culture did not affect process performance or stability against ammonia inhibition, and all four reactors deteriorated at high ammonia concentrations. Consequently, these findings further demonstrate the strong influence of ammonia on the methane-producing consortia and on the representative methanization pathway in mesophilic biogas reactors. PMID:22923397

Evaluation of autotrophic growth of ammonia-oxidizers associated with granular activated carbon used for drinking water purification by DNA-stable isotope probing.

Science.gov (United States)

Niu, Jia; Kasuga, Ikuro; Kurisu, Futoshi; Furumai, Hiroaki; Shigeeda, Takaaki

2013-12-01

Nitrification is an important biological function of granular activated carbon (GAC) used in advanced drinking water purification processes. Newly discovered ammonia-oxidizing archaea (AOA) have challenged the traditional understanding of ammonia oxidation, which considered ammonia-oxidizing bacteria (AOB) as the sole ammonia-oxidizers. Previous studies demonstrated the predominance of AOA on GAC, but the contributions of AOA and AOB to ammonia oxidation remain unclear. In the present study, DNA-stable isotope probing (DNA-SIP) was used to investigate the autotrophic growth of AOA and AOB associated with GAC at two different ammonium concentrations (0.14 mg N/L and 1.4 mg N/L). GAC samples collected from three full-scale drinking water purification plants in Tokyo, Japan, had different abundance of AOA and AOB. These samples were fed continuously with ammonium and (13)C-bicarbonate for 14 days. The DNA-SIP analysis demonstrated that only AOA assimilated (13)C-bicarbonate at low ammonium concentration, whereas AOA and AOB exhibited autotrophic growth at high ammonium concentration. This indicates that a lower ammonium concentration is preferable for AOA growth. Since AOA could not grow without ammonium, their autotrophic growth was coupled with ammonia oxidation. Overall, our results point towards an important role of AOA in nitrification in GAC filters treating low concentration of ammonium. Copyright © 2013 Elsevier Ltd. All rights reserved.

Functional recovery of biofilm bacterial communities after copper exposure

International Nuclear Information System (INIS)

Boivin, Marie-Elene Y.; Massieux, Boris; Breure, Anton M.; Greve, Gerdit D.; Rutgers, Michiel; Admiraal, Wim

2006-01-01

Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 μmol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 μmol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 μmol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days. - Genetically different bacterial communities can have similar functions and tolerance to copper

Inhibitory effects of C2 to C10 1-alkynes on ammonia oxidation in two Nitrososphaera species.

Science.gov (United States)

Taylor, A E; Taylor, K; Tennigkeit, B; Palatinszky, M; Stieglmeier, M; Myrold, D D; Schleper, C; Wagner, M; Bottomley, P J

2015-03-01

A previous study showed that ammonia oxidation by the Thaumarchaeota Nitrosopumilus maritimus (group 1.1a) was resistant to concentrations of the C8 1-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. In this study, the inhibitory effects of octyne and other C2 to C10 1-alkynes were evaluated on the nitrite production activity of two pure culture isolates from Thaumarchaeota group 1.1b, Nitrososphaera viennensis strain EN76 and Nitrososphaera gargensis. Both N. viennensis and N. gargensis were insensitive to concentrations of octyne that cause complete and irreversible inactivation of nitrite production by ammonia-oxidizing bacteria. However, octyne concentrations (≥20 μM) that did not inhibit N. maritimus partially inhibited nitrite production in N. viennensis and N. gargensis in a manner that did not show the characteristics of irreversible inactivation. In contrast to previous studies with an ammonia-oxidizing bacterium, Nitrosomonas europaea, octyne inhibition of N. viennensis was: (i) fully and immediately reversible, (ii) not competitive with NH4 (+), and (iii) without effect on the competitive interaction between NH4 (+) and acetylene. Both N. viennensis and N. gargensis demonstrated the same overall trend in regard to 1-alkyne inhibition as previously observed for N. maritimus, being highly sensitive to ≤C5 alkynes and more resistant to longer-chain length alkynes. Reproducible differences were observed among N. maritimus, N. viennensis, and N. gargensis in regard to the extent of their resistance/sensitivity to C6 and C7 1-alkynes, which may indicate differences in the ammonia monooxygenase binding and catalytic site(s) among the Thaumarchaeota. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Bacterial and archaeal communities in sediments of the north Chinese marginal seas.

Science.gov (United States)

Liu, Jiwen; Liu, Xiaoshou; Wang, Min; Qiao, Yanlu; Zheng, Yanfen; Zhang, Xiao-Hua

2015-07-01

Microbial communities of the Chinese marginal seas have rarely been reported. Here, bacterial and archaeal community structures and abundance in the surface sediment of four sea areas including the Bohai Sea (BS), North Yellow Sea (NYS), South Yellow Sea (SYS), and the north East China Sea (NECS) were surveyed by 16S ribosomal RNA (rRNA) gene pyrosequencing and quantitative PCR. The results showed that microbial communities of the four geographic areas were distinct from each other at the operational taxonomic unit (OTU) level, whereas the microbial communities of the BS, NYS, and SYS were more similar to each other than to the NECS at higher taxonomic levels. Across all samples, Bacteria were numerically dominant relative to Archaea, and among them, Gammaproteobacteria and Euryarchaeota were predominant in the BS, NYS, and SYS, while Deltaproteobacteria and Thaumarchaeota were prevalent in the NECS. The most abundant bacterial genera were putative sulfur oxidizer and sulfate reducer, suggesting that sulfur cycle processes might prevail in these areas, and the high abundance of dsrB (10(7)-10(8) copies g(-1)) in all sites verified the dominance of sulfate reducer in the north Chinese marginal seas. The differences in sediment sources among the sampling areas were potential explanations for the observed microbial community variations. Furthermore, temperature and dissolved oxygen of bottom water were significant environmental factors in determining both bacterial and archaeal communities, whereas chlorophyll a in sediment was significant only in structuring archaeal community. This study presented an outline of benthic microbial communities and provided insights into understanding the biogeochemical cycles in sediments of the north Chinese marginal seas.

Bacteria dominate ammonia oxidation in soils used for outdoor cattle overwintering

Czech Academy of Sciences Publication Activity Database

Radl, V.; Chroňáková, Alica; Čuhel, Jiří; Šimek, Miloslav; Elhottová, Dana; Welzl, G.; Schloter, M.

2014-01-01

Roč. 77, May (2014), s. 68-71 ISSN 0929-1393 R&D Projects: GA MŠk LC06066 Grant - others:Akademie věd ČR(CZ) D-CZ 45:05/06 Institutional support: RVO:60077344 Keywords : ammonia oxidation * bacteria * archaea * amoA diversity * urea * pasture Subject RIV: EH - Ecology, Behaviour Impact factor: 2.644, year: 2014

Resveratrol prevents ammonia toxicity in astroglial cells.

Directory of Open Access Journals (Sweden)

Larissa Daniele Bobermin

Full Text Available Ammonia is implicated as a neurotoxin in brain metabolic disorders associated with hyperammonemia. Acute ammonia toxicity can be mediated by an excitotoxic mechanism, oxidative stress and nitric oxide (NO production. Astrocytes interact with neurons, providing metabolic support and protecting against oxidative stress and excitotoxicity. Astrocytes also convert excess ammonia and glutamate into glutamine via glutamine synthetase (GS. Resveratrol, a polyphenol found in grapes and red wines, exhibits antioxidant and anti-inflammatory properties and modulates glial functions, such as glutamate metabolism. We investigated the effect of resveratrol on the production of reactive oxygen species (ROS, GS activity, S100B secretion, TNF-α, IL-1β and IL-6 levels in astroglial cells exposed to ammonia. Ammonia induced oxidative stress, decreased GS activity and increased cytokines release, probably by a mechanism dependent on protein kinase A (PKA and extracellular signal-regulated kinase (ERK pathways. Resveratrol prevented ammonia toxicity by modulating oxidative stress, glial and inflammatory responses. The ERK and nuclear factor-κB (NF-κB are involved in the protective effect of resveratrol on cytokines proinflammatory release. In contrast, other antioxidants (e.g., ascorbic acid and trolox were not effective against hyperammonemia. Thus, resveratrol could be used to protect against ammonia-induced neurotoxicity.

Resveratrol Prevents Ammonia Toxicity in Astroglial Cells

Science.gov (United States)

Guerra, Maria Cristina; Leite, Marina Concli; Souza, Diogo Onofre; Gonçalves, Carlos-Alberto; Gottfried, Carmem

2012-01-01

Ammonia is implicated as a neurotoxin in brain metabolic disorders associated with hyperammonemia. Acute ammonia toxicity can be mediated by an excitotoxic mechanism, oxidative stress and nitric oxide (NO) production. Astrocytes interact with neurons, providing metabolic support and protecting against oxidative stress and excitotoxicity. Astrocytes also convert excess ammonia and glutamate into glutamine via glutamine synthetase (GS). Resveratrol, a polyphenol found in grapes and red wines, exhibits antioxidant and anti-inflammatory properties and modulates glial functions, such as glutamate metabolism. We investigated the effect of resveratrol on the production of reactive oxygen species (ROS), GS activity, S100B secretion, TNF-α, IL-1β and IL-6 levels in astroglial cells exposed to ammonia. Ammonia induced oxidative stress, decreased GS activity and increased cytokines release, probably by a mechanism dependent on protein kinase A (PKA) and extracellular signal-regulated kinase (ERK) pathways. Resveratrol prevented ammonia toxicity by modulating oxidative stress, glial and inflammatory responses. The ERK and nuclear factor-κB (NF-κB) are involved in the protective effect of resveratrol on cytokines proinflammatory release. In contrast, other antioxidants (e.g., ascorbic acid and trolox) were not effective against hyperammonemia. Thus, resveratrol could be used to protect against ammonia-induced neurotoxicity. PMID:23284918

Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell.

Science.gov (United States)

Vilar-Sanz, Ariadna; Puig, Sebastià; García-Lledó, Arantzazu; Trias, Rosalia; Balaguer, M Dolors; Colprim, Jesús; Bañeras, Lluís

2013-01-01

The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A · m(-3) NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A · m(-3) NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation.

Review of Options for Ammonia/Ammonium Management

Energy Technology Data Exchange (ETDEWEB)

Nash, C. A. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2016-05-06

This report is a review of literature supporting practical ammonia/ammonium destruction processes. Melter research supporting Hanford Low Activity Waste (LAW) glass production has shown that significant amounts of ammonia will be in the melter offgas condensate. Further work with secondary waste forms indicates the potential need to remove the ammonia, perhaps by an oxidative process. This review finds likely practical chemical methods to oxidize ammonia in aqueous solution at moderate temperatures and atmospheric pressure, using easily obtained reagents. Leading candidates include nitrite oxidation to produce nitrogen gas, various peroxide oxidative processes, and air stripping. This work reviews many other processes and provides reasoning to not consider those processes further for this application.

Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

OpenAIRE

Yakimov, Michail M.; La Cono, Violetta; Smedile, Francesco; DeLuca, Thomas H.; Juarez, Silvia; Ciordia, Sergio; Fernandez, Marisol; Albar, Juan Pablo; Ferrer, Manuel; Golyshin, Peter N.; Giuliano, Laura

2011-01-01

Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and u...

Soil bacterial community shifts associated with sugarcane straw removal

Science.gov (United States)

Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

2017-04-01

In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

THE BIOENERGETICS OF AMMONIA AND HYDROXYLAMINE OXIDATION IN NITROSOMONAS-EUROPAEA AT ACID AND ALKALINE PH

NARCIS (Netherlands)

FRIJLINK, MJ; ABEE, T; LAANBROEK, HJ; DEBOER, W; KONINGS, WN

Autotrophic ammonia oxidizers depend on alkaline or neutral conditions for optimal activity. Below pH 7 growth and metabolic activity decrease dramatically. Actively oxidizing cells of Nitrosomonas europaea do not maintain a constant internal pH when the external pH is varied from 5 to 8. Studies of

Bacterial Communities Associated with the Lichen Symbiosis▿ †

Science.gov (United States)

Bates, Scott T.; Cropsey, Garrett W. G.; Caporaso, J. Gregory; Knight, Rob; Fierer, Noah

2011-01-01

Lichens are commonly described as a mutualistic symbiosis between fungi and “algae” (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N2 fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N2 fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses. PMID:21169444

Enhanced sulfamethoxazole degradation through ammonia oxidizing bacteria co-metabolism and fate of transformation products.

