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Sample records for aerobic ammonia-oxidizing bacteria

  1. Role of ammonia-oxidizing bacteria in micropollutant removal from wastewater with aerobic granular sludge.

    PubMed

    Margot, Jonas; Lochmatter, Samuel; Barry, D A; Holliger, Christof

    2016-01-01

    Nitrifying wastewater treatment plants (WWTPs) are more efficient than non-nitrifying WWTPs to remove several micropollutants such as pharmaceuticals and pesticides. This may be related to the activity of nitrifying organisms, such as ammonia-oxidizing bacteria (AOBs), which could possibly co-metabolically oxidize micropollutants with their ammonia monooxygenase (AMO). The role of AOBs in micropollutant removal was investigated with aerobic granular sludge (AGS), a promising technology for municipal WWTPs. Two identical laboratory-scale AGS sequencing batch reactors (AGS-SBRs) were operated with or without nitrification (inhibition of AMOs) to assess their potential for micropollutant removal. Of the 36 micropollutants studied at 1 μg l(-1) in synthetic wastewater, nine were over 80% removed, but 17 were eliminated by less than 20%. Five substances (bisphenol A, naproxen, irgarol, terbutryn and iohexol) were removed better in the reactor with nitrification, probably due to co-oxidation catalysed by AMOs. However, for the removal of all other micropollutants, AOBs did not seem to play a significant role. Many compounds were better removed in aerobic condition, suggesting that aerobic heterotrophic organisms were involved in the degradation. As the AGS-SBRs did not favour the growth of such organisms, their potential for micropollutant removal appeared to be lower than that of conventional nitrifying WWTPs. PMID:26877039

  2. Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.

    PubMed

    Sauder, Laura A; Ross, Ashley A; Neufeld, Josh D

    2016-04-01

    Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representativeNitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway. PMID:26946536

  3. Identification of Bacteria Responsible for Ammonia Oxidation in Freshwater Aquaria

    PubMed Central

    Burrell, Paul C.; Phalen, Carol M.; Hovanec, Timothy A.

    2001-01-01

    Culture enrichments and culture-independent molecular methods were employed to identify and confirm the presence of novel ammonia-oxidizing bacteria (AOB) in nitrifying freshwater aquaria. Reactors were seeded with biomass from freshwater nitrifying systems and enriched for AOB under various conditions of ammonia concentration. Surveys of cloned rRNA genes from the enrichments revealed four major strains of AOB which were phylogenetically related to the Nitrosomonas marina cluster, the Nitrosospira cluster, or the Nitrosomonas europaea-Nitrosococcus mobilis cluster of the β subdivision of the class Proteobacteria. Ammonia concentration in the reactors determined which AOB strain dominated in an enrichment. Oligonucleotide probes and PCR primer sets specific for the four AOB strains were developed and used to confirm the presence of the AOB strains in the enrichments. Enrichments of the AOB strains were added to newly established aquaria to determine their ability to accelerate the establishment of ammonia oxidation. Enrichments containing the Nitrosomonas marina-like AOB strain were most efficient at accelerating ammonia oxidation in newly established aquaria. Furthermore, if the Nitrosomonas marina-like AOB strain was present in the original enrichment, even one with other AOB, only the Nitrosomonas marina-like AOB strain was present in aquaria after nitrification was established. Nitrosomonas marina-like AOB were 2% or less of the cells detected by fluorescence in situ hybridization analysis in aquaria in which nitrification was well established. PMID:11722936

  4. Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria.

    PubMed

    Liu, Shuai; Hu, Baolan; He, Zhanfei; Zhang, Bin; Tian, Guangming; Zheng, Ping; Fang, Fang

    2015-10-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05). PMID:26099334

  5. Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

    PubMed Central

    Sonthiphand, Puntipar; Hall, Michael W.; Neufeld, Josh D.

    2014-01-01

    Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments. PMID:25147546

  6. Ammonia Oxidizing Bacteria Community Dynamics in a Pilot-Scale Wastewater Treatment Plant

    PubMed Central

    Wang, Xiaohui; Wen, Xianghua; Xia, Yu; Hu, Ma; Zhao, Fang; Ding, Kun

    2012-01-01

    Background Chemoautotrophic ammonia oxidizing bacteria (AOB) have the metabolic ability to oxidize ammonia to nitrite aerobically. This metabolic feature has been widely used, in combination with denitrification, to remove nitrogen from wastewater in wastewater treatment plants (WWTPs). However, the relative influence of specific deterministic environmental factors to AOB community dynamics in WWTP is uncertain. The ecological principles underlying AOB community dynamics and nitrification stability and how they are related are also poorly understood. Methodology/Principal Findings The community dynamics of ammonia oxidizing bacteria (AOB) in a pilot-scale WWTP were monitored over a one-year period by Terminal Restriction Fragment Length Polymorphism (T-RFLP). During the study period, the effluent ammonia concentrations were almost below 2 mg/L, except for the first 60 days, indicting stable nitrification. T-RFLP results showed that, during the test period with stable nitrification, the AOB community structures were not stable, and the average change rate (every 15 days) of AOB community structures was 10%±8%. The correlations between T-RFLP profiles and 10 operational and environmental parameters were tested by Canonical Correlation Analysis (CCA) and Mantel test. The results indicated that the dynamics of AOB community correlated most strongly with Dissolved Oxygen (DO), effluent ammonia, effluent Biochemical Oxygen Demand (BOD) and temperature. Conclusions/Significance This study suggests that nitrification stability is not necessarily accompanied by a stable AOB community, and provides insight into parameters controlling the AOB community dynamics within bioreactors with stable nitrification. PMID:22558415

  7. Ammonia-Oxidizing Bacteria in Biofilters Removing Trihalomethanes Are Related to Nitrosomonas oligotropha

    EPA Science Inventory

    Nitrifying biofilters degrading the four regulated trihalomethanes (THMs) trichloromethane (TCM), bromodichloromethane (BDCM), dibromochloromethane (DBCM), and tribromomethane (TBM) -were analyzed for the presence and activity of ammonia-oxidizing bacteria (AOB). Biofilter perfor...

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

    PubMed Central

    Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2015-01-01

    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. PMID:25705674

  9. Impact of TiO₂ and ZnO nanoparticles at predicted environmentally relevant concentrations on ammonia-oxidizing bacteria cultures under ammonia oxidation.

    PubMed

    Luo, Zhuanxi; Qiu, Zhaozheng; Chen, Zheng; Du Laing, Gijs; Liu, Aifen; Yan, Changzhou

    2015-02-01

    Increased application of titanium dioxide and zinc oxide nanoparticles (nano-TiO2 and nano-ZnO) raises concerns related to their environmental impacts. The effects that such nanoparticles have on environmental processes and the bacteria that carry them out are largely unknown. In this study, ammonia-oxidizing bacteria (AOB) enrichment cultures, grown from surface sediments taken from an estuary wetland in Fujian Province, China, were spiked with nano-TiO2 and nano-ZnO (with an average size of 32 and 43 nm, respectively) at predicted environmentally relevant concentrations (≤2 mg L(-1)) to determine their impacts on ammonia oxidation and the mechanisms involved. Results showed that higher nano-TiO2 concentrations significantly inhibited ammonia oxidation in enrichment cultures. It is noteworthy that the average ammonia oxidation rate was significantly correlated to the Shannon index, the Simpson's index, and AOB abundance. This suggested that ammonia oxidation inhibition primarily resulted from a reduction of AOB biodiversity and abundance. However, AOB biodiversity and abundance as well as the average ammonia oxidation rate were not inhibited by nano-ZnO at predicted environmentally relevant concentrations. Accordingly, an insignificant correlation was established between biodiversity and abundance of the AOB amoA gene and the average ammonia oxidation rate under nano-ZnO treatments. AOB present in samples belonged to the β-Proteobacteria class with an affinity close to Nitrosospira and Nitrosomonas genera. This suggested that identified impacts of nano-TiO2 and nano-ZnO on ammonia oxidation processes can be extrapolated to some extent to natural aquatic environments. Complex impacts on AOB may result from different nanomaterials present in aquatic environments at various ambient conditions. Further investigation on how and to what extent different nanomaterials influence AOB diversity and abundance and their subsequent ammonia oxidation processes is therefore

  10. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation.

    PubMed

    Könneke, Martin; Schubert, Daniel M; Brown, Philip C; Hügler, Michael; Standfest, Sonja; Schwander, Thomas; Schada von Borzyskowski, Lennart; Erb, Tobias J; Stahl, David A; Berg, Ivan A

    2014-06-01

    Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments. PMID:24843170

  11. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

    PubMed Central

    Könneke, Martin; Schubert, Daniel M.; Brown, Philip C.; Hügler, Michael; Standfest, Sonja; Schwander, Thomas; Schada von Borzyskowski, Lennart; Erb, Tobias J.; Stahl, David A.; Berg, Ivan A.

    2014-01-01

    Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments. PMID:24843170

  12. pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China.

    PubMed

    Li, Hu; Weng, Bo-Sen; Huang, Fu-Yi; Su, Jian-Qiang; Yang, Xiao-Ru

    2015-07-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity. PMID:25744648

  13. Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments

    PubMed Central

    Li, Meng; Cao, Huiluo; Hong, Yiguo

    2010-01-01

    We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to mangrove forest in the territories of Hong Kong. Both the archaeal and bacterial amoA genes (encoding ammonia monooxygenase subunit A) from all samples supported distinct phylogenetic groups, indicating the presences of niche-specific AOA and AOB in mangrove sediments. The higher AOB abundances than AOA in mangrove sediments, especially in the vicinity of the mangrove trees, might indicate the more important role of AOB on nitrification. The spatial distribution showed that AOA had higher diversity and abundance in the surface layer sediments near the mangrove trees (0 and 10 m) but lower away from the mangrove trees (1,000 m), and communities of AOA could be clustered into surface and bottom sediment layer groups. In contrast, AOB showed a reverse distributed pattern, and its communities were grouped by the distances between sites and mangrove trees, indicating mangrove trees might have different influences on AOA and AOB community structures. Furthermore, the strong correlations among archaeal and bacterial amoA gene abundances and their ratio with NH4+, salinity, and pH of sediments indicated that these environmental factors have strong influences on AOA and AOB distributions in mangrove sediments. In addition, AOA diversity and abundances were significantly correlated with hzo gene abundances, which encodes the key enzyme for transformation of hydrazine into N2 in anaerobic ammonium-oxidizing (anammox) bacteria, indicating AOA and anammox bacteria may interact with each other or they are influenced by the same controlling factors, such as NH4+. The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients. Electronic supplementary material The online version of this

  14. Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean.

    PubMed

    Xu, Wei; Li, Meng; Ding, Jie-Fei; Gu, Ji-Dong; Luo, Zhu-Hua

    2014-09-01

    Ammonia oxidation is the first and rate-limiting step of nitrification, which is carried out by two groups of microorganisms: ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). In this study, diversity and abundance of AOB and AOA were investigated in five rock samples from a deep-sea hydrothermal vent site at the Mid-Atlantic Ridge (MAR) of the South Atlantic Ocean. Both bacterial and archaeal ammonia monooxygenase subunit A (amoA) gene sequences obtained in this study were closely related to the sequences retrieved from deep-sea environments, indicating that AOB and AOA in this hydrothermal vent site showed typical deep ocean features. AOA were more diverse but less abundant than AOB. The ratios of AOA/AOB amoA gene abundance ranged from 1/3893 to 1/242 in all investigate samples, indicating that bacteria may be the major members responding to the aerobic ammonia oxidation in this hydrothermal vent site. Furthermore, diversity and abundance of AOA and AOB were significantly correlated with the contents of total nitrogen and total sulfur in investigated samples, suggesting that these two environmental factors exert strong influences on distribution of ammonia oxidizers in deep-sea hydrothermal vent environment. PMID:24893665

  15. Agreement between Theory and Measurement in Quantification of Ammonia-Oxidizing Bacteria

    PubMed Central

    Coskuner, Gulnur; Ballinger, Stuart J.; Davenport, Russell J.; Pickering, Rheanne L.; Solera, Rosario; Head, Ian M.; Curtis, Thomas P.

    2005-01-01

    Autotrophic ammonia-oxidizing bacteria (AOB) are of vital importance to wastewater treatment plants (WWTP), as well as being an intriguing group of microorganisms in their own right. To date, corroboration of quantitative measurements of AOB by fluorescence in situ hybridization (FISH) has relied on assessment of the ammonia oxidation rate per cell, relative to published values for cultured AOB. Validation of cell counts on the basis of substrate transformation rates is problematic, however, because published cell-specific ammonia oxidation rates vary by over two orders of magnitude. We present a method that uses FISH in conjunction with confocal scanning laser microscopy to quantify AOB in WWTP, where AOB are typically observed as microcolonies. The method is comparatively simple, requiring neither detailed cell counts or image analysis, and yet it can give estimates of either cell numbers or biomass. Microcolony volume and diameter were found to have a log-normal distribution. We were able to show that virtually all (>96%) of the AOB biomass occurred as microcolonies. Counts of microcolony abundance and measurement of their diameter coupled with a calibration of microcolony dimensions against cell numbers or AOB biomass were used to determine AOB cell numbers and biomass in WWTP. Cell-specific ammonia oxidation rates varied between plants by over three orders of magnitude, suggesting that cell-specific ammonia oxidation is an important process variable. Moreover, when measured AOB biomass was compared with process-based estimates of AOB biomass, the two values were in agreement. PMID:16204554

  16. Abundance of ammonia oxidizing bacteria and archaea under long-term maize cropping systems.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nitrification involves the oxidation of ammonium and is an important component of the overall N cycle. Nitrification occurs in two steps; first by oxidizing ammonium to nitrite, and then to nitrate. The first step is often the rate limiting step. Until recently ammonia-oxidizing bacteria were though...

  17. Phylogenetically diverse denitrifying and ammonia-oxidizing bacteria in corals Alcyonium gracillimum and Tubastraea coccinea.

    PubMed

    Yang, Shan; Sun, Wei; Zhang, Fengli; Li, Zhiyong

    2013-10-01

    To date, the association of coral-bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis. PMID:23564007

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

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed Central

    Sauder, Laura A.; Mosquera, Mariela; Neufeld, Josh D.; Boon, Nico

    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

  20. Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

    PubMed

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

    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

  1. Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems.

    PubMed

    Ding, Kun; Wen, Xianghua; Li, Yuyang; Shen, Bo; Zhang, Bing

    2015-02-01

    So far, the contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation in wastewater treatment processes has not been well understood. In this study, two soil aquifer treatment (SATs) systems were built up to treat synthetic domestic wastewater (column 1) and secondary effluent (column 4), accomplishing an average of 95% ammonia removal during over 550 days of operation. Except at day 322, archaeal amoA genes always outnumbered bacterial amoA genes in both SATs as determined by using quantitative polymerase chain reaction (q-PCR). The ratios of archaeal amoA to 16S rRNA gene averaged at 0.70 ± 0.56 and 0.82 ± 0.62 in column 1 and column 4, respectively, indicating that all the archaea could be AOA carrying amoA gene in the SATs. The results of MiSeq-pyrosequencing targeting on archaeal and bacterial 16S rRNA genes with the primer pair of modified 515R/806R indicated that Nitrososphaera cluster affiliated with thaumarchaeal group I.1b was the dominant AOA species, while Nitrosospira cluster was the dominant ammonia-oxidizing bacteria (AOB). The statistical analysis showed significant relationship between AOA abundance (compared to AOB abundance) and inorganic and total nitrogen concentrations. Based on the mathematical model calculation for microbial growth, AOA had much greater capacity of ammonia oxidation as compared to the specific influent ammonia loading for AOA in the SATs, implying that a small fraction of the total AOA would actively work to oxidize ammonia chemoautotrophically whereas most of AOA would exhibit some level of functional redundancy. These results all pointed that AOA involved in microbial ammonia oxidation in the SATs. PMID:25381908

  2. Detection and analysis of two serotypes of ammonia-oxidizing bacteria in sewage plants by flow cytometry.

    PubMed Central

    Völsch, A; Nader, W F; Geiss, H K; Nebe, G; Birr, C

    1990-01-01

    Two different serotypes of the genus Nitrosomonas were isolated from samples of the sewage plant Heidelberg. These nitrifiers were enumerated in activated sludge of various other sewage plants after immunofluorescent labeling and staining with propidium iodide by flow cytometry. The concentrations of these serotypes of Nitrosomonas spp. were in the range of 0.1 to 2%. Also, a test for the determination of the activity of ammonia-oxidizing bacteria was developed. Nitrite-oxidizing bacteria were specifically inhibited with sodium chlorate, and the activity of ammonia-oxidizing bacteria could be calculated from the increase of nitrite. Concentrations and activities of ammonia oxidizers were measured for a period of 6 months in the sewage plant Heidelberg. With one exception, activities and concentrations of ammonia-oxidizing bacteria decreased and increased in parallel. PMID:2403253

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

    PubMed

    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. PMID:24401864

  4. The abundance and diversity of ammonia-oxidizing bacteria in activated sludge under autotrophic domestication.

    PubMed

    Li, Qiang; Ma, Chao; Sun, Shifang; Xie, Hui; Zhang, Wei; Feng, Jun; Song, Cunjiang

    2013-04-01

    Ammonia-oxidizing bacteria (AOB) play a key role in nitrogen-removal wastewater treatment plants (WWTPs) as they can transform ammonia into nitrite. AOB can be enriched in activated sludge through autotrophic domestication although they are difficult to be isolated. In this study, autotrophic domestication was carried out in a lab-scale sequencing-batch-reactor (SBR) system with two activated sludge samples. The ammonia removal capacity of the sludge samples increased during the domestication, and pH exhibited a negative correlation with the ammonia removal amount, which indicated that it was one important factor of microbial ammonia oxidation. The count of AOB, measured by the most probable number (MPN) method, increased significantly during autotrophic domestication as ammonia oxidation efficiency was enhanced. We investigated the changes in the community structure of AOB before and after domestication by amoA clone library and T-RFLP profile. It showed that AOB had been successfully enriched and the community structure significantly shifted during the domestication. Two groups of AOB were found in sludge samples: Nitrosomonas-like group remained predominant all the time and Nitrosospira-like group changed obviously. Simultaneously, the total heterotrophic bacteria were investigated by MPN and Biolog assay. The metabolic diversity of heterotrophs had changed minutely, although the count of them decreased significantly and lost superiority of microbial communities in the sludge. PMID:24620598

  5. Efficient cryopreservation protocol enables accessibility of a broad range of ammonia-oxidizing bacteria for the scientific community.

    PubMed

    Hoefman, Sven; Pommerening-Röser, Andreas; Samyn, Emly; De Vos, Paul; Heylen, Kim

    2013-05-01

    Long-term storage of the fastidious ammonia-oxidizing bacteria has proven difficult, which limits their public availability and results in a loss of cultured biodiversity. To enable their accessibility to the scientific community, an effective protocol for cryopreservation of ammonia-oxidizing cultures at -80 °C and in liquid nitrogen was developed. Long-term storage could be achieved using 5% DMSO as cryoprotectant, preferably in a cryoprotective preservation medium containing tenfold-diluted trypticase soy broth and 1% trehalose. As such, successful activity and growth recovery was observed for a diverse set of ammonia-oxidizing cultures. PMID:23376087

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

    PubMed

    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. PMID:26938496

  7. Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest.

    PubMed

    Zhang, Li-Mei; Wang, Mu; Prosser, James I; Zheng, Yuan-Ming; He, Ji-Zheng

    2009-11-01

    To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000-6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800-6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amoA abundance was greater than bacterial amoA abundance in lower altitude soils (or=5700 m a.s.l.). Both archaeal and bacterial amoA abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amoA cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amoA sequences fell within soil and sediment clusters, and the proportions of the major archaeal amoA clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils. PMID:19780828

  8. Epiphyton as a Niche for Ammonia-Oxidizing Bacteria: Detailed Comparison with Benthic and Pelagic Compartments in Shallow Freshwater Lakes▿

    PubMed Central

    Coci, M.; Bodelier, P. L. E.; Laanbroek, H. J.

    2008-01-01

    Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated. PMID:18263748

  9. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California

    PubMed Central

    Beman, J. M.; Bertics, Victoria J.; Braunschweiler, Thomas; Wilson, Jesse M.

    2012-01-01

    Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation–reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another – yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O2, NH4+, and NO3−) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24–0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 107 genes g–1) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria. PMID:22837756

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

    NASA Astrophysics Data System (ADS)

    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;

  11. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria.

    PubMed

    Nicol, Graeme W; Leininger, Sven; Schleper, Christa; Prosser, James I

    2008-11-01

    Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils. PMID:18707610

  12. Biotransformation of pharmaceuticals by ammonia oxidizing bacteria in wastewater treatment processes.

    PubMed

    Xu, Yifeng; Yuan, Zhiguo; Ni, Bing-Jie

    2016-10-01

    Pharmaceutical residues could potentially pose detrimental effects on aquatic ecosystems and human health, with wastewater treatment being one of the major pathways for pharmaceuticals to enter into the environment. Enhanced removal of pharmaceuticals by ammonia oxidizing bacteria (AOB) has been widely observed in wastewater treatment processes. This article reviews the current knowledge on the biotransformation of pharmaceuticals by AOB. The relationship between the pharmaceuticals removal and nitrification process was revealed. The important role of AOB-induced cometabolism on the biotransformation of pharmaceuticals as well as their transformation products and pathways was elucidated. Kinetics and mathematical models describing the biotransformation of pharmaceuticals by AOB were also reviewed. The results highlighted the high degradation capabilities of AOB toward some refractory pharmaceuticals, with their degradations being clearly related to the nitrification rate and their transformation products being identified, which may exhibit similar or higher ecotoxicological impacts compared to the parent compound. PMID:27243932

  13. Comparison of the community structures of ammonia-oxidizing bacteria and archaea in rhizoplanes of floating aquatic macrophytes.

    PubMed

    Wei, Bo; Yu, Xin; Zhang, Shuting; Gu, Li

    2011-09-20

    Some common floating aquatic macrophytes could remove nutrients, such as nitrogen, from eutrophic water. However, the relationship between these macrophytes and the ammonia-oxidizing microorganisms on their rhizoplanes is still unknown. In this study, we examined communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) on the rhizoplanes of common floating aquatic macrophytes (Eichhornia crassipes, Pistia stratiotes and Ipomoea aquatic) in a eutrophic reservoir.The results show that AOB were the predominant ammonia-oxidizer on the three rhizoplanes. The principal AOB were Nitrosomonas europaea and Nitrosomonas ureae clades. The principal group of AOA was most similar to the clone from activated sludge. The ratio of AOB amoA gene copies to AOA varied from 1.36 (on E. crassipes) to 41.90 (on P. stratiotes). Diversity of AOA was much lower than that of AOB in most samples, with the exception of P. stratiotes. PMID:21239153

  14. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond

    PubMed Central

    Lu, Shimin; Liu, Xingguo; Ma, Zhuojun; Liu, Qigen; Wu, Zongfan; Zeng, Xianlei; Shi, Xu; Gu, Zhaojun

    2016-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster. PMID:26834709

  15. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond.

    PubMed

    Lu, Shimin; Liu, Xingguo; Ma, Zhuojun; Liu, Qigen; Wu, Zongfan; Zeng, Xianlei; Shi, Xu; Gu, Zhaojun

    2015-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0-50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0-10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0-2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10-15 and 20-25 cm depths) were grouped into the Nitrosopumilus cluster. PMID:26834709

  16. Active Autotrophic Ammonia-Oxidizing Bacteria in Biofilm Enrichments from Simulated Creek Ecosystems at Two Ammonium Concentrations Respond to Temperature Manipulation▿†

    PubMed Central

    Avrahami, Sharon; Jia, Zhongjun; Neufeld, Josh D.; Murrell, J. Colin; Conrad, Ralf; Küsel, Kirsten

    2011-01-01

    The first step of nitrification, the oxidation of ammonia to nitrite, is important for reducing eutrophication in freshwater environments when coupled with anammox (anaerobic ammonium oxidation) or denitrification. We analyzed active formerly biofilm-associated aerobic ammonia-oxidizing communities originating from Ammerbach (AS) and Leutra South (LS) stream water (683 ± 550 [mean ± standard deviation] and 16 ± 7 μM NH4+, respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using 13CO2, we found that members of the Bacteria and not Archaea were the functionally dominant autotrophic ammonia oxidizers at all temperatures under relatively high ammonium loads. The copy numbers of bacterial amoA genes in 13C-labeled DNA were lower at 30°C than at 13°C in both stream enrichment cultures. However, the community composition of the ammonia-oxidizing bacteria (AOB) in the 13C-labeled DNA responded differently to temperature manipulation at two ammonium concentrations. In LS enrichments incubated at the in situ temperature (13°C), Nitrosomonas oligotropha-like sequences were retrieved with sequences from Nitrosospira AmoA cluster 4, while the proportion of Nitrosospira sequences increased at higher temperatures. In AS enrichments incubated at 13°C and 20°C, AmoA cluster 4 sequences were dominant; Nitrosomonas nitrosa-like sequences dominated at 30°C. Biofilm-associated AOB communities were affected differentially by temperature at two relatively high ammonium concentrations, implicating them in a potential role in governing contaminated freshwater AOB distributions. PMID:21890674

  17. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil

    PubMed Central

    Sterngren, Anna E.; Hallin, Sara; Bengtson, Per

    2015-01-01

    Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil. PMID:26648926

  18. Aerobic Anoxygenic Phototrophic Bacteria

    PubMed Central

    Yurkov, Vladimir V.; Beatty, J. Thomas

    1998-01-01

    The aerobic anoxygenic phototrophic bacteria are a relatively recently discovered bacterial group. Although taxonomically and phylogenetically heterogeneous, these bacteria share the following distinguishing features: the presence of bacteriochlorophyll a incorporated into reaction center and light-harvesting complexes, low levels of the photosynthetic unit in cells, an abundance of carotenoids, a strong inhibition by light of bacteriochlorophyll synthesis, and the inability to grow photosynthetically under anaerobic conditions. Aerobic anoxygenic phototrophic bacteria are classified in two marine (Erythrobacter and Roseobacter) and six freshwater (Acidiphilium, Erythromicrobium, Erythromonas, Porphyrobacter, Roseococcus, and Sandaracinobacter) genera, which phylogenetically belong to the α-1, α-3, and α-4 subclasses of the class Proteobacteria. Despite this phylogenetic information, the evolution and ancestry of their photosynthetic properties are unclear. We discuss several current proposals for the evolutionary origin of aerobic phototrophic bacteria. The closest phylogenetic relatives of aerobic phototrophic bacteria include facultatively anaerobic purple nonsulfur phototrophic bacteria. Since these two bacterial groups share many properties, yet have significant differences, we compare and contrast their physiology, with an emphasis on morphology and photosynthetic and other metabolic processes. PMID:9729607

  19. Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.