Science.gov (United States)

Kassotaki, Elissavet; Buttiglieri, Gianluigi; Ferrando-Climent, Laura; Rodriguez-Roda, Ignasi; Pijuan, Maite

2016-05-01

The occurrence of the widely-used antibiotic sulfamethoxazole (SFX) in wastewaters and surface waters has been reported in a large number of studies. However, the results obtained up-to-date have pointed out disparities in its removal. This manuscript explores the enhanced biodegradation potential of an enriched culture of Ammonia Oxidizing Bacteria (AOB) towards SFX. Several sets of batch tests were conducted to establish a link between SFX degradation and specific ammonia oxidation rate. The occurrence, degradation and generation of SFX and some of its transformation products (4-Nitro SFX, Desamino-SFX and N(4)-Acetyl-SFX) was also monitored. A clear link between the degradation of SFX and the nitrification rate was found, resulting in an increased SFX removal at higher specific ammonia oxidation rates. Moreover, experiments conducted under the presence of allylthiourea (ATU) did not present any removal of SFX, suggesting a connection between the AMO enzyme and SFX degradation. Long term experiments (up to 10 weeks) were also conducted adding two different concentrations (10 and 100 μg/L) of SFX in the influent of a partial nitrification sequencing batch reactor, resulting in up to 98% removal. Finally, the formation of transformation products during SFX degradation represented up to 32%, being 4-Nitro-SFX the most abundant. Copyright © 2016 Elsevier Ltd. All rights reserved.

The origin of mouth-exhaled ammonia.

Science.gov (United States)

Chen, W; Metsälä, M; Vaittinen, O; Halonen, L

2014-09-01

It is known that the oral cavity is a production site for mouth-exhaled NH3. However, the mechanism of NH3 production in the oral cavity has been unclear. Since bacterial urease in the oral cavity has been found to produce ammonia from oral fluid urea, we hypothesize that oral fluid urea is the origin of mouth-exhaled NH3. Our results show that under certain conditions a strong correlation exists between oral fluid urea and oral fluid ammonia (NH4(+)+NH3) (rs = 0.77, p oral fluid NH3 and mouth-exhaled NH3 (rs = 0.81, p oral fluid pH. Bacterial urease catalyses the hydrolysis of oral fluid urea to ammonia (NH4(+)+NH3). Oral fluid ammonia (NH4(+)+NH3) and pH determine the concentration of oral fluid NH3, which evaporates from oral fluid into gas phase and turns to mouth-exhaled NH3.

Oxygen Distribution and Potential Ammonia Oxidation in Floating, Liquid Manure Crusts

DEFF Research Database (Denmark)

Nielsen, Daniel Aagren; Nielsen, Lars Peter; Schramm, Andreas

2010-01-01

Floating, organic crusts on liquid manure, stored as a result of animal production, reduce emission of ammonia (NH3) and other volatile compounds during storage. The occurrence of NO2- and NO3- in the crusts indicate the presence of actively metabolizing NH3 oxidizing bacteria (AOB) which may...... be partly responsible for this mitigation effect. Six manure tanks with organic covers (straw and natural) were surveyed to investigate the prevalence and potential activity of AOB and its dependence on the O2 availability in the crust matrix as studied by electrochemical profiling. Oxygen penetration...... microorganisms, including AOB. The microbial activity may thus contribute to a considerable reduction of ammonia emissions from slurry tanks with well-developed crusts....

Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

Science.gov (United States)

Daebeler, Anne; Herbold, Craig W.; Vierheilig, Julia; Sedlacek, Christopher J.; Pjevac, Petra; Albertsen, Mads; Kirkegaard, Rasmus H.; de la Torre, José R.; Daims, Holger; Wagner, Michael

2018-01-01

Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation§. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and

Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

Directory of Open Access Journals (Sweden)

Anne Daebeler

2018-02-01

Full Text Available Ammonia-oxidizing archaea (AOA within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85% enrichment from biofilm of an Icelandic hot spring (73°C. This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO generation§. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately

Mineral phosphate solubilizing bacterial community in agro-ecosystem

African Journals Online (AJOL)

Mineral phosphate solubilizing bacterial community in agro-ecosystem. N Saha, S Biswas. Abstract. The present communication deals with the assessment of phosphate solubilizing bacterial community structure across artificially created fertility gradient with regards to N, P and K status of soil in the experimental site.

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

Energy Technology Data Exchange (ETDEWEB)

Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

2010-03-01

Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy).

Science.gov (United States)

Quéméneur, Marianne; Palvadeau, Alexandra; Postec, Anne; Monnin, Christophe; Chavagnac, Valérie; Ollivier, Bernard; Erauso, Gaël

2015-09-01

The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing Methanobacteriales and Methanosarcinales (Euryarchaeota) together with ammonia-oxidizing Nitrososphaerales (Thaumarchaeota) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Verrucomicrobia phyla, altogether accounting for 92.2% of total retrieved bacterial 16S rRNA gene sequences. Amongst Bacteria, potential chemolithotrophy was mainly associated with Alpha- and Betaproteobacteria classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera Azospirillum, Methylosinus, and Hydrogenophaga/'Serpentinomonas', respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of Actinobacteria and Planctomycetales phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems.

Influence of environmental ammonia on the production of nitric oxide and expression of inducible nitric oxide synthase in the freshwater air-breathing catfish (Heteropneustes fossilis)

Energy Technology Data Exchange (ETDEWEB)

Choudhury, Mahua G. [Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022 (India); Saha, Nirmalendu, E-mail: nsaha@nehu.ac.in [Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022 (India)

2012-07-15

Highlights: Black-Right-Pointing-Pointer High environmental ammonia caused more production and accumulation of NO in air-breathing catfish (Heteropneustes fossilis). Black-Right-Pointing-Pointer Hyper-ammonia stress caused induction and zonal specific expression of iNOS enzyme protein, mRNA expression in different tissues. Black-Right-Pointing-Pointer Activation of NF{kappa}B that resulted under hyper-ammonia stress was believed to be the cause of induction of iNOS gene. - Abstract: Nitric oxide (NO) is a highly versatile and unique ubiquitous signaling molecule, and is known to play diverse physiological functions in mammals including those of adaptation to various stresses. The present study reports on the influence of exposure to high external ammonia (HEA) on the production of nitric oxide (NO) and the expression of inducible nitric oxide synthase (iNOS), that produces NO from L-arginine in the freshwater air-breathing catfish (Heteropneustes fossilis), which is reported to tolerate a very HEA. Some levels of NO were found to be present in all the tissues and also in plasma of control fish, which further enhanced significantly in fishes treated with high concentrations of environmental ammonia (25 and 50 mM ammonium chloride) for 7 days, accompanied by more efflux of NO from the perfused liver. This was accomplished by the induction of iNOS activity in different tissues of fish exposed to HEA, which otherwise was not detectable in control fish. Exposure to 25 mM ammonium chloride also led to a significant expression of iNOS protein in different tissues, followed by further increase at 50 mM ammonium chloride. Further, there was an increase in the expression of iNOS mRNA in ammonia-treated fish, thus suggesting that the expression of iNOS gene under hyper-ammonia stress was probably regulated at the transcriptional level. Immunocytochemical analysis indicated that the expression of iNOS in different tissues was zonal specific and not expressed uniformly

Influence of environmental ammonia on the production of nitric oxide and expression of inducible nitric oxide synthase in the freshwater air-breathing catfish (Heteropneustes fossilis)

International Nuclear Information System (INIS)

Choudhury, Mahua G.; Saha, Nirmalendu

2012-01-01

Highlights: ► High environmental ammonia caused more production and accumulation of NO in air-breathing catfish (Heteropneustes fossilis). ► Hyper-ammonia stress caused induction and zonal specific expression of iNOS enzyme protein, mRNA expression in different tissues. ► Activation of NFκB that resulted under hyper-ammonia stress was believed to be the cause of induction of iNOS gene. - Abstract: Nitric oxide (NO) is a highly versatile and unique ubiquitous signaling molecule, and is known to play diverse physiological functions in mammals including those of adaptation to various stresses. The present study reports on the influence of exposure to high external ammonia (HEA) on the production of nitric oxide (NO) and the expression of inducible nitric oxide synthase (iNOS), that produces NO from L-arginine in the freshwater air-breathing catfish (Heteropneustes fossilis), which is reported to tolerate a very HEA. Some levels of NO were found to be present in all the tissues and also in plasma of control fish, which further enhanced significantly in fishes treated with high concentrations of environmental ammonia (25 and 50 mM ammonium chloride) for 7 days, accompanied by more efflux of NO from the perfused liver. This was accomplished by the induction of iNOS activity in different tissues of fish exposed to HEA, which otherwise was not detectable in control fish. Exposure to 25 mM ammonium chloride also led to a significant expression of iNOS protein in different tissues, followed by further increase at 50 mM ammonium chloride. Further, there was an increase in the expression of iNOS mRNA in ammonia-treated fish, thus suggesting that the expression of iNOS gene under hyper-ammonia stress was probably regulated at the transcriptional level. Immunocytochemical analysis indicated that the expression of iNOS in different tissues was zonal specific and not expressed uniformly throughout the organ. Hyper-ammonia stress also led to activation and nuclear

Start-up and bacterial community compositions of partial nitrification in moving bed biofilm reactor.

Science.gov (United States)

Liu, Tao; Mao, Yan-Jun; Shi, Yan-Ping; Quan, Xie

2017-03-01

Partial nitrification (PN) has been considered as one of the promising processes for pretreatment of ammonium-rich wastewater. In this study, a kind of novel carriers with enhanced hydrophilicity and electrophilicity was implemented in a moving bed biofilm reactor (MBBR) to start up PN process. Results indicated that biofilm formation rate was higher on modified carriers. In comparison with the reactor filled with traditional carriers (start-up period of 21 days), it took only 14 days to start up PN successfully with ammonia removal efficiency and nitrite accumulation rate of 90 and 91%, respectively, in the reactor filled with modified carriers. Evident changes of spatial distributions and community structures had been detected during the start-up. Free-floating cells existed in planktonic sludge, while these microorganisms trended to form flocs in the biofilm. High-throughput pyrosequencing results indicated that Nitrosomonas was the predominant ammonia-oxidizing bacterium (AOB) in the PN system, while Comamonas might also play a vital role for nitrogen oxidation. Additionally, some other bacteria such as Ferruginibacter, Ottowia, Saprospiraceae, and Rhizobacter were selected to establish stable footholds. This study would be potentially significant for better understanding the microbial features and developing efficient strategies accordingly for MBBR-based PN operation.

Amorphous structure of iron oxide of bacterial origin

Energy Technology Data Exchange (ETDEWEB)

Hashimoto, Hideki; Fujii, Tatsuo [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Kohara, Shinji [Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198 (Japan); Asaoka, Hiroshi [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Kusano, Yoshihiro [Department of Fine and Applied Arts, Kurashiki University of Science and the Arts, Kurashiki, Okayama 712-8505 (Japan); Ikeda, Yasunori [Research Institute for Production Development, Sakyo-ku, Kyoto 606-0805 (Japan); Nakanishi, Makoto [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Benino, Yasuhiko; Nanba, Tokuro [Graduate School of Environmental Science, Okayama University, Okayama 700-8530 (Japan); Takada, Jun, E-mail: jtakada@cc.okayama-u.ac.jp [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); JST, CREST, Okayama 700-8530 (Japan)

2012-12-14

In nature, there are various iron oxides produced by the water-habitant bacterial group called 'iron-oxidizing bacteria'. These iron oxides have been studied mainly from biological and geochemical perspectives. Today, attempts are made to use such iron oxides as novel functional materials in several applications. However, their quantitative structural characteristics are still unclear. We studied the structure of iron oxide of microtubular form consisting of amorphous nanoparticles formed by an iron-oxidizing bacterium, Leptothrix ochracea, using a combination of high-energy X-ray diffraction and reverse Monte Carlo simulation. We found that its structure consists of a framework of corner- and edge-sharing distorted FeO{sub 6} octahedral units, while SiO{sub 4} tetrahedral units are isolated in the framework. The results reveal the atomic arrangement of iron oxide of bacterial origin, which is essential for investigating its potential as a functional material. -- Highlights: Black-Right-Pointing-Pointer The amorphous structure of bacterial iron oxide was investigated. Black-Right-Pointing-Pointer The structure was simulated by high-energy X-ray diffraction and reverse Monte Carlo simulation. Black-Right-Pointing-Pointer The structure was constructed of a framework of corner- and edge-sharing distorted FeO{sub 6} octahedral units. Black-Right-Pointing-Pointer SiO{sub 4} tetrahedral units were distributed isolatedly in the framework of FeO{sub 6} octahedral units.