    PubMed

    Sher, Yonatan; Ronen, Zeev; Nejidat, Ali

    2016-08-01

    Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were < 1 independent of niche or water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions. PMID:27037935

  20. Gold and silver nanoparticle effects on ammonia-oxidizing bacteria cultures under ammoxidation.

    PubMed

    Luo, Zhuanxi; Chen, Zheng; Qiu, Zhaozheng; Li, Yancai; Laing, Gijs Du; Liu, Aifen; Yan, Changzhou

    2015-02-01

    Owing to their wide application in industry and manufacturing, understanding the environmental safety of gold (Au) and silver (Ag) nanoparticles entering aquatic environment is a global issue of concern. For this study, ammonia-oxidizing bacteria (AOB) enrichment cultures reproduced from surface sediments taken from the Jiulong River estuary wetlands (Fujian Province, China) were spiked with nano-Ag and nano-Au to determine their impact on ammoxidation and the mechanisms involved in the process. Results showed that nano-Ag significantly inhibited bacterial ammoxidation in aquatic environment, with the average ammoxidation rate decreasing with increasing nano-Ag concentration. The average ammoxidation rate was significantly correlated to the Shannon index, the Simpson index, and AOB abundance. This suggested that ammoxidation inhibition resulted primarily from AOB biodiversity and abundance reduction, caused by the antibacterial property of nano-Ag. However, AOB biodiversity and abundance as well as bacterial ammoxidation were not inhibited by nano-Au (with a maximum experimental concentration of 2 mg L(-1)). Moreover, an insignificant correlation was found between AOB biodiversity and abundance and the average ammoxidation rate under the nano-Au treatment. Given that ammoxidation is regarded as a rate-limiting procedure in nitrogen (N) circulation, nano-Ag would affect N cycling but nano-Au would not after entering aquatic environments. Identified nano-Ag and nano-Au impacts on ammonium nitrogen transformation could be generalized in aquatic environment according to their extensive representation in the phylogenetic tree. PMID:24559932

  1. Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico.

    PubMed

    Flood, Matthew; Frabutt, Dylan; Floyd, Dalton; Powers, Ashley; Ezegwe, Uche; Devol, Allan; Tiquia-Arashiro, Sonia M

    2015-01-01

    The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability. PMID:25409591

  2. Modeling of nitrous oxide production by autotrophic ammonia-oxidizing bacteria with multiple production pathways.

    PubMed

    Ni, Bing-Jie; Peng, Lai; Law, Yingyu; Guo, Jianhua; Yuan, Zhiguo

    2014-04-01

    Autotrophic ammonia oxidizing bacteria (AOB) have been recognized as a major contributor to N2O production in wastewater treatment systems. However, so far N2O models have been proposed based on a single N2O production pathway by AOB, and there is still a lack of effective approach for the integration of these models. In this work, an integrated mathematical model that considers multiple production pathways is developed to describe N2O production by AOB. The pathways considered include the nitrifier denitrification pathway (N2O as the final product of AOB denitrification with NO2(-) as the terminal electron acceptor) and the hydroxylamine (NH2OH) pathway (N2O as a byproduct of incomplete oxidation of NH2OH to NO2(-)). In this model, the oxidation and reduction processes are modeled separately, with intracellular electron carriers introduced to link the two types of processes. The model is calibrated and validated using experimental data obtained with two independent nitrifying cultures. The model satisfactorily describes the N2O data from both systems. The model also predicts shifts of the dominating pathway at various dissolved oxygen (DO) and nitrite levels, consistent with previous hypotheses. This unified model is expected to enhance our ability to predict N2O production by AOB in wastewater treatment systems under varying operational conditions. PMID:24571180

  3. Modelling nitrous and nitric oxide emissions by autotrophic ammonia-oxidizing bacteria.

    PubMed

    Mampaey, K E; Beuckels, B; Kampschreur, M J; Kleerebezem, R; van Loosdrecht, M C M; Volcke, E I P

    2013-01-01

    The emission of greenhouse gases, such as N2O, from wastewater treatment plants is a matter of growing concern. Denitrification by ammonia-oxidizing bacteria (AOB) has been identified as the main N2O producing pathway. To estimate N2O emissions during biological nitrogen removal, reliable mathematical models are essential. In this work, a mathematical model for NO (a precursor for N2O formation) and N2O formation by AOB is presented. Based on mechanistic grounds, two possible reaction mechanisms for NO and N2O formation are distinguished, which differ in the origin of the reducing equivalents needed for denitrification by AOB. These two scenarios have been compared in a simulation study, assessing the influence of the aeration/stripping rate and the resulting dissolved oxygen (DO) concentration on the NO and N2O emission from a SHARON partial nitritation reactor. The study of the simulated model behaviour and its comparison with previously published experimental data serves in elucidating the true NO and N2O formation mechanism. PMID:24191490

  4. Evaluating Primers for Profiling Anaerobic Ammonia Oxidizing Bacteria within Freshwater Environments

    PubMed Central

    Sonthiphand, Puntipar; Neufeld, Josh D.

    2013-01-01

    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 analysis, A438f/A684r

  5. The distribution and relative abundance of ammonia-oxidizing bacteria in lakes of the McMurdo Dry Valley, Antarctica

    USGS Publications Warehouse

    Voytek, M.A.; Priscu, J.C.; Ward, B.B.

    1999-01-01

    Marked differences in the concentrations of major ions and cations, macronutrient chemistry and general trophic status exist among the lakes of the McMurdo dry valleys in Antarctica. These differences have been attributed to both variations in stream inputs and in situ lake processes (Priscu, 1995; Lizotte et al., 1996, Spigel and Priscu, 1996). This study examines the role of nitrifying bacteria in nitrogen transformations in these lakes. Applying two polymerase chain reaction (PCR) assays targeting the 16S rRNA genes of ammonia-oxidizing bacteria and the active site of the ammonia monooxygenase gene (amoA), the distribution of ammonia-oxidizers was examined in six Antarctic lakes: Lake Bonney, Lake Hoare, Lake Fryxell and Lake Joyce in the Taylor Valley, Lake Miers in the the Miers Valley and Lake Vanda in the Wright Valley. Using a two stage amplification procedure, ammonia-oxidizers from both the beta and gamma- subclasses of the Proteobacteria were detected and their relative abundances were determined in samples collected from all sites. Ammonia-oxidizers were detected in all lakes sampled. Members of the gamma subclass were only present in the saline lakes. In general, nitrifiers were most abundant at depths above the pycnocline and were usually associated with lower concentrations of NH4 and elevated concentrations of NO3 or NO2. The distribution of nitrifiers suggests that the primary N2O peak observed in most of the lakes was produced via nitrification. Preliminary data on the rate of nitrification (Priscu et al., 1996) support the occurrence of nitrification and the presence of nitrifiers at the depth intervals where nitrifiers were detected. In all lakes, except Lake Miers, the data indicate that nitrifying bacteria have an important role in the vertical distribution of nitrogen compounds in these systems.

  6. Acclimatization of communities of ammonia oxidizing bacteria to seasonal changes in optimal conditions in a coke wastewater treatment plant.

    PubMed

    Kim, Young Mo

    2013-11-01

    The goal of this study was to investigate the correlation between optimal conditions of ammonia oxidation rates (AORs) and communities of ammonia oxidizing bacteria (AOB) adapting to seasonal changes in a full-scale wastewater treatment plant (WWTP). The optimal temperature and pH of specific AORs reflected seasonal variation patterns, showing the lowest values during the cold season, while the highest values in the warm season. Throughout the study period, Nitrosomonas europaea/eutropha and Nitrosomonas nitrosa remained the dominant AOB, indicating resistance to the influences of a changing environment. These results show that the optimal conditions for AOR can be adjusted to accommodate changing environmental conditions, relying on the acclimatization of a stable AOB community to given conditions, without any visible shift in the AOB community. PMID:24001689

  7. Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients

    PubMed Central

    Delgado-Baquerizo, Manuel; Maestre, Fernando T.; Eldridge, David J.; Singh, Brajesh K.

    2016-01-01

    Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered. PMID:27148194

  8. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria.

    PubMed

    Kozlowski, Jessica A; Kits, K Dimitri; Stein, Lisa Y

    2016-01-01

    Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity. PMID:27462312

  9. Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients.

    PubMed

    Delgado-Baquerizo, Manuel; Maestre, Fernando T; Eldridge, David J; Singh, Brajesh K

    2016-01-01

    Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered. PMID:27148194

  10. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria

    PubMed Central

    Kozlowski, Jessica A.; Kits, K. Dimitri; Stein, Lisa Y.

    2016-01-01

    Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity. PMID:27462312

  11. Ammonia-oxidizing bacteria in a chloraminated distribution system: seasonal occurrence, distribution and disinfection resistance.

    PubMed Central

    Wolfe, R L; Lieu, N I; Izaguirre, G; Means, E G

    1990-01-01

    Nitrification in chloraminated drinking water can have a number of adverse effects on water quality, including a loss of total chlorine and ammonia-N and an increase in the concentration of heterotrophic plate count bacteria and nitrite. To understand how nitrification develops, a study was conducted to examine the factors that influence the occurrence of ammonia-oxidizing bacteria (AOB) in a chloraminated distribution system. Samples were collected over an 18-month period from a raw-water source, a conventional treatment plant effluent, and two covered, finished-water reservoirs that previously experienced nitrification episodes. Sediment and biofilm samples were collected from the interior wall surfaces of two finished-water pipelines and one of the covered reservoirs. The AOB were enumerated by a most-probable-number technique, and isolates were isolated and identified. The resistance of naturally occurring AOB to chloramines and free chlorine was also examined. The results of the monitoring program indicated that the levels of AOB, identified as members of the genus Nitrosomonas, were seasonally dependent in both source and finished waters, with the highest levels observed in the warm summer months. The concentrations of AOB in the two reservoirs, both of which have floating covers made of synthetic rubber (Hypalon; E.I. du Pont de Nemours & Co., Inc., Wilmington, Del.), had most probable numbers that ranged from less than 0.2 to greater than 300/ml and correlated significantly with temperature and levels of heterotrophic plate count bacteria. No AOB were detected in the chloraminated reservoirs when the water temperature was below 16 to 18 degrees C. The study indicated that nitrifiers occur throughout the chloraminated distribution system. Higher concentrations of AOB were found in the reservoir and pipe sediment materials than in the pipe biofilm samples. The AOB were approximately 13 times more resistant to monochloramine than to free chlorine. After 33 min

  12. Diversity of Ammonia-Oxidizing Archaea and Bacteria Across Physical-Chemical Gradients in San Francisco Bay Estuary Sediments

    NASA Astrophysics Data System (ADS)

    Mosier, A. C.; Francis, C. A.

    2006-12-01

    A combination of recent metagenomic analyses and the cultivation of a novel, ammonia-oxidizing, marine crenarchaeota revealed the first evidence for nitrification within the Archaeal domain. Further genetic and metagenomic studies demonstrated the presence of ammonia-oxidizing crenarchaea in diverse marine and terrestrial environments. These discoveries challenge the currently accepted view of the global nitrogen cycle and validate the need for further research on microbial diversity and function. In particular, it is imperative to reexamine the microbial communities involved in ammonia oxidation in marine and estuarine sediments, where this process plays a pivotal role in the cycling and removal of nitrogen. Using phylogenetic analyses of ammonia monooxygenase subunit A (amoA) gene sequences, we examined the distribution and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in San Francisco Bay, the largest estuary on the West coast of the United States. The highly impacted bay, encompassing nearly 178,000 km2, effectively connects two estuaries with varying physical-chemical characteristics to the Pacific Ocean. We recovered archaeal and bacterial amoA genes from 11 sites distributed throughout the bay, spanning the northern and southern estuaries and the central region where they connect to the ocean. Richness estimates varied considerably across all sites examined, with archaeal amoA estimates being generally higher than bacterial amoA. Several of the bacterial amoA libraries were represented by fewer than 3 genotypes. Archaeal amoA sequences were phylogenetically diverse and grouped within previously described sediment and soil/sediment clusters. Several sequences were closely related to the only cultivated AOA, Nitrosopumilus maritimus. Both the archaeal and bacterial amoA sequences showed significant regional specificity. Distinct populations exist in the northern and southern estuaries and sequences from the northernmost and southernmost sites

  13. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NASA Astrophysics Data System (ADS)

    Zheng, Y.; Huang, R.; Wang, B. Z.; Bodelier, P. L. E.; Jia, Z. J.

    2014-06-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and functional genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity 6-fold during a 19-day incubation period, while ammonia oxidation activity was significantly suppressed in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like MOB, and nitrifying communities appeared to be partially inhibited by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to an equal increase in Methylosarcina and Methylobacter-related type Ia MOB, indicating the differential growth requirements of representatives of these genera. An increase in 13C assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition partially inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, as well as growth of nitrite-oxidizing bacteria. These

  14. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NASA Astrophysics Data System (ADS)

    Zheng, Y.; Huang, R.; Wang, B. Z.; Bodelier, P. L. E.; Jia, Z. J.

    2014-03-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and pmoA genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity by 6-fold during a 19 day incubation period, while ammonia oxidation activity was significantly inhibited in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like type Ia MOB, and nitrifying communities appeared to be suppressed by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to equal increase in Methylosarcina and Methylobacter-related MOB, indicating the differential growth requirements of representatives of these genera. Strikingly, type Ib MOB did not respond to methane nor to urea. Increase in 13C-assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, in addition of nitrite

  15. Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India.

    PubMed

    Subrahmanyam, Gangavarapu; Shen, Ju-Pei; Liu, Yu-Rong; Archana, Gattupalli; He, Ji-Zheng

    2014-07-01

    Soil nitrifiers have been showing an important role in assessing environmental pollution as sensitive biomarkers. In this study, the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in long-term industrial waste effluent (IWE) polluted soils. Three different IWE polluted soils characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) were collected in triplicate along Mahi River basin, Gujarat, Western India. Quantitative numbers of ammonia monooxygenase α-subunit (amoA) genes as well as 16S rRNA genes indicated apparent deleterious effect of IWE on abundance of soil AOA, AOB, bacteria, and archaeal populations. Relatively, AOB was more abundant than AOA in the highly contaminated soil R3, while predominance of AOA was noticed in uncontaminated (R1) and moderately contaminated (R2) soils. Soil potential nitrification rate (PNR) significantly (P < 0.05) decreased in polluted soils R2 and R3. Reduced diversity accompanied by apparent community shifts of both AOB and AOA populations was detected in R2 and R3 soils. AOB were dominated with Nitrosospira-like sequences, whereas AOA were dominated by Thaumarchaeal "group 1.1b (Nitrososphaera clusters)." We suggest that the significant reduction in abundance and diversity AOA and AOB could serve as relevant bioindicators for soil quality monitoring of polluted sites. These results could be further useful for better understanding of AOB and AOA communities in polluted soils. PMID:24554021

  16. Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenerative life support

    NASA Technical Reports Server (NTRS)

    Sakano, Yuko; Pickering, Karen D.; Strom, Peter F.; Kerkhof, Lee J.; Janes, H. W. (Principal Investigator)

    2002-01-01

    Bioregenerative life support systems may be necessary for long-term space missions due to the high cost of lifting supplies and equipment into orbit. In this study, we investigated two biological wastewater treatment reactors designed to recover potable water for a spacefaring crew being tested at Johnson Space Center. The experiment (Lunar-Mars Life Support Test Project-Phase III) consisted of four crew members confined in a test chamber for 91 days. In order to recycle all water during the experiment, an immobilized cell bioreactor (ICB) was employed for organic carbon removal and a trickling filter bioreactor (TFB) was utilized for ammonia removal, followed by physical-chemical treatment. In this study, the spatial distribution of various microorganisms within each bioreactor was analyzed by using biofilm samples taken from four locations in the ICB and three locations in the TFB. Three target genes were used for characterization of bacteria: the 16S rRNA gene for the total bacterial community, the ammonia monooxygenase (amoA) gene for ammonia-oxidizing bacteria, and the nitrous oxide reductase (nosZ) gene for denitrifying bacteria. A combination of terminal restriction fragment length polymorphism (T-RFLP), sequence, and phylogenetic analyses indicated that the microbial community composition in the ICB and the TFB consisted mainly of Proteobacteria, low-G+C gram-positive bacteria, and a Cytophaga-Flexibacter-Bacteroides group. Fifty-seven novel 16S rRNA genes, 8 novel amoA genes, and 12 new nosZ genes were identified in this study. Temporal shifts in the species composition of total bacteria in both the ICB and the TFB and ammonia-oxidizing and denitrifying bacteria in the TFB were also detected when the biofilms were compared with the inocula after 91 days. This result suggests that specific microbial populations were either brought in by the crew or enriched in the reactors during the course of operation.

  17. Rapid and dissimilar response of ammonia oxidizing archaea and bacteria to nitrogen and water amendment in two temperate forest soils.

    PubMed

    Szukics, Ute; Hackl, Evelyn; Zechmeister-Boltenstern, Sophie; Sessitsch, Angela

    2012-01-20

    Biochemical processes relevant to soil nitrogen (N) cycling are performed by soil microorganisms affiliated with diverse phylogenetic groups. For example, the oxidation of ammonia, representing the first step of nitrification, can be performed by ammonia oxidizing bacteria (AOB) and, as recently reported, also by ammonia oxidizing archaea (AOA). However, the contribution to ammonia oxidation of the phylogenetically separated AOA versus AOB and their respective responsiveness to environmental factors are still poorly understood. The present study aims at comparing the capacity of AOA and AOB to momentarily respond to N input and increased soil moisture in two contrasting forest soils. Soils from the pristine Rothwald forest and the managed Schottenwald forest were amended with either NH(4)(+)-N or NO(3)(-)-N and were incubated at 40% and 70% water-filled pore space (WFPS) for four days. Nitrification rates were measured and AOA and AOB abundance and community composition were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP) analysis of bacterial and archaeal amoA genes. Our study reports rapid and distinct changes in AOA and AOB abundances in the two forest soils in response to N input and increased soil moisture but no significant effects on net nitrification rates. Functional microbial communities differed significantly in the two soils and responded specifically to the treatments during the short-term incubation. In the Rothwald soil the abundance and community composition of AOA were affected by the water content, whereas AOB communities responded to N amendment. In the Schottenwald soil, by contrast, AOA responded to N addition. These results suggest that AOA and AOB may be selectively influenced by soil and management factors. PMID:21632226

  18. Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments.

    PubMed

    Zheng, Yanling; Hou, Lijun; Liu, Min; Lu, Min; Zhao, Hui; Yin, Guoyu; Zhou, Junliang

    2013-09-01

    Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 10(4)-6.47 × 10(5) copies g(-1) sediment) was always greater than that of AOA amoA gene (7.98 × 10(3)-3.51 × 10(5) copies g(-1) sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03-5.39 pmol N copy(-1) day(-1)) compared with winter (0.16-0.38 pmol N copy(-1) day(-1)), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons. PMID:23108528

  19. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay.

    PubMed

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

    2016-07-01

    The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge. PMID:26960319

  20. Abundance, Activity, and Diversity of Ammonia-oxidizing Bacteria and Archaea in Oligotrophic Alpine Lakes of Yosemite National Park, California

    NASA Astrophysics Data System (ADS)

    Beman, J.; Hayden, C.

    2013-12-01

    Lakes play critical roles in biogeochemical cycles as integrators of carbon and nitrogen cycling across watersheds. They are also ';sentinels' that may be strongly affected by environmental change--yet the responses of lake biogeochemical processes are dictated by microbial communities that we still know little about. We quantified nitrification rates, carbon respiration rates, and the abundance and diversity of involved microbes, within lakes located along an elevational gradient in Yosemite National Park, USA. Temperature, atmospheric nitrogen (N) deposition, and exposure to UV all vary along this transect, allowing us to test how these variables may act together to influence microbial biogeochemical processes. We found surprisingly high abundances of ammonia-oxidizing bacteria (AOB)--despite low nutrient conditions and high light levels that may favor other organisms, and/or inhibit AOB. We also examined community composition and diversity of AOB and ammonia-oxidizjng archaea (AOA) using Illumina sequencing of 16S rRNA genes, and measured ammonia oxidation rates using 15N tracer. All of these data are indicative of active N cycling by a dynamic microbial community. In Yosemite and other wilderness areas, atmospheric N deposition supplies a critical nutrient that may alter naturally nutrient-poor ecosystems; in the Sierra Nevada, much of this deposition occurs in the form of ammonium, suggesting a key role for nitrification in converting deposited N into more mobile forms. Our data indicate that oligotrophic alpine lakes may be nitrification hotspots in Yosemite.

  1. N2O production by ammonia oxidizing bacteria in an enriched nitrifying sludge linearly depends on inorganic carbon concentration.

    PubMed

    Peng, Lai; Ni, Bing-Jie; Ye, Liu; Yuan, Zhiguo

    2015-05-01

    The effect of inorganic carbon (IC) on nitrous oxide (N2O) production by ammonia oxidizing bacteria (AOB) was investigated over a concentration range of 0-12 mmol C/L, encompassing typical IC levels in a wastewater treatment reactors. The AOB culture was enriched along with nitrite-oxidizing bacteria (NOB) in a sequencing batch reactor (SBR) to perform complete nitrification. Batch experiments were conducted with continuous carbon dioxide (CO2) stripping or at controlled IC concentrations. The results revealed a linear relationship between N2O production rate (N2OR) and IC concentration (R(2) = 0.97) within the IC range studied, suggesting a substantial effect of IC on N2O production by AOB. Similar results were also obtained with an AOB culture treating anaerobic sludge digestion liquor. The fundamental mechanism responsible for this dependency is unclear; however, in agreement with previous studies, it was observed that the ammonia oxidation rate (AOR) was also influenced by the IC concentration, which could be well described by the Monod kinetics. These resulted in an exponential relationship between N2OR and AOR, as previously observed in experiments where AOR was altered by varying dissolved oxygen and ammonia concentrations. It is therefore possible that IC indirectly affected N2OR by causing a change in AOR. The observation in this study indicates that alkalinity (mostly contributed by IC) could be a significant factor influencing N2O production and should be taken into consideration in estimating and mitigating N2O emissions in wastewater treatment systems. PMID:25706224

  2. Latitudinal Distribution of Ammonia-Oxidizing Bacteria and Archaea in the Agricultural Soils of Eastern China

    PubMed Central

    Huang, Liuqin; Deng, Ye; Wang, Shang; Zhou, Yu; Liu, Li

    2014-01-01

    The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients. PMID:25002421

  3. Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China.

    PubMed

    Jiang, Hongchen; Huang, Liuqin; Deng, Ye; Wang, Shang; Zhou, Yu; Liu, Li; Dong, Hailiang

    2014-09-01

    The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients. PMID:25002421

  4. Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake.

    PubMed

    Yang, Yuyin; Li, Ningning; Zhao, Qun; Yang, Mengxi; Wu, Zhen; Xie, Shuguang; Liu, Yong

    2016-08-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure. PMID:27109114

  5. Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil▿

    PubMed Central

    Kelly, John J.; Policht, Katherine; Grancharova, Tanya; Hundal, Lakhwinder S.

    2011-01-01

    The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare−1 year−1) and double the agronomic rate (54 Mg hectare−1 year−1), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare−1 year−1). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterial amoA genes. In addition, only archaeal amoA gene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaeal amoA genes were significantly higher than copy numbers of bacterial amoA genes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches. PMID:21803892

  6. Spatial Interaction of Archaeal Ammonia-Oxidizers and Nitrite-Oxidizing Bacteria in an Unfertilized Grassland Soil

    PubMed Central

    Stempfhuber, Barbara; Richter-Heitmann, Tim; Regan, Kathleen M.; Kölbl, Angelika; Wüst, Pia K.; Marhan, Sven; Sikorski, Johannes; Overmann, Jörg; Friedrich, Michael W.; Kandeler, Ellen; Schloter, Michael

    2016-01-01

    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 onward, indicating its important role in nitrite oxidation. PMID:26834718

  7. Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

    PubMed

    Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

    2015-01-01

    The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields. PMID:25736866

  8. Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh

    PubMed Central

    Peng, Xuefeng; Yando, Erik; Hildebrand, Erica; Dwyer, Courtney; Kearney, Anne; Waciega, Alex; Valiela, Ivan; Bernhard, Anne E.

    2013-01-01

    Since the discovery of ammonia-oxidizing archaea (AOA), new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing bacteria (AOB). We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF), high (HF), and extra high (XF) levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C). Terminal restriction fragment length polymorphism analysis of the amoA genes revealed distinct shifts in AOB communities related to fertilization treatment, but the response patterns of AOA were less consistent. Four AOB operational taxonomic units (OTUs) predictably and significantly responded to fertilization, but only one AOA OTU showed a significant pattern. Betaproteobacterial amoA gene sequences within the Nitrosospira-like cluster dominated at C and LF sites, while sequences related to Nitrosomonas spp. dominated at HF and XF sites. We identified some clusters of AOA sequences recovered primarily from high fertilization regimes, but other clusters consisted of sequences recovered from all fertilization treatments, suggesting greater physiological diversity. Surprisingly, fertilization appeared to have little impact on abundance of AOA or AOB. In summary, our data reveal striking patterns for AOA and AOB in response to long-term fertilization, and also suggest a missing link between community composition and abundance and nitrogen processing in the marsh. PMID:23346081

  9. Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre.

    PubMed

    Lagostina, Lorenzo; Goldhammer, Tobias; Røy, Hans; Evans, Thomas W; Lever, Mark A; Jørgensen, Bo B; Petersen, Dorthe G; Schramm, Andreas; Schreiber, Lars

    2015-06-01

    Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle. PMID:25581373

  10. Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California, on the basis of 16S rRNA sequences.

    PubMed

    Ward, B B; Martino, D P; Diaz, M C; Joye, S B

    2000-07-01

    Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the beta subdivision of the division Proteobacteria (beta-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different beta-subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the gamma subdivision of the Proteobacteria, did not amplify target from any samples. PMID:10877781

  11. Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil.

    PubMed

    Scharko, Nicole K; Schütte, Ursel M E; Berke, Andrew E; Banina, Lauren; Peel, Hannah R; Donaldson, Melissa A; Hemmerich, Chris; White, Jeffrey R; Raff, Jonathan D

    2015-12-01

    Nitrous acid (HONO) is a photochemical source of hydroxyl radical and nitric oxide in the atmosphere that stems from abiotic and biogenic processes, including the activity of ammonia-oxidizing soil microbes. HONO fluxes were measured from agricultural and urban soil in mesocosm studies aimed at characterizing biogenic sources and linking them to indigenous microbial consortia. Fluxes of HONO from agricultural and urban soil were suppressed by addition of a nitrification inhibitor and enhanced by amendment with ammonium (NH4(+)), with peaks at 19 and 8 ng m(-2) s(-1), respectively. In addition, both agricultural and urban soils were observed to convert (15)NH4(+) to HO(15)NO. Genomic surveys of soil samples revealed that 1.5-6% of total expressed 16S rRNA sequences detected belonged to known ammonia oxidizing bacteria and archaea. Peak fluxes of HONO were directly related to the abundance of ammonia-oxidizer sequences, which in turn depended on soil pH. Peak HONO fluxes under fertilized conditions are comparable in magnitude to fluxes reported during field campaigns. The results suggest that biogenic HONO emissions will be important in soil environments that exhibit high nitrification rates (e.g., agricultural soil) although the widespread occurrence of ammonia oxidizers implies that biogenic HONO emissions are also possible in the urban and remote environment. PMID:26248160

  12. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

    PubMed Central

    Soares, Johnny R.; Cassman, Noriko A.; Kielak, Anna M.; Pijl, Agata; Carmo, Janaína B.; Lourenço, Kesia S.; Laanbroek, Hendrikus J.; Cantarella, Heitor; Kuramae, Eiko E.

    2016-01-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane. PMID:27460335

  13. Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR.