Bacterial community structure in the Cerasus sachalinensis Kom ...

African Journals Online (AJOL)

Jane

2011-07-21

Jul 21, 2011 ... The bacterial community structures of the Cerasus sachalinensis Kom. rhizosphere in wild and cultivated soil were studied and the community changes in different growth stages were analyzed by the PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that the bacterial ...

Development of the kinetic model of platinum catalyzed ammonia oxidation in a microreactor

NARCIS (Netherlands)

Rebrov, E.V.; Croon, de M.H.J.M.; Schouten, J.C.

2002-01-01

The ammonia oxidation reaction on supported polycrystalline platinum catalyst was investigated in an aluminum-based microreactor. An extensive set of reactions was included in the chemical reactor modeling to facilitate the construction of a kinetic model capable of satisfactory predictions for a

Site-Specific Reactivity of Copper Chabazite Zeolites with Nitric Oxide, Ammonia, and Oxygen

DEFF Research Database (Denmark)

Godiksen, Anita; Isaksen, Oliver L.; Rasmussen, Søren B.

2018-01-01

In-situ electron paramagnetic resonance (EPR) spectroscopy was applied to dilute copper chabazite (CHA) zeolites under gas flows relevant for the selective catalytic reduction of NO with ammonia (NH3-SCR). Under both reducing and oxidizing conditions, we observed differences in reactivity between...

Enhanced and selective ammonia sensing of reduced graphene oxide based chemo resistive sensor at room temperature

Science.gov (United States)

Kumar, Ramesh; Kaur, Amarjeet

2016-05-01

The reduced graphene oxide thin films were fabricated by using the spin coating method. The reduced graphene oxide samples were characterised by Raman studies to obtain corresponding D and G bands at 1360 and 1590 cm-1 respectively. Fourier transform infra-red (FTIR) spectra consists of peak corresponds to sp2 hybridisation of carbon atoms at 1560 cm-1. The reduced graphene oxide based chemoresistive sensor exhibited a p-type semiconductor behaviour in ambient conditions and showed good sensitivity to different concentration of ammonia from 25 ppm to 500 ppm and excellent selectivity at room temperature. The sensor displays selectivity to several hazardous vapours such as methanol, ethanol, acetone and hydrazine hydrate. The sensor demonstrated a sensitivity of 9.8 at 25 ppm concentration of ammonia with response time of 163 seconds.

Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea.

Science.gov (United States)

Stieglmeier, Michaela; Mooshammer, Maria; Kitzler, Barbara; Wanek, Wolfgang; Zechmeister-Boltenstern, Sophie; Richter, Andreas; Schleper, Christa

2014-05-01

Soil emissions are largely responsible for the increase of the potent greenhouse gas nitrous oxide (N2O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil is unclear as is the mechanism by which they produce it. Here we investigate the potential of Nitrososphaera viennensis, the first pure culture of AOA from soil, to produce N2O and compare its activity with that of a marine AOA and an ammonia-oxidizing bacterium (AOB) from soil. N. viennensis produced N2O at a maximum yield of 0.09% N2O per molecule of nitrite under oxic growth conditions. N2O production rates of 4.6±0.6 amol N2O cell(-1) h(-1) and nitrification rates of 2.6±0.5 fmol NO2(-) cell(-1) h(-1) were in the same range as those of the AOB Nitrosospira multiformis and the marine AOA Nitrosopumilus maritimus grown under comparable conditions. In contrast to AOB, however, N2O production of the two archaeal strains did not increase when the oxygen concentration was reduced, suggesting that they are not capable of denitrification. In (15)N-labeling experiments we provide evidence that both ammonium and nitrite contribute equally via hybrid N2O formation to the N2O produced by N. viennensis under all conditions tested. Our results suggest that archaea may contribute to N2O production in terrestrial ecosystems, however, they are not capable of nitrifier-denitrification and thus do not produce increasing amounts of the greenhouse gas when oxygen becomes limiting.

Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

Directory of Open Access Journals (Sweden)

E Charlotte E Kvennefors

Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

Structural transformations of heat-treated bacterial iron oxide

Energy Technology Data Exchange (ETDEWEB)

Hashimoto, Hideki, E-mail: hideki-h@cc.okayama-u.ac.jp [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); JST, CREST, Okayama 700-8530 (Japan); Fujii, Tatsuo [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Kohara, Shinji [Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198 (Japan); Nakanishi, Koji [Office of Society-Academia Collaboration for Innovation, Kyoto University, Uji 611-0011 (Japan); Yogi, Chihiro [SR Center, Ritsumeikan University, Kusatsu, Shiga 525-8577 (Japan); Peterlik, Herwig [Faculty of Physics, University of Vienna, A-1090 Vienna (Austria); Nakanishi, Makoto [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Takada, Jun [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); JST, CREST, Okayama 700-8530 (Japan)

2015-04-01

A bacterial siliceous iron oxide microtubule (diameter: ca. 1 μm, 15Fe{sub 2}O{sub 3}·8SiO{sub 2}·P{sub 2}O{sub 5}·30H{sub 2}O) produced by Leptothrix ochracea was heat treated in air and its structural transformation was investigated in detail by microscopy, diffractometry, and spectroscopy. Although the heat-treated bacterial iron oxide retained its original microtubular structure, its nanoscopic, middle-range, and local structures changed drastically. Upon heat treatment, nanosized pores were formed and their size changed depending on temperature. The Fe–O–Si linkages were gradually cleaved with increasing temperature, causing the progressive separation of Fe and Si ions into iron oxide and amorphous silicate phases, respectively. Concomitantly, global connectivity and local structure of FeO{sub 6} octahedra in the iron oxide nanoparticles systematically changed depending on temperature. These comprehensive investigations clearly revealed various structural changes of the bacterial iron oxide which is an important guideline for the future exploration of novel bio-inspired materials. - Highlights: • Structural transformation of a bacterial iron oxide microtubule was investigated. • Si–O–Fe was cleaved with increasing temperature to form α-Fe{sub 2}O{sub 3}/silicate composite. • Crystallization to 2Fh started at 500 °C to give α-Fe{sub 2}O{sub 3} >700 °C. • FeO{sub 6} octahedra were highly distorted <500 °C. • Formation of face-sharing FeO{sub 6} was promoted >500 °C, releasing the local strain of FeO{sub 6}.

Ammonia, nitrous oxide and hydrogen cyanide emissions from five passenger vehicles

International Nuclear Information System (INIS)

Karlsson, Hua Lu

2004-01-01

In this paper, three unregulated components, ammonia, nitrous oxide and hydrogen cyanide, emitted from five passenger vehicles are investigated. With focus upon emission factors from existing production technology, vehicles produced between 1989 and 1998 with considerable mileage (7000 to 280,000) are chosen. Among the five vehicles, four were sold in the European market, whereas one was sold in the US market. The vehicles are tested on a chassis dynamometer. An EU2000 Driving Cycle (NEDC) and a US Urban Driving Cycle (UDC) of the Federal Test Procedure 75 (FTP-75) are used in the study. The regulated emissions are measured using a Horiba Mexa series. Unregulated emissions, ammonia (NH 3 ), nitrous oxide (N 2 O) and hydrogen cyanide (HCN) are analysed by mass spectrometer, gas chromatography and CNT-NA, TIM315-74W method, respectively. Both the unregulated emissions and the regulated emissions show driving cycle dependency; and they are also improved with newer vehicle and emission control technology. However, a gasoline direct injection vehicle (relatively new technology in this study) has rather high regulated emissions, whereas the NH 3 , N 2 O and HCN emissions are low

Ammonia, nitrous oxide and hydrogen cyanide emissions from five passenger vehicles.

Science.gov (United States)

Karlsson, Hua Lu

2004-12-01

In this paper, three unregulated components, ammonia, nitrous oxide and hydrogen cyanide, emitted from five passenger vehicles are investigated. With focus upon emission factors from existing production technology, vehicles produced between 1989 and 1998 with considerable mileage (7000 to 280,000) are chosen. Among the five vehicles, four were sold in the European market, whereas one was sold in the US market. The vehicles are tested on a chassis dynamometer. An EU2000 Driving Cycle (NEDC) and a US Urban Driving Cycle (UDC) of the Federal Test Procedure 75 (FTP-75) are used in the study. The regulated emissions are measured using a Horiba Mexa series. Unregulated emissions, ammonia (NH(3)), nitrous oxide (N(2)O) and hydrogen cyanide (HCN) are analysed by mass spectrometer, gas chromatography and CNT-NA, TIM315-74W method, respectively. Both the unregulated emissions and the regulated emissions show driving cycle dependency; and they are also improved with newer vehicle and emission control technology. However, a gasoline direct injection vehicle (relatively new technology in this study) has rather high regulated emissions, whereas the NH(3), N(2)O and HCN emissions are low.

Effect of calcium cyanamide, ammonium bicarbonate and lime mixture, and ammonia water on survival of Ralstonia solanacearum and microbial community

Science.gov (United States)

Liu, Lijuan; Sun, Chengliang; Liu, Xingxing; He, Xiaolin; Liu, Miao; Wu, Hao; Tang, Caixian; Jin, Chongwei; Zhang, Yongsong

2016-01-01

The inorganic nitrogenous amendments calcium cyanamide (CC), ammonia water (AW), and a mixture of ammonium bicarbonate with lime (A+L) are popularly used as fumigants to control soil-borne disease in China. However, it is unclear which of these fumigants is more effective in controlling R. solanacearum. This present study compared the efficiencies of the three nitrogenous amendments listed above at four nitrogen levels in suppressing the survival of R. solanacearum in soil. The CC showed the best ability to suppress R. solanacearum due to its highest capacity to increase soil and NO2− contents and pH. However, AW was more suitable to controlling bacterial wilt caused by R. solanacearum because it had a lower cost and its application rate of 0.25 g N kg−1 soil could effectively suppress the survival of R. solanacearum. Additionally, soil microbial activity and community populations were restored to their initial state four weeks after the application of each fumigant, indicating that the three fumigants had few detrimental impacts on soil microbial activity and community structure with an exception of the suppression of R. solanacearum. The present study provides guidance for the selection of a suitable alkaline nitrogenous amendment and its application rate in controlling bacterial wilt. PMID:26738601

Effect of calcium cyanamide, ammonium bicarbonate and lime mixture, and ammonia water on survival of Ralstonia solanacearum and microbial community

Science.gov (United States)

Liu, Lijuan; Sun, Chengliang; Liu, Xingxing; He, Xiaolin; Liu, Miao; Wu, Hao; Tang, Caixian; Jin, Chongwei; Zhang, Yongsong

2016-01-01

The inorganic nitrogenous amendments calcium cyanamide (CC), ammonia water (AW), and a mixture of ammonium bicarbonate with lime (A+L) are popularly used as fumigants to control soil-borne disease in China. However, it is unclear which of these fumigants is more effective in controlling R. solanacearum. This present study compared the efficiencies of the three nitrogenous amendments listed above at four nitrogen levels in suppressing the survival of R. solanacearum in soil. The CC showed the best ability to suppress R. solanacearum due to its highest capacity to increase soil and NO2- contents and pH. However, AW was more suitable to controlling bacterial wilt caused by R. solanacearum because it had a lower cost and its application rate of 0.25 g N kg-1 soil could effectively suppress the survival of R. solanacearum. Additionally, soil microbial activity and community populations were restored to their initial state four weeks after the application of each fumigant, indicating that the three fumigants had few detrimental impacts on soil microbial activity and community structure with an exception of the suppression of R. solanacearum. The present study provides guidance for the selection of a suitable alkaline nitrogenous amendment and its application rate in controlling bacterial wilt.

Ice formation and growth shape bacterial community structure in Baltic Sea drift ice.

Science.gov (United States)

Eronen-Rasimus, Eeva; Lyra, Christina; Rintala, Janne-Markus; Jürgens, Klaus; Ikonen, Vilma; Kaartokallio, Hermanni

2015-02-01

Drift ice, open water and under-ice water bacterial communities covering several developmental stages from open water to thick ice were studied in the northern Baltic Sea. The bacterial communities were assessed with 16S rRNA gene terminal-restriction fragment length polymorphism and cloning, together with bacterial abundance and production measurements. In the early stages, open water and pancake ice were dominated by Alphaproteobacteria and Actinobacteria, which are common bacterial groups in Baltic Sea wintertime surface waters. The pancake ice bacterial communities were similar to the open-water communities, suggesting that the parent water determines the sea-ice bacterial community in the early stages of sea-ice formation. In consolidated young and thick ice, the bacterial communities were significantly different from water bacterial communities as well as from each other, indicating community development in Baltic Sea drift ice along with ice-type changes. The thick ice was dominated by typical sea-ice genera from classes Flavobacteria and Gammaproteobacteria, similar to those in polar sea-ice bacterial communities. Since the thick ice bacterial community was remarkably different from that of the parent seawater, results indicate that thick ice bacterial communities were recruited from the rarer members of the seawater bacterial community. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular comparison of bacterial communities within iron-containing flocculent mats associated with submarine volcanoes along the Kermadec Arc.

Science.gov (United States)

Hodges, Tyler W; Olson, Julie B

2009-03-01

Iron oxide sheaths and filaments are commonly found in hydrothermal environments and have been shown to have a biogenic origin. These structures were seen in the flocculent material associated with two submarine volcanoes along the Kermadec Arc north of New Zealand. Molecular characterization of the bacterial communities associated with the flocculent samples indicated that no known Fe-oxidizing bacteria dominated the recovered clone libraries. However, clones related to the recently described Fe-oxidizing bacterium Mariprofundus ferrooxydans were obtained from both the iron-containing flocculent (Fe-floc) and sediment samples, and peaks corresponding to Mariprofundus ferrooxydans, as well as the related clones, were observed in several of our terminal restriction fragment length polymorphism profiles. A large group of epsilonproteobacterial sequences, for which there is no cultured representative, dominated clones from the Fe-floc libraries and were less prevalent in the sediment sample. Phylogenetic analyses indicated that several operational taxonomic units appeared to be site specific, and statistical analyses of the clone libraries found that all samples were significantly different from each other. Thus, the bacterial communities in the Fe-floc samples were not more closely related to each other than to the sediment communities.

Influence of organic substrates on the kinetics of bacterial As(III) oxidation

Science.gov (United States)

Lescure, T.; Joulian, C.; Bauda, P.; Hénault, C.; Battaglia-Brunet, F.

2012-04-01

on the bacterial speciation of arsenic in contaminated soils. Moreover, the biogeochemical consequences of this phenomenon on the mobility and ecotoxicity of this metalloid will be studied. The first task of this program is the precise and systematic investigation of the influence of different types and concentrations of organic matters on the activity of As(III)-oxidizing pure strains. Influence of aspartate, succinate (simple substrates) and yeast extract (complex substrate) on As(III)-oxidation kinetics has been studied. For each experiment, the bacterial growth and the expression of genes involved in the speciation of arsenic, i.e. aio and ars genes, has been monitored. A direct perspective of this work will be to perform experiments with humic and fulvic acids (complex organic matter commonly found in soils), and with water-extracted organic matter from polluted soils. Then the As(III)-oxidation activity of bacterial communities extracted from contaminated soils will be followed. These assays should allow the screening of conditions which will be applied in subsequent experiments with several real contaminated soils, including a former mining site, impacted industrial sites, and a forest soil heavily contaminated after arsenical ammunitions storage. This work is co-funded by BRGM and ADEME (convention TEZ 11-16).

The role of adsorbates in the electrochemical oxidation of ammonia on noble and transition metal electrodes

NARCIS (Netherlands)

Vooys, de A.C.A.; Koper, M.T.M.; Santen, van R.A.; Veen, van J.A.R.

2001-01-01

The activity for ammonia oxidation and the intermediates formed during the reaction have been studied on platinum, palladium, rhodium, ruthenium, iridium, copper, silver and gold electrodes. The activity in the selective oxidation to N-2 is related directly to the nature of the species at the

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.

Science.gov (United States)

Ma, Xiao; Vikram, Amit; Casson, Leonard; Bibby, Kyle

2017-07-05

Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.

Enhanced and selective ammonia sensing of reduced graphene oxide based chemo resistive sensor at room temperature

Energy Technology Data Exchange (ETDEWEB)

Kumar, Ramesh, E-mail: rameshphysicsdu@gmail.com; Kaur, Amarjeet, E-mail: amarkaur@physics.du.ac.in [Department of Physics and Astrophysics, University of Delhi, Delhi-110007 (India)

2016-05-06

The reduced graphene oxide thin films were fabricated by using the spin coating method. The reduced graphene oxide samples were characterised by Raman studies to obtain corresponding D and G bands at 1360 and 1590 cm{sup −1} respectively. Fourier transform infra-red (FTIR) spectra consists of peak corresponds to sp{sup 2} hybridisation of carbon atoms at 1560 cm{sup −1}. The reduced graphene oxide based chemoresistive sensor exhibited a p-type semiconductor behaviour in ambient conditions and showed good sensitivity to different concentration of ammonia from 25 ppm to 500 ppm and excellent selectivity at room temperature. The sensor displays selectivity to several hazardous vapours such as methanol, ethanol, acetone and hydrazine hydrate. The sensor demonstrated a sensitivity of 9.8 at 25 ppm concentration of ammonia with response time of 163 seconds.

Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit.

Science.gov (United States)

Diaby, N; Dold, B; Rohrbach, E; Holliger, C; Rossi, P

2015-11-15

Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation

Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics

DEFF Research Database (Denmark)

Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq

2017-01-01

Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures......, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion...

Biochar type and factors affecting N transformation, ammonia volatilization, and nitrous oxide emissions

Science.gov (United States)

Soil amendment with biochar has shown the potential to improve nitrogen (N) availability for plant uptake and reduce environmental losses via ammonia (NH3) and nitrous oxide (N2O) emissions. There are still many unknowns on how biochar type and soil conditions affect N dynamics and processes associa...

Manganese oxidation and bacterial diversity on different filter media coatings during the start-up of drinking water biofilters

DEFF Research Database (Denmark)

Breda, I. L.; Ramsay, L.; Roslev, P.

2017-01-01

Manganese removal is a typical concern in drinking water production. Biofiltration may be used when treating groundwater sources but the onset of manganese removal in virgin biofilters can vary considerably. The aim of this study was to investigate the effect of different filter media on manganese...... by manganese oxide, while 48, 57 and 72 days were required by virgin quartz, calcium carbonate and polystyrene, respectively. The bacterial community was investigated using DAPI staining, quantitative polymerase chain reaction (qPCR), 16S rRNA gene pyrosequencing, and bacterial enrichments. Bacterial abundance...

Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

Science.gov (United States)

Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

2017-05-01

The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mercury alters the bacterial community structure and diversity in soil even at concentrations lower than the guideline values.

Science.gov (United States)

Mahbub, Khandaker Rayhan; Subashchandrabose, Suresh Ramraj; Krishnan, Kannan; Naidu, Ravi; Megharaj, Mallavarapu

2017-03-01

This study evaluated the effect of inorganic mercury (Hg) on bacterial community and diversity in different soils. Three soils-neutral, alkaline and acidic-were spiked with six different concentrations of Hg ranging from 0 to 200 mg kg -1 and aged for 90 days. At the end of the ageing period, 18 samples from three different soils were investigated for bacterial community structure and soil physicochemical properties. Illumina MiSeq-based 16s ribosomal RNA (rRNA) amplicon sequencing revealed the alteration in the bacterial community between un-spiked control soils and Hg-spiked soils. Among the bacterial groups, Actinobacteria (22.65%) were the most abundant phyla in all samples followed by Proteobacteria (21.95%), Bacteroidetes (4.15%), Firmicutes (2.9%) and Acidobacteria (2.04%). However, the largest group showing increased abundance with higher Hg doses was the unclassified group (45.86%), followed by Proteobacteria. Mercury had a considerable negative impact on key soil functional bacteria such as ammonium oxidizers and nitrifiers. Canonical correspondence analysis (CCA) indicated that among the measured soil properties, Hg had a major influence on bacterial community structure. Furthermore, nonlinear regression analysis confirmed that Hg significantly decreased soil bacterial alpha diversity in lower organic carbon containing neutral and alkaline soils, whereas in acidic soil with higher organic carbon there was no significant correlation. EC 20 values obtained by a nonlinear regression analysis indicated that Hg significantly decreased soil bacterial diversity in concentrations lower than several guideline values.

Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing

Energy Technology Data Exchange (ETDEWEB)

Zhou, Jiemin [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhou, Xuemei; Li, Yuguang [101 Institute, Ministry of Civil Affairs, Beijing 100070 (China); Xing, Jianmin, E-mail: jmxing@ipe.ac.cn [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China)

2015-09-15

Highlights: • Bacterial communities of haloalkaliphilic bioreactors were investigated. • MiSeq was first used in analysis of communities of haloalkaliphilic bioreactors. • Electron donors had significant effect on bacterial communities. - Abstract: Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.

Bacterial community diversity of the deep-sea octocoral Paramuricea placomus

Directory of Open Access Journals (Sweden)

Christina A. Kellogg

2016-09-01

Full Text Available Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

Quantitative analysis of ammonia-oxidizing bacteria in a combined system of MBR and worm reactors treating synthetic wastewater.

Science.gov (United States)

Liu, Jia; Tian, Yu; Wang, Dezhen; Lu, Yaobin; Zhang, Jun; Zuo, Wei

2014-12-01

The Static Sequencing Batch Worm Reactor (SSBWR) followed by the MBR (S-MBR) is one of the advanced excess sludge treatments. In this paper, the control MBR (C-MBR) and the SSBWR-MBR were operated in parallel to study the changes of NH3-N removal and ammonia oxidizing bacteria (AOB). The results showed that the capacity of NH3-N removal of the S-MBR was improved by the worm reactors along with the operation. The S-MBR was favorable because it selected for the higher activity of the ammonia oxidization and better cells appearance of the sludge. The five species (Nitrosomonas, Betaproteobacteria, Clostridium, Dechloromonas and Bacteria) were found to be significantly correlate with the ammonia oxidization functions and performance of NH3-N removal in the C-MBR and S-MBR. The Nitrosomonas, Betaproteobacteria and Dechloromonas remained and eventually enriched in the S-MBR played a primary role in the NH3-N removal of the S-MBR. Copyright © 2014 Elsevier Ltd. All rights reserved.

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

Directory of Open Access Journals (Sweden)

Jacob D. Hosen

2017-08-01

Full Text Available Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition

Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

Science.gov (United States)

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments

Directory of Open Access Journals (Sweden)

Ramona Marasco

2013-01-01

Full Text Available Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches. According to 16S rRNA gene PCR-DGGE, the structure of endosphere and rhizosphere bacterial communities was highly diverse (P=0.03 and was associated with a cultivar/latitudinal/climatic effect. Despite being diverse, the bacterial communities associated with Egyptian grapevines shared a higher similarity with the Tunisian grapevines than those cultivated in North Italy. A similar distribution, according to the cultivar/latitude/aridity gradients, was observed for the cultivable bacteria. Many isolates (23% presented in vitro multiple stress resistance capabilities and PGP activities, the most frequent being auxin synthesis (82%, insoluble phosphate solubilisation (61%, and ammonia production (70%. The comparable numbers and types of potential PGP traits among the three different environmental settings indicate a strong functional homeostasis of beneficial bacteria associated with grape root.

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

KAUST Repository

Tian, R.-M.

2014-11-04

Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. IMPORTANCE This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper

Pyrosequencing Reveals Soil Enzyme Activities and Bacterial Communities Impacted by Graphene and Its Oxides.