    PubMed

    Dechesne, Arnaud; Musovic, Sanin; Palomo, Alejandro; Diwan, Vaibhav; Smets, Barth F

    2016-07-01

    Molecular methods to investigate functional groups in microbial communities rely on the specificity and selectivity of the primer set towards the target. Here, using rapid sand filters for drinking water production as model environment, we investigated the consistency of two commonly used quantitative PCR methods to enumerate ammonia-oxidizing bacteria (AOB): one targeting the phylogenetic gene 16S rRNA and the other, the functional gene amoA. Cloning-sequencing with both primer sets on DNA from two waterworks revealed contrasting images of AOB diversity. The amoA-based approach preferentially recovered sequences belonging to Nitrosomonas Cluster 7 over Cluster 6A ones, while the 16S rRNA one yielded more diverse sequences belonging to three AOB clusters, but also a few non-AOB sequences, suggesting broader, but partly unspecific, primer coverage. This was confirmed by an in silico coverage analysis against sequences of AOB (both isolates and high-quality environmental sequences). The difference in primer coverage significantly impacted the estimation of AOB abundance at the waterworks with high Cluster 6A prevalence, with estimates up to 50-fold smaller for amoA than for 16S rRNA. In contrast, both approaches performed very similarly at waterworks with high Cluster 7 prevalence. Our results highlight that caution is warranted when comparing AOB abundances obtained using different qPCR primer sets. PMID:27166579

  14. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil.

    PubMed

    Soares, Johnny R; Cassman, Noriko A; Kielak, Anna M; Pijl, Agata; Carmo, Janaína B; Lourenço, Kesia S; Laanbroek, Hendrikus J; Cantarella, Heitor; Kuramae, Eiko E

    2016-01-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4(+)-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane. PMID:27460335

  15. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

    NASA Astrophysics Data System (ADS)

    Soares, Johnny R.; Cassman, Noriko A.; Kielak, Anna M.; Pijl, Agata; Carmo, Janaína B.; Lourenço, Kesia S.; Laanbroek, Hendrikus J.; Cantarella, Heitor; Kuramae, Eiko E.

    2016-07-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.

  16. Influence of land use intensity on the diversity of ammonia oxidizing bacteria and archaea in soils from grassland ecosystems.

    PubMed

    Meyer, Annabel; Focks, Andreas; Radl, Viviane; Welzl, Gerhard; Schöning, Ingo; Schloter, Michael

    2014-01-01

    In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates. PMID:24141944

  17. The intracellular proton gradient enables anaerobic ammonia oxidizing (anammox) bacteria to tolerate NO2 - inhibition.

    PubMed

    Carvajal-Arroyo, José M; Puyol, Daniel; Li, Guangbin; Sierra-Álvarez, Reyes; Field, Jim A

    2014-12-20

    Anammox bacteria are inhibited by nitrite, which is one of their substrates. By utilizing 2,4 dinitrophenol and carbonyl cyanide m-chlorophenyl hydrazone, two uncouplers of respiration, we demonstrate that nitrite tolerance of anammox cells is strongly dependent on their ability to maintain a proton gradient, which may be the driving force for active nitrite transport system. PMID:25449017

  18. The effect of dissolved oxygen on N2O production by ammonia-oxidizing bacteria in an enriched nitrifying sludge.

    PubMed

    Peng, Lai; Ni, Bing-Jie; Erler, Dirk; Ye, Liu; Yuan, Zhiguo

    2014-12-01

    Dissolved oxygen (DO) is commonly recognized as an important factor influencing nitrous oxide (N2O) production by ammonia-oxidizing bacteria (AOB). However, it has been difficult to separate the true effect of DO from that of nitrite, as DO variation often affects nitrite accumulation. The effect of DO on N2O production by an enriched nitrifying sludge, consisting of both AOB and nitrite-oxidizing bacteria (NOB), was investigated in this study. Nitrite accumulation was minimised by augmenting nitrite oxidation through the addition of an enriched NOB sludge. It was demonstrated that the specific N2O production rate increased from 0 to 1.9 ± 0.09 (n = 3) mg N2O-N/hr/g VSS with an increase of DO concentration from 0 to 3.0 mg O2/L, whereas N2O emission factor (the ratio between N2O nitrogen emitted and the ammonium nitrogen converted) decreased from 10.6 ± 1.7% (n = 3) at DO = 0.2 mg O2/L to 2.4 ± 0.1% (n = 3) at DO = 3.0 mg O2/L. The site preference measurements indicated that both the AOB denitrification and hydroxylamine (NH2OH) oxidation pathways contributed to N2O production, and DO had an important effect on the relative contributions of the two pathways. This finding is supported by analysis of the process data using an N2O model describing both pathways. As DO increased from 0.2 to 3.0 mg O2/L, the contribution of AOB denitrification decreased from 92% - 95%-66% - 73%, accompanied by a corresponding increase in the contribution by the NH2OH oxidation pathway. PMID:25179869

  19. Influence of season and plant species on the abundance and diversity of sulfate reducing bacteria and ammonia oxidizing bacteria in constructed wetland microcosms.

    PubMed

    Faulwetter, Jennifer L; Burr, Mark D; Parker, Albert E; Stein, Otto R; Camper, Anne K

    2013-01-01

    Constructed wetlands offer an effective means for treatment of wastewater from a variety of sources. An understanding of the microbial ecology controlling nitrogen, carbon and sulfur cycles in constructed wetlands has been identified as the greatest gap for optimizing performance of these promising treatment systems. It is suspected that operational factors such as plant types and hydraulic operation influence the subsurface wetland environment, especially redox, and that the observed variation in effluent quality is due to shifts in the microbial populations and/or their activity. This study investigated the biofilm associated sulfate reducing bacteria and ammonia oxidizing bacteria (using the dsrB and amoA genes, respectively) by examining a variety of surfaces within a model wetland (gravel, thick roots, fine roots, effluent), and the changes in activity (gene abundance) of these functional groups as influenced by plant species and season. Molecular techniques were used including quantitative PCR and denaturing gradient gel electrophoresis (DGGE), both with and without propidium monoazide (PMA) treatment. PMA treatment is a method for excluding from further analysis those cells with compromised membranes. Rigorous statistical analysis showed an interaction between the abundance of these two functional groups with the type of plant and season (p < 0.05). The richness of the sulfate reducing bacterial community, as indicated by DGGE profiles, increased in planted vs. unplanted microcosms. For ammonia oxidizing bacteria, season had the greatest impact on gene abundance and diversity (higher in summer than in winter). Overall, the primary influence of plant presence is believed to be related to root oxygen loss and its effect on rhizosphere redox. PMID:22961363

  20. Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

    PubMed Central

    Wessén, Ella; Söderström, Mats; Stenberg, Maria; Bru, David; Hellman, Maria; Welsh, Allana; Thomsen, Frida; Klemedtson, Leif; Philippot, Laurent; Hallin, Sara

    2011-01-01

    Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers. PMID:21228891

  1. Ammonia-Oxidizing Bacteria along Meadow-to-Forest Transects in the Oregon Cascade Mountains†

    PubMed Central

    Mintie, A. T.; Heichen, R. S.; Cromack, Jr., K.; Myrold, D. D.; Bottomley, P. J.

    2003-01-01

    Although nitrification has been well studied in coniferous forests of Western North America, communities of NH3-oxidizing bacteria in these forests have not been characterized. Studies were conducted along meadow-to-forest transects at two sites (Lookout and Carpenter) in the H. J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon. Soil samples taken at 10- or 20-m intervals along the transects showed that several soil properties, including net nitrogen mineralization and nitrification potential rates changed significantly between vegetation zones. Nonetheless, terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR-amplified NH3 monooxygenase subunit A gene (amoA) showed the same DNA fragments (TaqI [283 bp], CfoI [66 bp], and AluI [392 bp]) to dominate ≥45 of 47 soil samples recovered from both sites. Two fragments (491-bp AluI [AluI491] and CfoI135) were found more frequently in meadow and transition zone soil samples than in forest samples at both sites. At the Lookout site the combination AluI491-CfoI135 was found primarily in meadow samples expressing the highest N mineralization rates. Four unique amoA sequences were identified among 15 isolates recovered into pure culture from various transect locations. Six isolates possessed the most common T-RFLP amoA fingerprint of the soil samples (TaqI283-AluI392-CfoI66), and their amoA sequences shared 99.8% similarity with a cultured species, Nitrosospira sp. strain Ka4 (cluster 4). The other three amoA sequences were most similar to sequences of Nitrosospira sp. strain Nsp1 and Nitrosospira briensis (cluster 3). 16S ribosomal DNA sequence analysis confirmed the affiliation of these isolates with Nitrosospira clusters 3 and 4. Two amoA clone sequences matched T-RFLP fingerprints found in soil, but they were not found among the isolates. PMID:12788707

  2. Responses of soil hydrolytic enzymes, ammonia-oxidizing bacteria and archaea to nitrogen applications in a temperate grassland in Inner Mongolia.

    PubMed

    Zhang, Xinyu; Tang, Yuqian; Shi, Yao; He, Nianpeng; Wen, Xuefa; Yu, Qiang; Zheng, Chunyu; Sun, Xiaomin; Qiu, Weiwen

    2016-01-01

    We used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392 kg N ha(-1 )yr(-1) treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4(+)-N content. However, the AOB gene copies were positively correlated with NO3(-)-N content. Moderate N application rates (56-224 kg N ha(-1 )yr(-1)) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392 kg N ha(-1 )yr(-1)) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224 kg N ha(-1 )yr(-1) in temperate grasslands in Inner Mongolia. PMID:27596731

  3. Responses of soil hydrolytic enzymes, ammonia-oxidizing bacteria and archaea to nitrogen applications in a temperate grassland in Inner Mongolia

    PubMed Central

    Zhang, Xinyu; Tang, Yuqian; Shi, Yao; He, Nianpeng; Wen, Xuefa; Yu, Qiang; Zheng, Chunyu; Sun, Xiaomin; Qiu, Weiwen

    2016-01-01

    We used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392 kg N ha−1 yr−1 treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4+-N content. However, the AOB gene copies were positively correlated with NO3−-N content. Moderate N application rates (56–224 kg N ha−1 yr−1) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392 kg N ha−1 yr−1) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224 kg N ha−1 yr−1 in temperate grasslands in Inner Mongolia. PMID:27596731

  4. [Effects of Corbicula fluminea bioturbation on the community composition and abundance of ammonia-oxidizing archaea and bacteria in surface sediments].

    PubMed

    Wang, Xue; Zhao, Da-Yong; Zeng, Jin; Yu, Duo-Wei; Wu, Qing-Long

    2014-06-01

    To better understand the effects of Corbicula fluminea bioturbation on the ammonia-oxidizing microorganisms in the surface sediment, sediment-water microcosms with different densities of Corbicula fluminea were constructed. Clone libraries and real-time qPCR were applied to analyze the community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. The results obtained indicated that the bioturbation of Corbicula fluminea accelerated the release of nitrogen from the surface sediment. In the amoA gene clone libraries, the identified AOA amoA gene sequences affiliated with the two known clusters (marine and soil clusters). The identified AOB amoA gene sequences mostly belonged to the Nitrosomonas of beta-Proteobacteria. The abundance of the bacterial amoA gene was higher than that of the archaeal amoA gene in all treatments. With increasing density of Corbicula fluminea, decreased abundances of the bacterial amoA gene were observed. At the same time, the diversity of AOA and AOB reduced in the Corbicula fluminea containing microcosms. In conclusion, the bioturbation of Corbicula fluminea could affected the community composition and abundance of ammonia-oxidizing microorganisms in surface sediments. PMID:25158512

  5. Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars.

    PubMed

    Bertagnolli, Anthony D; Meinhardt, Kelley A; Pannu, Manmeet; Brown, Sally; Strand, Stuart; Fransen, Steven C; Stahl, David A

    2015-04-01

    Ammonia-oxidizing thaumarcheota (AOA) and ammonia-oxidizing bacteria (AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene (amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass (Panicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. Nitrosotalea-like and Nitrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with Nitrososphaera and Nitrosospira cluster 3A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses. PMID:25504683

  6. Selective isolation of ammonia-oxidizing bacteria from autotrophic nitrifying granules by applying cell-sorting and sub-culturing of microcolonies

    PubMed Central

    Fujitani, Hirotsugu; Kumagai, Asami; Ushiki, Norisuke; Momiuchi, Kengo; Tsuneda, Satoshi

    2015-01-01

    Nitrification is a key process in the biogeochemical nitrogen cycle and biological wastewater treatment that consists of two stepwise reactions, ammonia oxidation by ammonia-oxidizing bacteria (AOB) or archaea followed by nitrite oxidation by nitrite-oxidizing bacteria. One of the representatives of the AOB group is Nitrosomonas mobilis species. Although a few pure strains of this species have been isolated so far, approaches to their preservation in pure culture have not been established. Here, we report isolation of novel members of the N. mobilis species from autotrophic nitrifying granules used for ammonia-rich wastewater treatment. We developed an isolation method focusing on microcolonies formation of nitrifying bacteria. Two kinds of distinctive light scattering signatures in a cell-sorting system enabled to separate microcolonies from single cells and heterogeneous aggregates within granule samples. Inoculation of a pure microcolony into 96-well microtiter plates led to successful sub-culturing and increased probability of isolation. Obtained strain Ms1 is cultivated in the liquid culture with relatively high ammonia or nitrite concentration, not extremely slow growing. Considering environmental clones that were closely related to N. mobilis and detected in various environments, the availability of this novel strain would facilitate to reveal this member’s ecophysiology in a variety of habitats. PMID:26528282

  7. A novel control method for nitritation: The domination of ammonia-oxidizing bacteria by high concentrations of inorganic carbon in an airlift-fluidized bed reactor.

    PubMed

    Tokutomi, Takaaki; Shibayama, Chizu; Soda, Satoshi; Ike, Michihiko

    2010-07-01

    A novel nitritation method based on the addition of inorganic carbon (IC) was verified using an airlift-fluidized bed reactor packed with sponge cubes. A continuous-treatment experiment demonstrated that the type of nitrification-nitrite or nitrate accumulation-could be controlled by the addition of different alkalinity sources (NaHCO(3) or NaOH, respectively). The maximum rate of ammonia oxidation at 30 degrees C was 2.47kg-N/(m(3) d), with nitrate formation of less than 0.5% of the converted ammonia. Nitrite accumulation of over 90% was maintained stably over 250 days at 30 degrees C and was achieved even at 19 degrees C. Qualitative and quantitative shifts of nitrifying bacteria in the biofilm were monitored by real-time PCR and T-RFLP analysis. Ammonia-oxidizing bacteria (AOB) were dominant but nitrite-oxidizing bacteria (NOB) were eliminated in the reactor when NaHCO(3) was used as the alkalinity source. From the kinetic data, we inferred that high IC concentrations drive stable nitritation by promoting a higher growth rate for AOB than for NOB. PMID:20554306

  8. Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten wastewater treatment systems.