Science.gov (United States)

Rong, Yan; Wang, Yi; Guan, Yina; Ma, Jiangtao; Cai, Zhiqiang; Yang, Guanghua; Zhao, Xiyue

2017-10-25

Graphene (GN) and graphene oxides (GOs) are novel carbon nanomaterial; they have been attracting much attention because of their excellent properties and are widely applied in many areas, including energy, electronics, biomedicine, environmental science, etc. With industrial production and consumption of GN/GO, they will inevitably enter the soil and water environments. GN/GO may directly cause certain harm to microorganisms and lead to ecological and environmental risks. GOs are GN derivatives with abundant oxygen-containing functional groups in their graphitic backbone. The structure and chemistry of GN show obvious differences compared to those of GO, which lead to the different environmental behaviors. In this study, four different types of soil (S1-S4) were employed to investigate the effect of GN and GO on soil enzymatic activity, microbial population, and bacterial community through pyrosequencing of 16S rRNA gene amplicons. The results showed that soil enzyme activity (invertase, protease, catalase, and urease) and microbial population (bacteria, actinomycetes, and fungi) changed after GN/GO release into soils. Soil microbial community species are more rich, and the diversity also increases after GO/GN application. The phylum of Proteobacteria increased at 90 days after treatment (DAT) after GN/GO application. The phylum of Chloroflexi occurred after GN application at 90 DAT in S1 soil and reached 4.6%. Proteobacteria was the most abundant phylum in S2, S3, and S4 soils; it ranged from 43.6 to 71.4% in S2 soil, from 45.6 to 73.7% in S3 soil, and from 38.1 to 56.7% in S4 soil. The most abundant genera were Bacillus (37.5-47.0%) and Lactococcus (28.0-39.0%) in S1 soil, Lysobacter and Flavobacterium in S2 soil, Pedobacter in S3 soil, and Massilia in S4 soil. The effect of GN and GO on the soil microbial community is time-dependent, and there are no significant differences between the samples at 10 and 90 DAT.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

Directory of Open Access Journals (Sweden)

Lidianne L. Rocha

2016-01-01

Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

Science.gov (United States)

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

Bacterial community profiles in low microbial abundance sponges

KAUST Repository

Giles, Emily

2012-09-04

It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

Biodegradation of BOD and ammonia-free using bacterial consortium in aerated fixed film bioreactor (AF2B)

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Prayitno, Rulianah, Sri; Saroso, Hadi; Meilany, Diah

2017-06-01

BOD and Ammonia-free (NH3-N) are pollutants of hospital wastewater which often exceed the quality standards. It is because biological processes in wastewater treatment plant (WWTP) have not been effective in degrading BOD and NH3-N. Therefore, a study on factors that influence the biodegradation of BOD and NH3-N by choosing the type of bacteria to improve the mechanisms of biodegradation processes is required. Bacterial consortium is a collection of several types of bacteria obtained from isolation process, which is known to be more effective than a single bacterial in degrading pollutants. On the other hand, AF2B is a type of reactor in wastewater treatment system. The AF2B contains a filter media that has a large surface area so that the biodegradation process of pollutants by microorganism can be improved. The objective of this research is to determine the effect of volume of starter and air supplies on decreasing BOD and NH3-N in hospital wastewater using bacterial consortium in the AF2B on batch process. The research was conducted in three stages: the making of the growth curve of the bacterial consortium, bacterial consortium acclimatization, and hospital wastewater treatment in the AF2B with batch process. The variables used are the volume of starter (65%, 75%, and 85% in volume) and air supplies (2.5, 5, and 7.5 L/min). Meanwhile, the materials used are hospital wastewater, bacterial consortium (Pseudomonas diminuta, Pseudomonas capica, Bacillius sp, and Nitrobacter sp), blower, and AF2B. AF2B is a plastic basin containing a filter media with a wasp-nest shape used as a medium for growing the bacterial consortium. In the process of making the growth curve, a solid form of bacterial consortium was dissolved in sterilized water, then grown in a nutrient broth (NB). Then, shaking and sampling were done at any time to determine the path growth of bacterial consortium. In the acclimatization process, bacterial isolates were grown using hospital wastewater as a

Impact of disinfection on drinking water biofilm bacterial community.

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Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-11-01

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination. Copyright © 2015. Published by Elsevier B.V.

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

Science.gov (United States)

Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.

2016-12-01

Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.

Ammonia chemistry in a flameless jet

Energy Technology Data Exchange (ETDEWEB)

Zieba, Mariusz; Schuster, Anja; Scheffknecht, Guenter [Institute of Process Engineering and Power Plant Technology, University of Stuttgart, Pfaffenwaldring 23, D-70569 Stuttgart (Germany); Brink, Anders; Hupa, Mikko [Process Chemistry Centre, Aabo Akademi University, Biskopsgatan 8, 20500 Aabo (Finland)

2009-10-15

In this paper, the nitrogen chemistry in an ammonia (NH{sub 3}) doped flameless jet is investigated using a kinetic reactor network model. The reactor network model is used to explain the main differences in ammonia chemistry for methane (CH{sub 4})-containing fuels and methane-free fuels. The chemical pathways of nitrogen oxides (NO{sub x}) formation and destruction are identified using rate-of-production analysis. The results show that in the case of natural gas, ammonia reacts relatively late at fuel lean condition leading to high NO{sub x} emissions. In the pre-ignition zone, the ammonia chemistry is blocked due to the absence of free radicals which are consumed by methane-methyl radical (CH{sub 3}) conversion. In the case of methane-free gas, the ammonia reacted very rapidly and complete decomposition was reached in the fuel rich region of the jet. In this case the necessary radicals for the ammonia conversion are generated from hydrogen (H{sub 2}) oxidation. (author)

Long-term high-solids anaerobic digestion of food waste: Effects of ammonia on process performance and microbial community.

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Peng, Xuya; Zhang, ShangYi; Li, Lei; Zhao, Xiaofei; Ma, Yao; Shi, Dezhi

2018-04-22

A long-term high solids anaerobic digestion of food waste was conducted to identify microbial mechanisms of ammonia inhibition during digestion and to clarify correlations between ammonia accumulation, microbial community dynamics (diversity, composition, and interactions), and process stability. Results show that the effects of ammonia on process performance and microbial community were indirectly caused by volatile fatty acid accumulation. Excess free ammonia blocked acetate metabolism, leading to process instability. Accumulated acetate caused feedback inhibition at the acetogenesis stage, which resulted in considerable accumulation of propionate, valerate, and other long-chain fatty acids. This high concentration of volatile fatty acids reduced the abundance of syntrophic acetogenic bacteria and allowed hydrolytic fermentative bacteria to dominate. The normally interactive and orderly metabolic network was broken, which further exacerbated the process instability. These results improve the understanding of microbial mechanisms which contribute to process instability and provide guidance for the microbial management of anaerobic digesters. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

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Wu, M.; Wang, H.; Wang, N.; Wang, M.

2017-12-01

Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system.

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She, Siyuan; Niu, Jiaojiao; Zhang, Chao; Xiao, Yunhua; Chen, Wu; Dai, Linjian; Liu, Xueduan; Yin, Huaqun

2017-03-01

Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

Structure of the bacterial community in a biofilter during dimethyl sulfide (DMS) removal processes.

Science.gov (United States)

Chung, Ying-Chien; Cheng, Chiu-Yu; Chen, Tzu-Yu; Hsu, Jo-Shan; Kui, Chun-Chi

2010-09-01

We report here both the successful treatment of DMS in a biofilter and the dynamic changes that occur in the composition of the bacterial community of the biofilter during this process. Denaturing gradient gel electrophoresis of eubacterial 16S rDNA samples taken from packing material at different DMS removal stages revealed 11 distinct bands. Phylogenetic analysis showed that the sequences of these bands were closest to sequences of species of the Proteobacteria, Firmicutes, and Actinobacteria. The specific occurrence of these bacterial species varied mainly with DMS load, but it was also affected by the addition of glucose and by ambient temperature. Based on the characteristics of the identified species, the system is conducive for such processes as sulfur oxidation, sulfate reduction, carbon oxidation, and fermentation. The strains identified in this study are potential candidates for purifying waste gas effluents containing DMS gas. Copyright 2010 Elsevier Ltd. All rights reserved.

Ammonia-Oxidizing β-Proteobacteria from the Oxygen Minimum Zone off Northern Chile▿

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Molina, Verónica; Ulloa, Osvaldo; Farías, Laura; Urrutia, Homero; Ramírez, Salvador; Junier, Pilar; Witzel, Karl-Paul

2007-01-01

The composition of ammonia-oxidizing bacteria from the β-Proteobacteria subclass (βAOB) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, ∼200 to 44 μM O2) and within the oxygen minimum zone (OMZ) suboxic waters (50- to 400-m depth, ≤10 μM O2) of the eastern South Pacific off northern Chile. This study was carried out through cloning and sequencing of genes coding for 16S rRNA and the ammonia monooxygenase enzyme active subunit (amoA). Sequences affiliated with Nitrosospira-like cluster 1 dominated the 16S rRNA gene clone libraries constructed from both oxic and suboxic waters. Cluster 1 consists exclusively of yet-uncultivated βAOB from marine environments. However, a single clone, out of 224 obtained from the OMZ, was found to belong to Nitrosospira lineage cluster 0. To our knowledge, cluster 0 sequences have been derived from βAOB isolated only from sand, soil, and freshwater environments. Sequences in clone libraries of the amoA gene from the surface and upper oxycline could be grouped in a marine subcluster, also containing no cultured representatives. In contrast, all 74 amoA sequences originating from the OMZ were either closely affiliated with cultured Nitrosospira spp. from clusters 0 and 2 or with other yet-uncultured βAOB from soil and an aerated-anoxic Orbal process waste treatment plant. Our results reveal the presence of Nitrosospira-like βAOB in both oxic and suboxic waters associated with the OMZ but with a clear community shift at the functional level (amoA) along the strong oxygen gradient. PMID:17416686

Denitrification of groundwater using a sulfur-oxidizing autotrophic denitrifying anaerobic fluidized-bed MBR: performance and bacterial community structure.

Science.gov (United States)

Zhang, Lili; Zhang, Chao; Hu, Chengzhi; Liu, Huijuan; Qu, Jiuhui

2015-03-01

This paper investigates a novel sulfur-oxidizing autotrophic denitrifying anaerobic fluidized bed membrane bioreactor (AnFB-MBR) that has the potential to overcome the limitations of conventional sulfur-oxidizing autotrophic denitrification systems. The AnFB-MBR produced consistent high-quality product water when fed by a synthetic groundwater with NO3 (-)-N ranging 25-80 mg/L and operated at hydraulic retention times of 0.5-5.0 h. A nitrate removal rate of up to 4.0 g NO3 (-)-N/Lreactord was attained by the bioreactor, which exceeded any reported removal capacity. The flux of AnFB-MBR was maintained in the range of 1.5-15 L m(-2) h(-1). Successful membrane cleaning was practiced with cleaning cycles of 35-81 days, which had no obvious effect on the AnFB-MBR performance. The (15) N-tracer analyses elucidated that nitrogen was converted into (15) N2-N and (15) N-biomass accounting for 88.1-93.1 % and 6.4-11.6 % of the total nitrogen produced, respectively. Only 0.3-0.5 % of removed nitrogen was in form of (15)N2O-N in sulfur-oxidizing autotrophic denitrification process, reducing potential risks of a significant amount of N2O emissions. The sulfur-oxidizing autotrophic denitrifying bacterial consortium was composed mainly of bacteria from Proteobacteria, Chlorobi, and Chloroflexi phyla, with genera Thiobacillus, Sulfurimonas, and Ignavibacteriales dominating the consortium. The pyrosequencing assays also suggested that the stable microbial communities corresponded to the elevated performance of the AnFB-MBR. Overall, this research described relatively high nitrate removal, acceptable flux, indicating future potential for the technology in practice.

Energy-mediated versus ammonium-regulated gene expression in the obligate ammonia-oxidizing bacterium, Nitrosococcus oceani

Directory of Open Access Journals (Sweden)

Lisa Y Stein

2013-09-01

Full Text Available Ammonia serves as the source of energy and reductant and as a signaling molecule that regulates gene expression in obligate ammonia-oxidizing chemolithotrophic microorganisms. The gammaproteobacterium, Nitrosococcus oceani, was the first obligate ammonia-oxidizer isolated from seawater and is one of the model systems for ammonia chemolithotrophy. We compared global transcriptional responses to ammonium and the catabolic intermediate, hydroxylamine, in ammonium-starved and non-starved cultures of N. oceani to discriminate transcriptional effects of ammonium from a change in overall energy and redox status upon catabolite availability. The most highly expressed genes from ammonium- or hydroxylamine-treated relative to starved cells are implicated in catabolic electron flow, carbon fixation, nitrogen assimilation, ribosome structure and stress tolerance. Catabolic inventory-encoding genes, including electron flow-terminating Complexes IV, FoF1 ATPase, transporters, and transcriptional regulators were among the most highly expressed genes in cells exposed only to ammonium relative to starved cells, although the differences compared to steady-state transcript levels were less pronounced. Reduction in steady-state mRNA levels from hydroxylamine-treated relative to starved-cells were less than five-fold. In contrast, several transcripts from ammonium-treated relative to starved cells were significantly less abundant including those for forward Complex I and a gene cluster of cytochrome c encoding proteins. Identified uneven steady-state transcript levels of co-expressed clustered genes support previously reported differential regulation at the levels of transcription and transcript stability. Our results differentiated between rapid regulation of core genes upon a change in cellular redox status versus those responsive to ammonium as a signaling molecule in N. oceani, both confirming and extending our knowledge of metabolic modules involved in ammonia

The bacterial community of entomophilic nematodes and host beetles.

Science.gov (United States)

Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

2016-05-01

Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. © 2016 John Wiley & Sons Ltd.

Microstructure and electrical-optical properties of cesium tungsten oxides synthesized by solvothermal reaction followed by ammonia annealing

International Nuclear Information System (INIS)

Liu Jingxiao; Ando, Yoshihiko; Dong Xiaoli; Shi Fei; Yin Shu; Adachi, Kenji; Chonan, Takeshi; Tanaka, Akikazu; Sato, Tsugio

2010-01-01

Cesium tungsten oxides (Cs x WO 3 ) were synthesized by solvothermal reactions using ethanol and 57.1 vol% ethanol aqueous solution at 200 o C for 12 h, and the effects of post annealing in ammonia atmosphere on the microstructure and electrical-optical properties were investigated. Agglomerated particles consisting of disk-like nanoparticles and nanorods of Cs x WO 3 were formed in the pure ethanol and ethanol aqueous solutions, respectively. The samples retained the original morphology and crystallinity after annealing in ammonia atmosphere up to 500 o C, while a small amount of nitrogen ion were incorporated in the lattice. The as-prepared Cs x WO 3 sample showed excellent near infrared (NIR) light shielding ability as well as high transparency in the visible light region. The electrical resistivity of the pressed pellets of the powders prepared in pure ethanol and 57.1 vol% ethanol aqueous solution greatly decreased after ammonia annealing at 500 o C, i.e., from 734 to 31.5 and 231 to 3.58 Ω cm, respectively. - Graphical abstract: Cesium tungsten oxides (Cs x WO 3 ) with different morphology were synthesized by solvothermal reaction, and the effects of post-ammonia annealing on the microstructure and electrical-optical properties were investigated.

Strategies for managing rival bacterial communities: Lessons from burying beetles.

Science.gov (United States)

Duarte, Ana; Welch, Martin; Swannack, Chris; Wagner, Josef; Kilner, Rebecca M

2018-03-01

The role of bacteria in animal development, ecology and evolution is increasingly well understood, yet little is known of how animal behaviour affects bacterial communities. Animals that benefit from defending a key resource from microbial competitors are likely to evolve behaviours to control or manipulate the animal's associated external microbiota. We describe four possible mechanisms by which animals could gain a competitive edge by disrupting a rival bacterial community: "weeding," "seeding," "replanting" and "preserving." By combining detailed behavioural observations with molecular and bioinformatic analyses, we then test which of these mechanisms best explains how burying beetles, Nicrophorus vespilloides, manipulate the bacterial communities on their carcass breeding resource. Burying beetles are a suitable species to study how animals manage external microbiota because reproduction revolves around a small vertebrate carcass. Parents shave a carcass and apply antimicrobial exudates on its surface, shaping it into an edible nest for their offspring. We compared bacterial communities in mice carcasses that were either fresh, prepared by beetles or unprepared but buried underground for the same length of time. We also analysed bacterial communities in the burying beetle's gut, during and after breeding, to understand whether beetles could be "seeding" the carcass with particular microbes. We show that burying beetles do not "preserve" the carcass by reducing bacterial load, as is commonly supposed. Instead, our results suggest they "seed" the carcass with bacterial groups which are part of the Nicrophorus core microbiome. They may also "replant" other bacteria from the carcass gut onto the surface of their carrion nest. Both these processes may lead to the observed increase in bacterial load on the carcass surface in the presence of beetles. Beetles may also "weed" the bacterial community by eliminating some groups of bacteria on the carcass, perhaps through

Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages

Directory of Open Access Journals (Sweden)

ANTONIUS SUWANTO

2010-04-01

Full Text Available Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages. Biodiversitas 11 (2: 65-68.Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to monitor the dynamics of the bacterial communities associated with early developmental stages of white shrimp (Litopenaeus vannamei larvae. Samples for analysis were egg, hatching nauplii, 24 hours old nauplii, and 48 hours old nauplii which were collected from one cycle of production at commercial hatchery. T-RFLP results indicated that the bacterial community associated with early stages of shrimp development might be transferred vertically from broodstock via egg. There was no significant difference between bacterial communities investigated, except the bacterial community of 48 hours old nauplii. Diversity analyses showed that the bacterial community of egg had the highest diversity and evenness, meanwhile the bacterial community of 48 hours old nauplii had the lowest diversity. Nine phylotypes were found at all stages with high abundance. Those TRFs were identified as γ- proteobacteria, α-proteobacteria, and bacteroidetes group.

Water addition regulates the metabolic activity of ammonia oxidizers responding to environmental perturbations in dry subhumid ecosystems.

Science.gov (United States)

Hu, Hang-Wei; Macdonald, Catriona A; Trivedi, Pankaj; Holmes, Bronwyn; Bodrossy, Levente; He, Ji-Zheng; Singh, Brajesh K

2015-02-01

Terrestrial arid and semi-arid ecosystems (drylands) constitute about 41% of the Earth's land surface and are predicted to experience increasing fluctuations in water and nitrogen availability. Mounting evidence has confirmed the significant importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in nitrification, plant nitrogen availability and atmospheric N2 O emissions, but their responses to environmental perturbations in drylands remain largely unknown. Here we evaluate how the factorial combinations of irrigation and fertilization in forests and land-use change from grassland to forest affects the dynamics of AOA and AOB following a 6-year dryland field study. Potential nitrification rates and AOA and AOB abundances were significantly higher in the irrigated plots, accompanied by considerable changes in community compositions, but their responses to fertilization alone were not significant. DNA-stable isotope probing results showed increased (13) CO2 incorporation into the amoA gene of AOA, but not of AOB, in plots receiving water addition, coupled with significantly higher net mineralization and nitrification rates. High-throughput microarray analysis revealed that active AOA assemblages belonging to Nitrosopumilus and Nitrosotalea were increasingly labelled by (13) CO2 following irrigation. However, no obvious effects of land-use changes on nitrification rates or metabolic activity of AOA and AOB could be observed under dry conditions. We provide evidence that water addition had more important roles than nitrogen fertilization in influencing the autotrophic nitrification in dryland ecosystems, and AOA are increasingly involved in ammonia oxidation when dry soils become wetted. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

The Effect of the 2015 Earthquake on the Bacterial Community Compositions in Water in Nepal

KAUST Repository

Uprety, Sital

2017-12-06

We conducted a study to examine the effect of seasonal variations and the disruptive effects of the 2015 Nepal earthquake on microbial communities associated with drinking water sources. We first characterized the microbial communities of water samples in two Nepali regions (Kathmandu and Jhapa) to understand the stability of microbial communities in water samples collected in 2014. We analyzed additional water samples from the same sources collected from May to August 2015, allowing the comparison of samples from dry-to-dry season and from dry-to-monsoon seasons. Emphasis was placed on microbes responsible for maintaining the geobiochemical characteristics of water (e.g., ammonia-oxidizing and nitrite-oxidizing bacteria and archaea and sulfate-reducing bacteria) and opportunistic pathogens often found in water (Acinetobacter). When examining samples from Jhapa, we identified that most geobiochemical microbe populations remained similar. When examining samples from Kathmandu, the abundance of microbial genera responsible for maintaining the geobiochemical characteristics of water increased immediately after the earthquake and decreased 8 months later (December 2015). In addition, microbial source tracking was used to monitor human fecal contamination and revealed deteriorated water quality in some specific sampling sites in Kathmandu post-earthquake. This study highlights a disruption of the environmental microbiome after an earthquake and the restoration of these microbial communities as a function of time and sanitation practices.

Architectural design drives the biogeography of indoor bacterial communities.

Science.gov (United States)

Kembel, Steven W; Meadow, James F; O'Connor, Timothy K; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G Z; Bohannan, Brendan J M; Green, Jessica L

2014-01-01

Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being.

Microbial community changes along the active seepage site of one cold seep in the Red Sea.

KAUST Repository

Cao, Huiluo

2015-07-21

The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

Microbial community changes along the active seepage site of one cold seep in the Red Sea.

KAUST Repository

Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

2015-01-01

The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

[Distribution and Diversity of Ammonium-oxidizing Archaea and Ammonium-oxidizing Bacteria in Surface Sediments of Oujiang River].

Science.gov (United States)

Li, Hu; Huang, Fu-yi; Su, Jian-qiang; Hong, You-wei; Yu, Shen

2015-12-01

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in the biogeochemical nitrogen cycle. Rivers are important ecosystems containing a large number of functional microbes in nitrogen cycle. In this study, denaturing gradient gel electrophoresis (DGGE ) and real-time quantitative PCR (qPCR) technology were used to analyze the distribution and diversity of AOA and AOB in sediments from Oujiang. The results showed that the AOA community structure was similar among various sites, while the AOB community structure was significantly different, in which all detected AOB sequences were classified into Nitrosospira and Nitrosomonas, and 90% affiliated to Nitrosospira. The community composition of AOA was influenced by NH₄⁺ and TS, in addition, the AOB composition was affected by NH₄⁺, EC, pH, NO₃⁻, TC and TN. Total sulfur (TS) and electrical conductivity (EC) were the major factors influencing the diversity of AOA and AOB, respectively. AOA abundance was significantly higher than that of AOB. EC, NH₄⁺-N and NO₃⁻-N were the main environmental factors affecting the abundance of AOA and AOB. This study indicated that the community composition and diversity of AOA and AOB were significantly influenced by environmental factors, and AOA might be dominant drivers in the ammonia oxidation process in Oujiang surface sediment.

Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments.

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Puntipar Sonthiphand

Full Text Available Anaerobic ammonia oxidizing (anammox bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library

Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

KAUST Repository

Tian, Ren-Mao

2014-01-01

Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2\\',4,4\\'-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge.

Characterization of Bioaerosol Bacterial Communities During Hazy and Foggy Weather in Qingdao, China

Science.gov (United States)

Qi, Jianhua; Li, Mengzhe; Zhen, Yu; Wu, Lijing

2018-06-01

This study was conducted to evaluate the impact of hazy and foggy weather on the bacterial communities in bioaerosols, for which samples were collected from the Qingdao coastal region on sunny, foggy, and hazy days in January and March 2013. Bacterial community compositions were determined using polymerase chain reaction denaturing gradient gel electrophoresis (PCRDGGE). The bacterial community diversity was found to be high on foggy and hazy days, and the dominant species differed during hazy weather. The Shannon-Wiener index revealed that the bacterial community diversity of coarse particles was higher than that of fine particles in the bioaerosols. The bacterial community diversity of fine particles significantly correlated with relative humidity (RH; r 2 = 0.986). The cluster analysis results indicated that the bacterial communities on sunny days differed from those on hazy and foggy days. Compared with sunny days, the bacterial communities in the fine particles during hazy weather exhibited greater changes than those in the coarse particles. Most of the sequenced bacteria were found to be closely affiliated with uncultured bacteria. During hazy weather, members of the classes Bacilli and Gammaproteobacteria ( Pseudomonas and Acinetobacter) were dominant. The DGGE analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, and their relative percentages to all the measured species changed significantly on hazy days, particularly in the fine particles. Haze and fog had a significant impact on the bacterial communities in bioaerosols, and the bacterial community diversity varied on different hazy days.

Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage.

Science.gov (United States)

Aida, Azrina A; Hatamoto, Masashi; Yamamoto, Masamitsu; Ono, Shinya; Nakamura, Akinobu; Takahashi, Masanobu; Yamaguchi, Takashi

2014-11-01

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Method for forming ammonia

Science.gov (United States)

Kong, Peter C.; Pink, Robert J.; Zuck, Larry D.

2008-08-19

A method for forming ammonia is disclosed and which includes the steps of forming a plasma; providing a source of metal particles, and supplying the metal particles to the plasma to form metal nitride particles; and providing a substance, and reacting the metal nitride particles with the substance to produce ammonia, and an oxide byproduct.

Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities

DEFF Research Database (Denmark)

Read, Daniel S.; Matzke, Marianne; Gweon, Hyun S.

2016-01-01

nanoparticles due to the practice of applying sewage sludge as a fertiliser or as an organic soil improver. However, understanding on the interactions between soil properties, nanoparticles and the organisms that live within soil is lacking, especially with regards to soil bacterial communities. We studied......Zinc oxide nanoparticles (ZnO NPs) are used in an array of products and processes, ranging from personal care products to antifouling paints, textiles, food additives, antibacterial agents and environmental remediation processes. Soils are an environment likely to be exposed to manmade...... the effects of nanoparticulate, non-nanoparticulate and ionic zinc (in the form of zinc chloride) on the composition of bacterial communities in soil with a modified pH range (from pH 4.5 to pH 7.2). We observed strong pH-dependent effects on the interaction between bacterial communities and all forms of zinc...

Effect of red clay on diesel bioremediation and soil bacterial community.

Science.gov (United States)

Jung, Jaejoon; Choi, Sungjong; Hong, Hyerim; Sung, Jung-Suk; Park, Woojun

2014-08-01

Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis

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Matt S. Conover

2016-04-01

Full Text Available Uropathogenic Escherichia coli (UPEC is the primary etiological agent of over 85% of community-acquired urinary tract infections (UTIs. Mouse models of infection have shown that UPEC can invade bladder epithelial cells in a type 1 pilus-dependent mechanism, avoid a TLR4-mediated exocytic process, and escape into the host cell cytoplasm. The internalized UPEC can clonally replicate into biofilm-like intracellular bacterial communities (IBCs of thousands of bacteria while avoiding many host clearance mechanisms. Importantly, IBCs have been documented in urine from women and children suffering acute UTI. To understand this protected bacterial niche, we elucidated the transcriptional profile of bacteria within IBCs using microarrays. We delineated the upregulation within the IBC of genes involved in iron acquisition, metabolism, and transport. Interestingly, lacZ was highly upregulated, suggesting that bacteria were sensing and/or utilizing a galactoside for metabolism in the IBC. A ΔlacZ strain displayed significantly smaller IBCs than the wild-type strain and was attenuated during competitive infection with a wild-type strain. Similarly, a galK mutant resulted in smaller IBCs and attenuated infection. Further, analysis of the highly upregulated gene yeaR revealed that this gene contributes to oxidative stress resistance and type 1 pilus production. These results suggest that bacteria within the IBC are under oxidative stress and, consistent with previous reports, utilize nonglucose carbon metabolites. Better understanding of the bacterial mechanisms used for IBC development and establishment of infection may give insights into development of novel anti-virulence strategies.

Anaerobic ammonia removal in presence of organic matter: A novel route

International Nuclear Information System (INIS)

Sabumon, P.C.

2007-01-01

This study describes the feasibility of anaerobic ammonia removal process in presence of organic matter. Different sources of biomass collected from diverse eco-systems containing ammonia and organic matter (OM) were screened for potential anaerobic ammonia removal. Sequential batch studies confirmed the possibility of anaerobic ammonia removal in presence of OM, but ammonia was oxidized anoxically to nitrate (at oxidation reduction potential; ORP -248 ± 25 mV) by an unknown mechanism unlike in the reported anammox process. The oxygen required for oxidation of ammonia might have been generated through catalase enzymatic activity of facultative anaerobes in mixed culture. The oxygen generation possibility by catalase enzyme route was demonstrated. Among the inorganic electron acceptors (NO 2 - , NO 3 - and SO 4 2- ) studied, NO 2 - was found to be most effective in total nitrogen removal. Denitrification by the developed culture was much effective and faster compared to ammonia oxidation. The results of this study show that anaerobic ammonia removal is feasible in presence of OM. The novel nitrogen removal route is hypothesized as enzymatic anoxic oxidation of NH 4 + to NO 3 - , followed by denitrification via autotrophic and/or heterotrophic routes. The results of batch study were confirmed in continuous reactor operation

Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

KAUST Repository

Barbato, Marta

2016-02-02

Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

Panamanian frog species host unique skin bacterial communities

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Lisa K. Belden

2015-10-01

Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

Science.gov (United States)

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

Science.gov (United States)

Kembel, Steven W.; O’Connor, Timothy K.; Arnold, Holly K.; Hubbell, Stephen P.; Wright, S. Joseph; Green, Jessica L.

2014-01-01

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function. PMID:25225376

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

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Justin Wright

2017-11-01

Full Text Available The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM, has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26 with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration

Characterization of TEMPO-oxidized bacterial cellulose; Caracterizacao de celulose bacteriana tempo-oxidada

Energy Technology Data Exchange (ETDEWEB)

Nascimento, Eligenes S.; Pereira, Andre L.S.; Lima, Helder L.; Barroso, Maria K. de A., E-mail: eligenessampaio@hotmail.com [Universidade Federal Ceara (UFC), Fortaleza, CE (Brazil); Barros, Matheus de O. [Instituto Federal do Ceara (IFCE), Fortaleza, CE (Brazil); Morais, Joao P.S. [Embrapa Algodao, Campina Grande, PB (Brazil); Borges, Maria de F.; Rosa, Morsyleide de F. [Embrapa Agroindustria Tropical, Fortaleza, CE (Brazil)

2015-07-01

The aim of this study was to characterize the TEMPO-oxidized bacterial cellulose, as a preliminary research for further application in nanocomposites. Bacterial cellulose (BC) was selectively oxidized at C-6 carbon by TEMPO radical. Oxidized bacterial cellulose (BCOX) was characterized by TGA, FTIR, XRD, and zeta potential. BCOX suspension was stable at pH 7.0, presented a crystallinity index of 83%, in spite of 92% of BC, because of decrease in the free hydroxyl number. FTIR spectra showed characteristic BC bands and, in addition, band of carboxylic group, proving the oxidation. BCOX DTG showed, in addition to characteristic BC thermal events, a maximum degradation peak at 233 °C, related to sodium anhydro-glucuronate groups formed during the cellulose oxidation. Thus, BC can be TEMPO-oxidized without great loss in its structure and properties. (author)

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Science.gov (United States)

2012-01-01

Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems.

Science.gov (United States)

Rachid, Caio T C C; Piccolo, Marisa C; Leite, Deborah Catharine A; Balieiro, Fabiano C; Coutinho, Heitor Luiz C; van Elsas, Jan Dirk; Peixoto, Raquel S; Rosado, Alexandre S

2012-08-08

Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Directory of Open Access Journals (Sweden)

Rachid Caio TCC

2012-08-01

Full Text Available Abstract Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane, next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA and denitrifying (nirK genes, greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil

Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

Science.gov (United States)

Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

2017-06-01

While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Characterisation of the bacterial community structures in the intestine of Lampetra morii.

Science.gov (United States)

Li, Yingying; Xie, Wenfang; Li, Qingwei

2016-07-01

The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response.

Diversity of ammonia-oxidizing bacteria in relation to soil environment in Ebinur Lake Wetland

Directory of Open Access Journals (Sweden)

Wenge Hu

2016-03-01

Full Text Available Ammonia oxidation is the first and rate-limiting step of nitrification and is carried out by ammonia-oxidizing bacteria (AOB. Ebinur Lake Wetland, the most representative temperate arid zone wetland ecosystem in China, is the centre of oasis and desertification of the northern slope of Tianshan conjugate. Soil samples were collected from three sites (Tamarix ramosissima, Halocnemum strobilaceum and Phragmites australis and different soil layers (0–5, 5–15, 15–25 and 25–35 cm in this wetland in spring, summer and autumn and were used to characterize the diversity of AOB based on the ammonia monooxygenase (amoA gene. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE and bivariate correlation analysis were used to analyse the relationship between the diversity of AOB and soil environment factors. The PCR-DGGE indicated that the diversity of AOB was high in the entire sample and the Shannon diversity index varied from 1.369 to 2.471. The phylogenetic analysis showed that the amoA fragments were grouped into Nitrosospira sp. and Nitrosomonas sp. Most amoA gene sequences fell within the Nitrosospira sp. cluster, and only a few sequences were clustered with Nitrosomonas sp., indicating that Nitrosospira sp. may be more adaptable than Nitrosomonas sp. in this area. Bivariate correlation analysis showed that the diversity of AOB was significantly correlated with soil organic matter, conductivity, total phosphorus and nitrate in the Ebinur Lake Wetland in Xinjiang.

Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

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Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

2017-11-01

The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia.

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Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

2014-02-01

Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds.

Methane-oxidizing seawater microbial communities from an Arctic shelf

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Uhlig, Christiane; Kirkpatrick, John B.; D'Hondt, Steven; Loose, Brice

2018-06-01

Marine microbial communities can consume dissolved methane before it can escape to the atmosphere and contribute to global warming. Seawater over the shallow Arctic shelf is characterized by excess methane compared to atmospheric equilibrium. This methane originates in sediment, permafrost, and hydrate. Particularly high concentrations are found beneath sea ice. We studied the structure and methane oxidation potential of the microbial communities from seawater collected close to Utqiagvik, Alaska, in April 2016. The in situ methane concentrations were 16.3 ± 7.2 nmol L-1, approximately 4.8 times oversaturated relative to atmospheric equilibrium. The group of methane-oxidizing bacteria (MOB) in the natural seawater and incubated seawater was > 97 % dominated by Methylococcales (γ-Proteobacteria). Incubations of seawater under a range of methane concentrations led to loss of diversity in the bacterial community. The abundance of MOB was low with maximal fractions of 2.5 % at 200 times elevated methane concentration, while sequence reads of non-MOB methylotrophs were 4 times more abundant than MOB in most incubations. The abundances of MOB as well as non-MOB methylotroph sequences correlated tightly with the rate constant (kox) for methane oxidation, indicating that non-MOB methylotrophs might be coupled to MOB and involved in community methane oxidation. In sea ice, where methane concentrations of 82 ± 35.8 nmol kg-1 were found, Methylobacterium (α-Proteobacteria) was the dominant MOB with a relative abundance of 80 %. Total MOB abundances were very low in sea ice, with maximal fractions found at the ice-snow interface (0.1 %), while non-MOB methylotrophs were present in abundances similar to natural seawater communities. The dissimilarities in MOB taxa, methane concentrations, and stable isotope ratios between the sea ice and water column point toward different methane dynamics in the two environments.

Plants of the fynbos biome harbour host species-specific bacterial communities.