    PubMed

    Gao, Jingfeng; Luo, Xin; Wu, Guixia; Li, Ting; Peng, Yongzhen

    2014-04-01

    The abundance and diversity of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in ten wastewater treatment systems (WTSs) by polymerase chain reaction (PCR), cloning, sequencing, and quantitative real-time PCR (qPCR). The ten WTSs included four full-scale municipal WTSs, three full-scale industrial WTSs, and three lab-scale WTSs. AOB were present in all the WTSs, whereas AOA were detected in nine WTSs. QPCR data showed that AOB amoA genes (4.625 × 10(4)-9.99 × 10(9) copies g(-1) sludge) outnumbered AOA amoA genes (ammonia oxidization in WTSs. Interestingly, it was found that AOA and AOB coexisted with anaerobic ammonia oxidation (anammox) bacteria in three anammox WTSs with relatively higher abundance. In a full-scale industrial WTS where effluent ammonia was higher than influent ammonia, both AOA and AOB showed higher abundance. The phylogenetic analysis of AOB amoA genes showed that genera Nitrosomonas was the most dominant species in the ten WTSs; Nitrosomonas europaea cluster was the dominant major cluster, followed by Nitrosomonas-like cluster and Nitrosomonas oligotropha cluster; and AOB species showed higher diversity than AOA species. AOA were found to be affiliated with two major clusters: Nitrososphaera cluster and Nitrosopumilus cluster. Nitrososphaera cluster was the most dominant species in different samples and distributed worldwide. PMID:24318009

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

    PubMed

    Chen, Zhu; Wu, Wenliang; Shao, Xiaoming; Li, Li; Guo, Yanbin; Ding, Guochun

    2015-01-01

    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. PMID:26172994

  10. 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

    PubMed Central

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

    2014-01-01

    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. PMID:25326303

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

    PubMed Central

    Chen, Zhu; Wu, Wenliang; Shao, Xiaoming; Li, Li; Guo, Yanbin; Ding, Guochun

    2015-01-01

    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. PMID:26172994

  12. 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.

    PubMed

    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. PMID:25326303

  13. Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.

    PubMed

    Song, He; Che, Zhao; Cao, Wenchao; Huang, Ting; Wang, Jingguo; Dong, Zhaorong

    2016-06-01

    Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation. PMID:26961528

  14. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization

    PubMed Central

    Xue, Chao; Zhang, Xu; Zhu, Chen; Zhao, Jun; Zhu, Ping; Peng, Chang; Ling, Ning; Shen, Qirong

    2016-01-01

    Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB. PMID:27356769

  15. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization.

    PubMed

    Xue, Chao; Zhang, Xu; Zhu, Chen; Zhao, Jun; Zhu, Ping; Peng, Chang; Ling, Ning; Shen, Qirong

    2016-01-01

    Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB. PMID:27356769

  16. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization

    NASA Astrophysics Data System (ADS)

    Xue, Chao; Zhang, Xu; Zhu, Chen; Zhao, Jun; Zhu, Ping; Peng, Chang; Ling, Ning; Shen, Qirong

    2016-06-01

    Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.

  17. Nitrification resilience and community dynamics of ammonia-oxidizing bacteria with respect to ammonia loading shock in a nitrification reactor treating steel wastewater.

    PubMed

    Cho, Kyungjin; Shin, Seung Gu; Lee, Joonyeob; Koo, Taewoan; Kim, Woong; Hwang, Seokhwan

    2016-08-01

    The aim of this study was to investigate the nitrification resilience pattern and examine the key ammonia-oxidizing bacteria (AOB) with respect to ammonia loading shocks (ALSs) in a nitrification bioreactor treating steel wastewater. The perturbation experiments were conducted in a 4-L bioreactor operated in continuous mode with a hydraulic retention time of 10 d. Three sequential ALSs were given to the bioreactor (120, 180 and 180 mg total ammonia nitrogen (TAN)/L. When the first shock was given, the nitrification process completely recovered after 14 d of further operation. However, the resilience duration was significantly reduced to ∼1 d after the second and third ALSs. In the bioreactor, Nitrosomonas aestuarii dominated the other AOB species, Nitrosomonas europaea and N. nitrosa, throughout the process. In addition, the population of N. aestuarii increased with ammonia utilization following each ALS; i.e., this species responded to acute ammonia overloadings by contributing to ammonia oxidation. This finding suggests that N. aestuarii could be exploited to achieve stable nitrification in industrial wastewaters that contain high concentrations of ammonia. PMID:26896313

  18. Comparative effects of 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) on ammonia-oxidizing bacteria and archaea in a vegetable soil.

    PubMed

    Chen, Qiuhui; Qi, Lingyu; Bi, Qingfang; Dai, Peibin; Sun, Dasheng; Sun, Chengliang; Liu, Wenjing; Lu, Lingli; Ni, Wuzhong; Lin, Xianyong

    2015-01-01

    Nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) have been used extensively to improve nitrogen fertilizer utilization in farmland. However, their comparative effects on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in agricultural soils are still unclear. Here, we compared the impacts of these two inhibitors on soil nitrification, AOA and AOB abundance as well as their community structure in a vegetable soil by using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP). Our results showed that urea application significantly increased the net nitrification rates, but were significantly inhibited by both NIs, and the inhibitory effect of DMPP was significantly greater than that of DCD. AOB growth was more greatly inhibited by DMPP than by DCD, and the net nitrification rate was significantly related to AOB abundance, but not to AOA abundance. Application of urea and NIs to soil did not change the diversity of the AOA community, with the T-RFs remaining in proportions that were similar to control soils, while the community structure of AOB exhibited obvious shifts within all different treatments compared to the control. Phylogenetic analysis showed that all AOA sequences fell within group 1.1a and group 1.1b, and the AOB community consisted of Nitrosospira cluster 3, cluster 0, and unidentified species. These results suggest that DMPP exhibited a stronger inhibitory effect on nitrification than DCD by inhibiting AOB rather than AOA. PMID:25172135

  19. Response of performance and ammonia oxidizing bacteria community to high salinity stress in membrane bioreactor with elevated ammonia loading.

    PubMed

    Wang, Zhu; Luo, Gan; Li, Jun; Chen, Shi-Yu; Li, Yan; Li, Wen-Tao; Li, Ai-Min

    2016-09-01

    Effect of elevated ammonia loading rate (ALR) and increasing salinity on the operation of membrane bioreactor (MBR) and the response of microbial community were investigated. Results showed that MBR started up with 1% NaCl stress achieved amazing nitrification performance at high salinity up to 4% when treating wastewater containing 1000mg/L NH(+)4-N. Further increasing salinity to 7% led to failure of MBR unrecoverably. Steep decline of sludge activity contributed to the extremely worse performance. High-throughput sequencing analysis showed that both ALR and salinity had selective effects on the microbial community structure. In genus level, Methyloversatilis and Maribacter were enriched during the operation. Survival of salt-resistant microbes contributed to the rising of richness and diversity at 2% and 4% NaCl stress. Analysis of amoA-gene-based cloning revealed Nitrosomonas marina are chiefly responsible for catalyzing ammonia oxidation in high ALR at high salinity stress. PMID:27290667

  20. Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria.

    PubMed

    Junier, Pilar; Kim, Ok-Sun; Molina, Verónica; Limburg, Petra; Junier, Thomas; Imhoff, Johannes F; Witzel, Karl-Paul

    2008-04-01

    Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study. PMID:18248438

  1. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

    PubMed Central

    Magalhães, Catarina M.; Machado, Ana; Frank-Fahle, Béatrice; Lee, Charles K.; Cary, S. Craig

    2014-01-01

    The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints. PMID:25324835

  2. Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China.

    PubMed

    Gan, Xian-Hua; Zhang, Fang-Qiu; Gu, Ji-Dong; Guo, Yue-Dong; Li, Zhao-Qing; Zhang, Wei-Qiang; Xu, Xiu-Yu; Zhou, Yi; Wen, Xiao-Ying; Xie, Guo-Guang; Wang, Yong-Feng

    2016-02-01

    In addition to ammonia-oxidizing bacteria (AOB) the more recently discovered ammonia-oxidizing archaea (AOA) can also oxidize ammonia, but little is known about AOA community structure and abundance in subtropical forest soils. In this study, both AOA and AOB were investigated with molecular techniques in eight types of forests at surface soils (0-2 cm) and deep layers (18-20 cm) in Nanling National Nature Reserve in subtropical China. The results showed that the forest soils, all acidic (pH 4.24-5.10), harbored a wide range of AOA phylotypes, including the genera Nitrosotalea, Nitrososphaera, and another 6 clusters, one of which was reported for the first time. For AOB, only members of Nitrosospira were retrieved. Moreover, the abundance of the ammonia monooxygenase gene (amoA) from AOA dominated over AOB in most soil samples (13/16). Soil depth, rather than forest type, was an important factor shaping the community structure of AOA and AOB. The distribution patterns of AOA and AOB in soil layers were reversed: AOA diversity and abundances in the deep layers were higher than those in the surface layers; on the contrary, AOB diversity and abundances in the deep layers were lower than those in the surface layers. Interestingly, the diversity of AOA was positively correlated with pH, but negatively correlated with organic carbon, total nitrogen and total phosphorus, and the abundance of AOA was negatively correlated with available phosphorus. Our results demonstrated that AOA and AOB were differentially distributed in acidic soils in subtropical forests and affected differently by soil characteristics. PMID:26626057

  3. Abundance and Diversity of Ammonia-Oxidizing Archaea and Bacteria in Sediments of Trophic End Members of the Laurentian Great Lakes, Erie and Superior

    PubMed Central

    Bollmann, Annette; Bullerjahn, George S.; McKay, Robert Michael

    2014-01-01

    Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes. PMID:24819357

  4. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys.

    PubMed

    Magalhães, Catarina M; Machado, Ana; Frank-Fahle, Béatrice; Lee, Charles K; Cary, S Craig

    2014-01-01

    The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints. PMID:25324835

  5. Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior.

    PubMed

    Bollmann, Annette; Bullerjahn, George S; McKay, Robert Michael

    2014-01-01

    Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes. PMID:24819357

  6. Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei.

    PubMed

    Feng, Guofang; Sun, Wei; Zhang, Fengli; Karthik, Loganathan; Li, Zhiyong

    2016-01-01

    Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei. PMID:27113140

  7. Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

    PubMed Central

    Feng, Guofang; Sun, Wei; Zhang, Fengli; Karthik, Loganathan; Li, Zhiyong

    2016-01-01

    Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei. PMID:27113140

  8. Bacterial and archaea community present in the Pine Barrens Forest of Long Island, NY: unusually high percentage of ammonia oxidizing bacteria.

    PubMed

    Shah, Vishal; Shah, Shreya; Kambhampati, Murty S; Ambrose, Jeffery; Smith, Nyesha; Dowd, Scot E; McDonnell, Kevin T; Panigrahi, Bishnu; Green, Timothy

    2011-01-01

    Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0-10 cm (Horizon O); 11-25 cm (Horizon A) and 26-40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil. PMID:22028845

  9. Bacterial and Archaea Community Present in the Pine Barrens Forest of Long Island, NY: Unusually High Percentage of Ammonia Oxidizing Bacteria

    SciTech Connect

    Shah, V.; Green, T.; Shah, V.; Shah, S.; Kambhampati, M.; Ambrose, J.; Smith, N.; Dowd, S.; McDonnell, K.; Panigrahi, B.

    2011-10-20

    Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0-10 cm (Horizon O); 11-25 cm (Horizon A) and 26-40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil.

  10. Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment.

    PubMed

    Hiorns, W D; Hastings, R C; Head, I M; McCarthy, A J; Saunders, J R; Pickup, R W; Hall, G H

    1995-11-01

    Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as specific PCR amplification primers and probes. The specificities of primer pairs for eubacterial, Nitrosospira and Nitrosomonas rRNA genes were established with sequence databases, and the primer pairs were used to amplify DNA from laboratory cultures and environmental samples. Eubacterial rRNA genes amplified from samples of soil and activated sludge hybridized with an oligonucleotide probe specific for Nitrosospira spp., but not with a Nitrosomonas-specific probe. Lakewater and sediment samples were analysed using a nested PCR technique in which eubacterial rRNA genes were subjected to a secondary amplification with Nitrosomonas or Nitrosospira specific primers. Again, the presence of Nitrosospira DNA, but not Nitrosomonas DNA, was detected and this was confirmed by hybridization of the amplified DNA with an internal oligonucleotide probe. Enrichments of lakewater and sediment samples, incubated for two weeks in the presence of ammonium, produced nitrite and were found to contain DNA from both Nitrosospira and Nitrosomonas as determined by nested PCR amplification and probing of 16S rRNA genes. This demonstrates that Nitrosospira spp. are widespread in the environment. The implications of the detection of Nitrosomonas DNA only after enrichment culture are discussed. PMID:8535507

  11. High Abundances of Potentially Active Ammonia-Oxidizing Bacteria and Archaea in Oligotrophic, High-Altitude Lakes of the Sierra Nevada, California, USA

    PubMed Central

    Hayden, Curtis J.; Beman, J. Michael

    2014-01-01

    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 (r2 = 0.32, p<0.1), whereas AOA abundance was inversely correlated with lake elevation (r2 = 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. PMID:25402442

  12. Bacterial and Archaea Community Present in the Pine Barrens Forest of Long Island, NY: Unusually High Percentage of Ammonia Oxidizing Bacteria

    PubMed Central

    Shah, Vishal; Shah, Shreya; Kambhampati, Murty S.; Ambrose, Jeffery; Smith, Nyesha; Dowd, Scot E.; McDonnell, Kevin T.; Panigrahi, Bishnu; Green, Timothy

    2011-01-01

    Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0–10 cm (Horizon O); 11–25 cm (Horizon A) and 26–40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil. PMID:22028845

  13. N2O emission in short-cut simultaneous nitrification and denitrification process: dynamic emission characteristics and succession of ammonia-oxidizing bacteria.