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Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Analysis of soil whole- and inner-microaggregate bacterial communities

Energy Technology Data Exchange (ETDEWEB)

Mummey, D L; Stahl, P D [University of Wyoming, Laramie, WY (United States). Dept. of Renewable Resources

2004-07-01

Although soil structure largely determines energy flows and the distribution and composition of soil microhabitats, little is known about how microbial community composition is influenced by soil structural characteristics and organic matter compartmentalization dynamics. A UV irradiation-based procedure was developed to specifically isolate inner-microaggregate microbial communities, thus providing the means to analyze these communities in relation to their environment. Whole- and inner-microaggregate fractions of undisturbed soil and soils reclaimed after disturbance by surface coal mining were analyzed using 16S rDNA terminal restriction fragment polymorphism (T-RFLP) and sequence analyses to determine salient bacterial community structural characteristics. We hypothesized that inner-microaggregate environments select for definable microbial communities and that, due to their sequestered environment, inner-microaggregate communities would not be significantly impacted by disturbance. However, T-RFLP analysis indicated distinct differences between bacterial populations of inner-microaggregates of undisturbed and reclaimed soils. While both undisturbed and reclaimed inner-microaggregate bacterial communities were dominated by Actinobacteria, undisturbed soils contained only Actinobacteridae, while in inner-microaggregates of reclaimed soils Rubrobacteridae predominate. Spatial stratification of division-level lineages within microaggregates was also seen. The fractionation methods employed in this study therefore represent a valuable tool for defining relationships between biodiversity and soil structure.

Parental material and cultivation determine soil bacterial community structure and fertility.

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Sun, Li; Gao, Jusheng; Huang, Ting; Kendall, Joshua R A; Shen, Qirong; Zhang, Ruifu

2015-01-01

Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate

Biosynthesis of poly (3-hydroxybutyrate-co-3-hydroxyvalerate) by bacterial community from propylene oxide saponification wastewater residual sludge.

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Wang, Yiwei; Zhu, Ying; Gu, Pengfei; Li, Yumei; Fan, Xiangyu; Song, Dongxue; Ji, Yan; Li, Qiang

2017-05-01

The saponification wastewater from the process of propylene oxide (PO) production is contaminated with high chemical oxygen demand (COD) and chlorine contents. Although the activated sludge process could treat the PO saponification wastewater effectively, the residual sludge was difficult to be disposed properly. In this research, microbes in PO saponification wastewater residual sludge were acclimated to produce poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from volatile fatty acids. Through Miseq Illumina highthroughput sequencing, the bacterial community discrepancy between the original and the acclimated sludge samples were analyzed. The proportions of Bacillus, Acinetobacter, Brevundimonas and Pseudomonas, the potential PHBV-producers in the residual sludge, were all obviously increased. In the batch fermentation, the production of PHBV could achieve 4.262g/L at 300min, with the content increased from 0.04% to 23.67% of mixed liquor suspended solid (MLSS) in the acclimated sludge, and the COD of the PO saponification wastewater was also decreased in the fermentation. This work would provide an effective solution for the utilization of PO saponification wastewater residual sludge. Copyright © 2017 Elsevier B.V. All rights reserved.

Understanding the efficacy of influent waste water on microbial ...

African Journals Online (AJOL)

acer

composition on the species structure and the diversity of bacterial consortia. The community ... 2010; Kim et al., 2011; Ye et al., 2011; Zhang et al.,. 2011a; b), greatly ..... molecular fine scale analysis of natural ammonia-oxidizing populations.

Microbial community shifts in a farm-scale anaerobic digester treating swine waste: Correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions.

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Cho, Kyungjin; Shin, Seung Gu; Kim, Woong; Lee, Joonyeob; Lee, Changsoo; Hwang, Seokhwan

2017-12-01

Microbial community structure in a farm-scale anaerobic digester treating swine manure was investigated during three process events: 1) prolonged starvation, and changes of 2) operating temperature (between meso- and thermophilic) and 3) hydraulic retention time (HRT). Except during the initial period, the digester was dominated by hydrogenotrophic methanogens (HMs). The bacterial community structure significantly shifted with operating temperature and HRT but not with long-term starvation. Clostridiales (26.5-54.4%) and Bacteroidales (2.5-13.7%) became dominant orders in the digester during the period of HM dominance. Abundance of diverse meso- and thermophilic bacteria increased during the same period; many of these species may be H 2 producers, and/or syntrophic acetate oxidizers. Some of these species showed positive correlations with [NH 4 + -N] (panaerobic digesters treating swine manure that contains high ammonia content. Copyright © 2017 Elsevier B.V. All rights reserved.

Effective bioleaching of chromium in tannery sludge with an enriched sulfur-oxidizing bacterial community.

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Zeng, Jing; Gou, Min; Tang, Yue-Qin; Li, Guo-Ying; Sun, Zhao-Yong; Kida, Kenji

2016-10-01

In this study, a sulfur-oxidizing community was enriched from activated sludge generated in tannery wastewater treatment plants. Bioleaching of tannery sludge containing 0.9-1.2% chromium was investigated to evaluate the effectiveness of the enriched community, the effect of chromium binding forms on bioleaching efficiency, and the dominant microbes contributing to chromium bioleaching. Sludge samples inoculated with the enriched community presented 79.9-96.8% of chromium leaching efficiencies, much higher than those without the enriched community. High bioleaching efficiencies of over 95% were achieved for chromium in reducible fraction, while 60.9-97.9% were observed for chromium in oxidizable and residual fractions. Acidithiobacillus thiooxidans, the predominant bacteria in the enriched community, played an important role in bioleaching, whereas some indigenous heterotrophic species in sludge might have had a supporting role. The results indicated that A. thiooxidans-dominant enriched microbial community had high chromium bioleaching efficiency, and chromium binding forms affected the bioleaching performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

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Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

2016-01-01

Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

Directory of Open Access Journals (Sweden)

Laura Delgado-Balbuena

Full Text Available Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826 accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485 inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100% > earthworms applied (92% > organic material applied (77% > untreated soil (57% > surfactant applied (34% after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil

Microbial community shifts and biogas conversion computation during steady, inhibited and recovered stages of thermophilic methane fermentation on chicken manure with a wide variation of ammonia.

Science.gov (United States)

Niu, Qigui; Qiao, Wei; Qiang, Hong; Li, Yu-You

2013-10-01

The thermophilic methane fermentation of chicken manure (10% TS) was investigated within a wide range of ammonia. Microbiological analysis showed significant shifts in Archaeal and Bacterial proportions with VFA accmulation and CH4 formation before and after inhibition. VFA accumulated sharply with lower methane production, 0.29 L/g VS, than during the steady stage, 0.32 L/g VS. Biogas production almost ceased with the synergy inhibition of TAN (8000 mg/L) and VFA (25,000 mg/L). Hydrogenotrophic Methanothermobacter thermautotrophicus str. was the dominate archaea with 95% in the inhibition stage and 100% after 40 days recovery compared to 9.3% in the steady stage. Aceticlastic Methanosarcina was not encountered with coincided phenomenal of high VFA in the inhibition stage as well as recovery stage. Evaluation of the microbial diversity and functional bacteria indicated the dominate phylum of Firmicutes were 94.74% and 84.4% with and without inhibition. The microbial community shifted significantly with elevated ammonia concentration affecting the performance. Copyright © 2013 Elsevier Ltd. All rights reserved.

Changes in the bacterial community of soybean rhizospheres during growth in the field.

Science.gov (United States)

Sugiyama, Akifumi; Ueda, Yoshikatsu; Zushi, Takahiro; Takase, Hisabumi; Yazaki, Kazufumi

2014-01-01

Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils.

Science.gov (United States)

Cao, Qing; Steinman, Alan D; Su, Xiaomei; Xie, Liqiang

2017-12-01

A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L -1 ) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application. In contrast, dehydrogenase activity was stimulated in the 1000 μg treatment, and a stimulatory effect also occurred with soil respiration in contaminated soil. The metabolic profiles of the microbial communities indicated that overall carbon metabolic activity in the soils treated with high microcystin concentrations was inhibited, and high concentrations of microcystin also led to different patterns of potential carbon utilization. High microcystin concentrations (100, 1000 μg eq. MC-LR L -1 in Soil A; 10, 100 1000 μg eq. MC-LR L -1 in Soil B) significantly decreased soil potential nitrification rate. Furthermore, the decrease in soil potential nitrification rate was positively correlated with the decrease of the amoA gene abundance, which corresponds to the ammonia-oxidizing bacterial community. We conclude that application of microcystin-enriched irrigation water can significantly impact soil microbial community structure and function. Copyright © 2017 Elsevier Ltd. All rights reserved.

Invasive lionfish harbor a different external bacterial community than native Bahamian fishes

Science.gov (United States)

Stevens, J. L.; Olson, J. B.

2013-12-01

The introduction and subsequent spread of lionfish into the Atlantic Ocean and Caribbean Sea has become a worldwide conservation issue. These highly successful invaders may also be capable of introducing non-native microorganisms to the invaded regions. This study compared the bacterial communities associated with lionfish external tissue to those of native Bahamian fishes and ambient water. Terminal restriction fragment length polymorphism analyses demonstrated that lionfish bacterial communities were significantly different than those associated with three native Bahamian fishes. Additionally, all fishes harbored distinct bacterial communities from the ambient bacterioplankton. Analysis of bacterial clone libraries from invasive lionfish and native squirrelfish indicated that lionfish communities were more diverse than those associated with squirrelfish, yet did not contain known fish pathogens. Using microscopy and molecular genetic approaches, lionfish eggs were examined for the presence of bacteria to evaluate the capacity for vertical transmission. Eggs removed from the ovaries of gravid females were free of bacteria, suggesting that lionfish likely acquire bacteria from the environment. This study was the first examination of bacterial communities associated with the invasive lionfish and indicated that they support different communities of environmentally derived bacteria than Caribbean reef fishes.

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

Science.gov (United States)

Luo, Gang; Angelidaki, Irini

2014-09-01

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

DEFF Research Database (Denmark)

Jurburg, Stephanie D.; Nunes, Ines Marques; Stegen, James C.

2017-01-01

The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In ord...... diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery....... to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days...... slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme...

Molecular characterization of soil bacterial community in a perhumid, low mountain forest.

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Lin, Yu-Te; Whitman, William B; Coleman, David C; Chih-Yu, Chiu

2011-01-01

Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.

Emissions of ammonia, nitrous oxide and methane during composting of organic household waste

International Nuclear Information System (INIS)

Gunnarsdotter Beck-Friis, Barbro

2001-01-01

In Sweden, composting of source-separated organic household waste is increasing, both domestically at the small-scale, and in larger municipal plants. Composting means a microbial decomposition of organic material, which results in the production of environmentally undesirable gases, such as ammonia (NH 3 ), nitrous oxide (N 2 O) and methane (CH 4 ). The aim of this thesis was to study the emissions of NH 3 , N 2 O and CH 4 to the atmosphere during composting of source-separated organic household waste. The studies were conducted in an experimental reactor under constant and controlled conditions and in municipal compost heaps. Emissions of NH 3 , N 2 O and CH 4 occurred at different phases during composting. Ammonia started to volatilise during the shift from mesophilic to thermophilic conditions when short-chained fatty acids were decomposed. Nitrous oxide was only emitted during the first days of composting and later during the cooling phase when nitrate was formed. Methane was only produced during the thermophilic phase. Large municipal compost heaps are a significant source for the production and emission of the greenhouse gases N 2 O and CH 4 . To avoid unwanted gaseous emissions to the atmosphere during composting, gaseous exchange with the atmosphere should be controlled in future composting plants

A gold electrode modified with silver oxide nanoparticle decorated carbon nanotubes for electrochemical sensing of dissolved ammonia

International Nuclear Information System (INIS)

Rahman, Mohammed M.; Asiri, Abdullah M.; Balkhoyor, Hasan B.; Marwani, Hadi M.

2016-01-01

We have prepared silver oxide nanoparticles with a diameter of ∼ 15 nm and decorated with carbon nanotube nanocomposites (Ag_2O/CNT NCs) by a facile wet chemical method using reducing agents in alkaline medium. These NCs were characterized by UV/vis, FTIR and energy dispersive X-ray spectroscopy, by X-ray powder diffraction and field emission scanning electron microscopy. The NCs were then deposited on a flat gold electrode with the help of a conducting binder to result in an electrochemical sensor for aqueous ammonia using the I-V technique. Response is based on surface oxidation of ammonium hydroxide with electrode-adsorbed oxygen to form nitrogen oxide, these simultaneously liberating free electrons in the conduction band. Sensor features include a sensitivity of 32.856 μA.μM"-"1.cm"-"2, a low detection limit (1.3 pM at a signal to noise ratio of 3), reliability, reproducibility, ease of integration, and long term stability. The response to dissolved ammonia is linear (r"2: 0.9778) over the 0.01 nM to 0.1 mM concentration range. (author)