    PubMed

    Yan, Yingyan; Li, Ping; Wu, Jinhua; Zhu, Nengwu; Wu, Pingxiao; Wang, Xiangde

    2014-01-01

    A sequencing batch airlift reactor was used to investigate the characteristics of nitrous oxide (N2O) emission and the succession of an ammonia-oxidizing bacteria (AOB) community. The bioreactor could successfully switch from the complete simultaneous nitrification and denitrification (SND) process to the short-cut SND process by increasing the influent pH from 7.0-7.3 to 8.0-8.3. The results obtained showed that, compared with the complete SND process, the TN removal rate and SND efficiency were improved in the short-cut SND process by approximately 13 and 11%, respectively, while the amount of N2O emission was nearly three times larger than that in the complete SND process. The N2O emission was closely associated to nitrite accumulation. Analysis of the AOB microbial community showed that nitrifier denitrification by Nitrosomonas-like AOB could be an important pathway for the enhancement of N2O emission in the short-cut SND process. PMID:24960019

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

    PubMed Central

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J.

    2015-01-01

    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 waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

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

    PubMed

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J

    2015-01-01

    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 waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

  16. The combined effect of dissolved oxygen and nitrite on N2O production by ammonia oxidizing bacteria in an enriched nitrifying sludge.

    PubMed

    Peng, Lai; Ni, Bing-Jie; Ye, Liu; Yuan, Zhiguo

    2015-04-15

    Both nitrite [Formula: see text] and dissolved oxygen (DO) play important roles in nitrous oxide (N2O) production by ammonia oxidizing bacteria (AOB). However, few studies focused on the combined effect of them on N2O production by AOB as well as the corresponding mechanisms. In this study, N2O production by an enriched nitrifying sludge, consisting of both AOB and nitrite-oxidizing bacteria (NOB), was investigated under various [Formula: see text] and DO concentrations. At each investigated DO level, both the biomass specific N2O production rate and the N2O emission factor (the ratio between N2O nitrogen emitted and the ammonium nitrogen converted) increased as [Formula: see text] concentration increased from 3 mg N/L to 50 mg N/L. However, at each investigated [Formula: see text] level, the maximum biomass specific N2O production rate occurred at DO of 0.85 mg O2/L, while the N2O emission factor decreased as DO increased from 0.35 to 3.5 mg O2/L. The analysis of the process data using a mathematical N2O model incorporating both the AOB denitrification and hydroxylamine (NH2OH) oxidation pathways indicated that the contribution of AOB denitrification pathway increased as [Formula: see text] concentration increased, but decreased as DO concentration increased, accompanied by a corresponding change in the contribution of NH2OH oxidation pathway to N2O production. The AOB denitrification pathway was predominant in most cases, with the NH2OH oxidation pathway making a comparable contribution only at high DO level (e.g. 3.5 mg O2/L). PMID:25644626

  17. Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

    PubMed Central

    2012-01-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research. PMID:22923400

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

    PubMed

    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. PMID:26463999

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

    PubMed Central

    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

  20. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria.

    PubMed Central

    Stephen, J R; McCaig, A E; Smith, Z; Prosser, J I; Embley, T M

    1996-01-01

    We have conducted a preliminary phylogenetic survey of ammonia-oxidizing beta-proteobacteria, using 16S rRNA gene libraries prepared by selective PCR and DNA from acid and neutral soils and polluted and nonpolluted marine sediments. Enrichment cultures were established from samples and analyzed by PCR. Analysis of 111 partial sequences of c. 300 bases revealed that the environmental sequences formed seven clusters, four of which are novel, within the phylogenetic radiation defined by cultured autotrophic ammonia oxidizers. Longer sequences from 13 cluster representatives support their phylogenetic positions relative to cultured taxa. These data suggest that known taxa may not be representative of the ammonia-oxidizing beta-proteobacteria in our samples. Our data provide further evidence that molecular and culture-based enrichment methods can select for different community members. Most enrichments contained novel Nitrosomonas-like sequences whereas novel Nitrosospira-like sequences were more common from gene libraries of soils and marine sediments. This is the first evidence for the occurrence of Nitrosospira-like strains in marine samples. Clear differences between the sequences of soil and marine sediment libraries were detected. Comparison of 16S rRNA sequences from polluted and nonpolluted sediments provided no strong evidence that the community composition was determined by the degree of pollution. Soil clone sequences fell into four clusters, each containing sequences from acid and neutral soils in varying proportions. Our data suggest that some related strains may be present in both samples, but further work is needed to resolve whether there is selection due to pH for particular sequence types. PMID:8900005

  1. Biology of Moderately Halophilic Aerobic Bacteria

    PubMed Central

    Ventosa, Antonio; Nieto, Joaquín J.; Oren, Aharon

    1998-01-01

    The moderately halophilic heterotrophic aerobic bacteria form a diverse group of microorganisms. The property of halophilism is widespread within the bacterial domain. Bacterial halophiles are abundant in environments such as salt lakes, saline soils, and salted food products. Most species keep their intracellular ionic concentrations at low levels while synthesizing or accumulating organic solutes to provide osmotic equilibrium of the cytoplasm with the surrounding medium. Complex mechanisms of adjustment of the intracellular environments and the properties of the cytoplasmic membrane enable rapid adaptation to changes in the salt concentration of the environment. Approaches to the study of genetic processes have recently been developed for several moderate halophiles, opening the way toward an understanding of haloadaptation at the molecular level. The new information obtained is also expected to contribute to the development of novel biotechnological uses for these organisms. PMID:9618450

  2. Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea)

    PubMed Central

    Lipsewers, Yvonne A.; Bale, Nicole J.; Hopmans, Ellen C.; Schouten, Stefan; Sinninghe Damsté, Jaap S.; Villanueva, Laura

    2014-01-01

    Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria. PMID:25250020

  3. Diversity and Abundance of Ammonia-Oxidizing Archaeal Nitrite Reductase (nirK) Genes in Estuarine Sediments of San Francisco Bay

    NASA Astrophysics Data System (ADS)

    Reji, L.; Lee, J. A.; Damashek, J.; Francis, C. A.

    2013-12-01

    Nitrification, the microbially-mediated aerobic oxidation of ammonia to nitrate via nitrite, is an integral component of the global biogeochemical nitrogen cycle. The first and rate-limiting step of nitrification, ammonia oxidation, is carried out by two distinct microbial groups: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Molecular ecological studies targeting the amoA gene have revealed the abundance and ubiquity of AOA in terrestrial as well as aquatic environments. In addition to the ammonia oxidation machinery that includes the amoA gene, AOA also encode a gene for copper-containing nitrite reductase (nirK). The distribution patterns and functional role of nirK in AOA remain mostly unknown; proposed functions include the indirect involvement in ammonia oxidation through the production of nitric oxide during nitrite reduction, and (2) nitrite detoxification. In the present study, the diversity and abundance of archaeal nirK genes in estuarine sediments were investigated using quantitative polymerase chain reaction, cloning and sequencing approaches. In sediment samples collected from the San Francisco Bay estuary, two archaeal nirK variants (AnirKa and AnirKb) were amplified using specific primer sets. Overall, AnirKa was observed to be significantly more abundant than AnirKb in the sediment samples, with variation in relative abundance spanning two to three orders of magnitude between sampling sites. Phylogenetic analysis revealed a number of unique archaeal nirK sequence types, as well as many that clustered with sequences from previous estuarine studies and cultured AOA isolates, such as Nitrosopumilus maritimus. This study yielded new insights into the diversity and abundance of archaeal nirK genes in estuarine sediments, and highlights the importance of further investigating the physiological role of this gene in AOA, as well as its suitability as a marker gene for studying AOA in the environment.

  4. Ammonia oxidation rates and nitrification in the Arabian Sea

    NASA Astrophysics Data System (ADS)

    Newell, Silvia E.; Babbin, Andrew R.; Jayakumar, Amal; Ward, Bess B.

    2011-12-01

    Nitrification rates, as well as the relationships between rates and ammonia oxidizer abundance (both archaeal and bacterial), were investigated in the Arabian Sea. Ammonia oxidation rates were measured directly using 15N-NH4+stable isotope additions in gas-impermeable, trace metal clean trilaminate bags (500 mL) at in situ temperature. Tracer incubations were performed at three stations at depths above, below, and within the oxycline of the open-ocean oxygen minimum zone (OMZ). Ammonia oxidation rates were similar to previous open-ocean measurements, ranging from undetectable to 21.6 ± 0.1 nmol L-1 d-1. The highest rates at each station occurred at the primary nitrite maximum (above the OMZ), and rates were very low at depths greater than 900 m. The abundances of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were estimated using theamoA gene by quantitative polymerase chain reaction (qPCR). Both AOA and AOB amoA were detected above, within, and below the OMZ, although the AOA were always more abundant than the AOB, by a factor of 35-216. Nitrification rates were not directly correlated to AOA or AOB amoA abundance. These rates offer new insight into the role of nitrification in the mesopelagic zone. The abundance of AOA amoA genes at 1000 m suggests that ˜50% of the microbial biomass could be autotrophic. Additionally, the integrated nitrification rate at depth implies that nitrification could consume most of the ammonium produced by the flux of organic carbon in the mesopelagic zone.

  5. Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon “Candidatus Nitrosotalea devanaterra”

    PubMed Central

    Sayavedra-Soto, Luis A.; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y.; Prosser, James I.; Nicol, Graeme W.

    2016-01-01

    Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer “Candidatus Nitrosotalea devanaterra” provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of “Ca. Nitrosotalea devanaterra” reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that “Ca. Nitrosotalea devanaterra” contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography–mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of “Ca. Nitrosotalea devanaterra” were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. PMID:26896134

  6. Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

    PubMed

    Lehtovirta-Morley, Laura E; Sayavedra-Soto, Luis A; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y; Prosser, James I; Nicol, Graeme W

    2016-05-01

    Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer "Candidatus Nitrosotalea devanaterra" provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of "Ca Nitrosotalea devanaterra" reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that "Ca Nitrosotalea devanaterra" contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of "Ca Nitrosotalea devanaterra" were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. PMID:26896134

  7. Ammonia oxidizing bacteria and archaea in horizontal flow biofilm reactors treating ammonia-contaminated air at 10 °C.

    PubMed

    Gerrity, Seán; Clifford, Eoghan; Kennelly, Colm; Collins, Gavin

    2016-05-01

    The objective of this study was to demonstrate the feasibility of novel, Horizontal Flow Biofilm Reactor (HFBR) technology for the treatment of ammonia (NH3)-contaminated airstreams. Three laboratory-scale HFBRs were used for remediation of an NH3-containing airstream at 10 °C during a 90-d trial to test the efficacy of low-temperature treatment. Average ammonia removal efficiencies of 99.7 % were achieved at maximum loading rates of 4.8 g NH3 m(3) h(-1). Biological nitrification of ammonia to nitrite (NO2 (-)) and nitrate (NO3 (-)) was mediated by nitrifying bacterial and archaeal biofilm populations. Ammonia-oxidising bacteria (AOB) were significantly more abundant than ammonia-oxidising archaea (AOA) vertically at each of seven sampling zones along the vertical HFBRs. Nitrosomonas and Nitrosospira, were the two most dominant bacterial genera detected in the HFBRs, while an uncultured archaeal clone dominated the AOA community. The bacterial community composition across the three HFBRs was highly conserved, although variations occurred between HFBR zones and were driven by physicochemical variables. The study demonstrates the feasibility of HFBRs for the treatment of ammonia-contaminated airstreams at low temperatures; identifies key nitrifying microorganisms driving the removal process; and provides insights for process optimisation and control. The findings are significant for industrial applications of gas oxidation technology in temperate climates. PMID:26879980

  8. Aerobic Denitrifying Bacteria That Produce Low Levels of Nitrous Oxide

    PubMed Central

    Takaya, Naoki; Catalan-Sakairi, Maria Antonina B.; Sakaguchi, Yasushi; Kato, Isao; Zhou, Zhemin; Shoun, Hirofumi

    2003-01-01

    Most denitrifiers produce nitrous oxide (N2O) instead of dinitrogen (N2) under aerobic conditions. We isolated and characterized novel aerobic denitrifiers that produce low levels of N2O under aerobic conditions. We monitored the denitrification activities of two of the isolates, strains TR2 and K50, in batch and continuous cultures. Both strains reduced nitrate (NO3−) to N2 at rates of 0.9 and 0.03 μmol min−1 unit of optical density at 540 nm−1 at dissolved oxygen (O2) (DO) concentrations of 39 and 38 μmol liter−1, respectively. At the same DO level, the typical denitrifier Pseudomonas stutzeri and the previously described aerobic denitrifier Paracoccus denitrificans did not produce N2 but evolved more than 10-fold more N2O than strains TR2 and K50 evolved. The isolates denitrified NO3− with concomitant consumption of O2. These results indicated that strains TR2 and K50 are aerobic denitrifiers. These two isolates were taxonomically placed in the β subclass of the class Proteobacteria and were identified as P. stutzeri TR2 and Pseudomonas sp. strain K50. These strains should be useful for future investigations of the mechanisms of denitrifying bacteria that regulate N2O emission, the single-stage process for nitrogen removal, and microbial N2O emission into the ecosystem. PMID:12788710

  9. Biodegradation of Asphalt Cement-20 by Aerobic Bacteria

    PubMed Central

    Pendrys, John P.

    1989-01-01

    Seven gram-negative, aerobic bacteria were isolated from a mixed culture enriched for asphalt-degrading bacteria. The predominant genera of these isolates were Pseudomonas, Acinetobacter, Alcaligenes, Flavimonas, and Flavobacterium. The mixed culture preferentially degraded the saturate and naphthene aromatic fractions of asphalt cement-20. A residue remained on the surface which was resistant to biodegradation and protected the underlying asphalt from biodegradation. The most potent asphalt-degrading bacterium, Acinetobacter calcoaceticus NAV2, excretes an emulsifier which is capable of emulsifying the saturate and naphthene aromatic fractions of asphalt cement-20. This emulsifier is not denatured by phenol. PMID:16347928

  10. Soil and sediment bacteria capable of aerobic nitrate respiration.

    PubMed Central

    Carter, J P; Hsaio, Y H; Spiro, S; Richardson, D J

    1995-01-01

    Several laboratory strains of gram-negative bacteria are known to be able to respire nitrate in the presence of oxygen, although the physiological advantage gained from this process is not entirely clear. The contribution that aerobic nitrate respiration makes to the environmental nitrogen cycle has not been studied. As a first step in addressing this question, a strategy which allows for the isolation of organisms capable of reducing nitrate to nitrite following aerobic growth has been developed. Twenty-nine such strains have been isolated from three soils and a freshwater sediment and shown to comprise members of three genera (Pseudomonas, Aeromonas, and Moraxella). All of these strains expressed a nitrate reductase with an active site located in the periplasmic compartment. Twenty-two of the strains showed significant rates of nitrate respiration in the presence of oxygen when assayed with physiological electron donors. Also isolated was one member of the gram-positive genus Arthrobacter, which was likewise able to respire nitrate in the presence of oxygen but appeared to express a different type of nitrate reductase. In the four environments studied, culturable bacteria capable of aerobic nitrate respiration were isolated in significant numbers (10(4) to 10(7) per g of soil or sediment) and in three cases were as abundant as, or more abundant than, culturable bacteria capable of denitrification. Thus, it seems likely that the corespiration of nitrate and oxygen may indeed make a significant contribution to the flux of nitrate to nitrite in the environment. PMID:7487017

  11. Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.

    PubMed

    Marusenko, Yevgeniy; Garcia-Pichel, Ferran; Hall, Sharon J

    2015-02-01

    In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability. PMID:25764551

  12. Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

    PubMed

    Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

    2014-03-01

    Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. PMID:23897748

  13. Distribution of ammonia oxidizers in relation to vegetation characteristics in the Qilian Mountains, northwestern China

    NASA Astrophysics Data System (ADS)

    Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.; Gao, T. P.

    2014-04-01

    Nitrogen is the major limiting nutrient in cold environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in alpine meadow soils in northwestern China, namely those catalyzing the rate-limiting step of ammonia oxidation. In this study, ammonia-oxidizing communities in alpine meadow soils were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. The results demonstrated that ammonia-oxidizing archaea (AOA) outnumbered ammonia-oxidizing bacteria (AOB) in the alpine meadow soils. Most of the AOA phylotypes detected in the study region fell within typical Group I.1b of Thaumarchaeota. Interestingly, a new ammonia-oxidizing archaeal group named "Kobresia meadow soil group" was found. Phylogenetic analysis of AOB communities exhibited a dominance of Nitrosospira-like sequences affiliated to beta-Proteobacteria. Compared with other alpine environments, Qilian Mountains had a great phylogenetic diversity of ammonia oxidizers. Principal Component Analysis (PCA) analysis showed that distinct AOA/AOB phylotype groups were attributed to different meadow types, reflecting an overall distribution of ammonia-oxidizing communities associated with meadow types. Redundancy Analysis (RDA) analysis showed that Axis 1 (90.9%) together with Axis 2 (9.1%) explained all the variables while Axis 1 exhibited a significant explanatory power. So that vegetation coverage mostly correlated to Axis 1 was the most powerful environmental factor in the study region. Characteristics of ammonia-oxidizing communities showed a close association with vegetation coverage.

  14. Bacterial domination over archaea in ammonia oxidation in a monsoon-driven tropical estuary.

    PubMed

    Puthiya Veettil, Vipindas; Abdulaziz, Anas; Chekidhenkuzhiyil, Jasmin; Kalanthingal Ramkollath, Lallu; Karayadi Hamza, Fausia; Kizhakkepat Kalam, Balachandran; Kallungal Ravunnikutty, Muraleedharan; Nair, Shanta

    2015-04-01

    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-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale. PMID:25344857

  15. Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

    PubMed Central

    Santoro, Alyson E; Casciotti, Karen L

    2011-01-01

    Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH3) to nitrite (NO2−). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15ɛNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15ɛNH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15ɛNH3 is similar. PMID:21562601

  16. Aerobic sulfur-oxidizing bacteria: Environmental selection and diversification

    NASA Technical Reports Server (NTRS)

    Caldwell, D.

    1985-01-01

    Sulfur-oxidizing bacteria oxidize reduced inorganic compounds to sulfuric acid. Lithotrophic sulfur oxidizer use the energy obtained from oxidation for microbial growth. Heterotrophic sulfur oxidizers obtain energy from the oxidation of organic compounds. In sulfur-oxidizing mixotrophs energy are derived either from the oxidation of inorganic or organic compounds. Sulfur-oxidizing bacteria are usually located within the sulfide/oxygen interfaces of springs, sediments, soil microenvironments, and the hypolimnion. Colonization of the interface is necessary since sulfide auto-oxidizes and because both oxygen and sulfide are needed for growth. The environmental stresses associated with the colonization of these interfaces resulted in the evolution of morphologically diverse and unique aerobic sulfur oxidizers.

  17. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant.

    PubMed

    Wu, Yi-Ju; Whang, Liang-Ming; Fukushima, Toshikazu; Chang, Shao-Hsiung

    2013-04-01

    The diversity and abundance of ammonia-oxidizing Betaproteobacteria and archaea were investigated in a full-scale municipal wastewater treatment plant where the wastewater conductivity level varied considerably (due to seawater salinity intrusion) during this study between 2004 and 2007. Based on the quantitative polymerase chain reaction of ammonia monooxygenase subunit A (amoA) genes, an increase in the ammonia oxidizing bacteria amoA gene copies occurred with a decrease in the wastewater salinity level. A corresponding decrease in the average ammonia-oxidizing archaea to bacteria ratio, from 1.22 (2004 and 2005), 0.17 (2006), and then to 0.07 (2007), was observed. Phylogenetic analyses on amoA gene sequences indicated that Nitrosomonas marina-like ammonia oxidizing bacteria and Thaumarcheota Ⅰ.1a (marina group) ammonia-oxidizing archaea were dominant when the wastewater salinity level fluctuated at high values with an average of 4.83 practical salinity unit (psu), while Nitrosomonas urea-like ammonia oxidizing bacteria and Thaumarcheota Ⅰ.1b (soil group) ammonia-oxidizing archaea became dominant when the wastewater salinity decreased to a more stable lower level with an average of 1.93 psu. Based on the amoA gene-based terminal restriction fragment length polymorphism analyses, results from this study demonstrated that the observed shift in ammonia oxidizing bacteria and archaea populations is likely caused by a change of the wastewater salinity level. PMID:23232030

  18. Ammonia-oxidizing Archaea in laboratory-scale activated sludge systems for wastewater of low- or high-ammonium concentration.

    PubMed

    Oishi, Ryu; Hirooka, Kayako; Otawa, Kenichi; Tada, Chika; Nakai, Yutaka

    2012-07-01

    Ammonia-oxidizing bacteria (AOB) is known as ammonia-oxidizer in wastewater treatment systems. However, ammonia-oxidizing Archaea (AOA) is found from various environments, including wastewater treatment systems. In this study, to investigate the relationships between AOA population and ammonia concentration, AOA was monitored in two laboratory-scale reactors treating artificial wastewater of different ammonium concentrations by denaturing gradient gel electrophoresis targeting ammonia monooxygenase genes. At day 60 of the operation, AOA populations dominant in each reactor differed, suggesting the importance of influent ammonia concentration in dominant AOA selection. PMID:22776796

  19. Aerobic salivary bacteria in wild and captive Komodo dragons.

    PubMed

    Montgomery, Joel M; Gillespie, Don; Sastrawan, Putra; Fredeking, Terry M; Stewart, George L

    2002-07-01

    During the months of November 1996, August 1997, and March 1998, saliva and plasma samples were collected for isolation of aerobic bacteria from 26 wild and 13 captive Komodo dragons (Varanus komodoensis). Twenty-eight Gram-negative and 29 Gram-positive species of bacteria were isolated from the saliva of the 39 Komodo dragons. A greater number of wild than captive dragons were positive for both Gram-negative and Gram-positive bacteria. The average number of bacterial species within the saliva of wild dragons was 46% greater than for captive dragons. While Escherichia coli was the most common bacterium isolated from the saliva of wild dragons, this species was not present in captive dragons. The most common bacteria isolated from the saliva of captive dragons were Staphylococcus capitis and Staphylococcus capitis and Staphylococcus caseolyticus, neither of which were found in wild dragons. High mortality was seen among mice injected with saliva from wild dragons and the only bacterium isolated from the blood of dying mice was Pasteurella multocida. A competitive inhibition enzyme-linked immunosorbent assay revealed the presence of anti-Pasteurella antibody in the plasma of Komodo dragons. Four species of bacteria isolated from dragon saliva showed resistance to one or more of 16 antimicrobics tested. The wide variety of bacteria demonstrated in the saliva of the Komodo dragon in this study, at least one species of which was highly lethal in mice and 54 species of which are known pathogens, support the observation that wounds inflicted by this animal are often associated with sepsis and subsequent bacteremia in prey animals. PMID:12238371

  20. Development of a simultaneous partial nitrification, anaerobic ammonia oxidation and denitrification (SNAD) bench scale process for removal of ammonia from effluent of a fertilizer industry.

    PubMed

    Keluskar, Radhika; Nerurkar, Anuradha; Desai, Anjana

    2013-02-01

    A simultaneous partial nitrification, anammox and denitrification (SNAD) process was developed for the treatment of ammonia laden effluent of a fertilizer industry. Autotrophic aerobic and anaerobic ammonia oxidizing biomass was enriched and their ammonia removal ability was confirmed in synthetic effluent system. Seed consortium developed from these was applied in the treatment of effluent in an oxygen limited bench scale SNAD type (1L) reactor run at ambient temperature (∼30°C). Around 98.9% ammonia removal was achieved with ammonia loading rate 0.35kgNH(4)(+)-N/m(3)day in the presence of 46.6mg/L COD at 2.31days hydraulic retention time. Qualitative and quantitative analysis of the biomass from upper and lower zone of the reactor revealed presence of autotrophic ammonia oxidizing bacteria (AOB), Planctomycetes and denitrifiers as the dominant bacteria carrying out anoxic oxidation of ammonia in the reactor. Physiological and molecular studies strongly indicate presence of anammox bacteria in the anoxic zone of the SNAD reactor. PMID:23313684

  1. Phosphatase activity of aerobic and facultative anaerobic bacteria.

    PubMed

    Pácová, Z; Kocur, M

    1978-10-01

    1115 strains of aerobic and facultatively anaerobic bacteria were tested for phosphatase activity by a conventional plate method and a microtest. The microtest was devised to allow results to be read after 4 h cultivation. Phosphatase activity was found in wide range of species and strains. Besides staphylococci, where the test for phosphatase is successfully used, it may be applied as one of the valuable tests for the differentiation of the following species: Bacillus cereus, B. licheniformis, Aeromonas spp., Vibrio parahaemolyticus, Actinobacillus spp., Pasteurella spp., Xanthomonas spp., Flavobacterium spp., Alteromonas putrefaciens, Pseudomonas maltophilia, Ps. cepacia, and some other species of Pseudomonas. The species which gave uniformly negative phosphatase reaction were as follows: Staph. saprophyticus, Acinetobacter calcoaceticus, Alcaligenes faecalis, and Bordetella bronchiseptica. PMID:216188

  2. Poplar lignin decomposition by gram-negative aerobic bacteria

    SciTech Connect

    Odier, E.; Janin, G.; Monties, B.

    1981-02-01

    Eleven gram-negative aerobic bacteria (Pseudomonadaceae and Neisseriaceae) out of 122 soil isolates were selected for their ability to assimilate poplar dioxane lignin without a cosubstrate. Dioxane lignin and milled wood lignin degradation rates ranged between 20 and 40% of initial content after 7 days in mineral medium, as determined by a loss of absorbance at 280 nm; 10 strains could degrade in situ lignin, as evidenced by the decrease of the acetyl bromide lignin content of microtome wood sections. No degradation of wood polysaccharides was detected. Lignin biodegradation by Pseudomonas 106 was confirmed by 14CO2 release from labeled poplar wood, although in lower yields compared with results obtained through chemical analysis based on acetyl bromide residual lignin determination. (Refs. 31).

  3. Ammonia Oxidizers in a Pilot-Scale Multilayer Rapid Infiltration System for Domestic Wastewater Treatment

    PubMed Central

    Lian, Yingli; Xu, Meiying; Zhong, Yuming; Yang, Yongqiang; Chen, Fanrong; Guo, Jun

    2014-01-01

    A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed contrary tendency. In the flowing phase (water effluent), AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO), NO3-N and NH3-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD). NH3-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS. PMID:25479611

  4. Ammonia oxidizers in a pilot-scale multilayer rapid infiltration system for domestic wastewater treatment.

    PubMed

    Lian, Yingli; Xu, Meiying; Zhong, Yuming; Yang, Yongqiang; Chen, Fanrong; Guo, Jun

    2014-01-01

    A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed contrary tendency. In the flowing phase (water effluent), AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO), NO3-N and NH3-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD). NH3-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS. PMID:25479611

  5. Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen

    PubMed Central

    Fitzgerald, Colin M.; Camejo, Pamela; Oshlag, J. Zachary; Noguera, Daniel R.

    2015-01-01

    Ammonia-oxidizing microbial communities involved in ammonia oxidation under low dissolved oxygen (DO) conditions (<0.3 mg/L) were investigated using chemostat reactors. One lab-scale reactor (NS_LowDO) was seeded with sludge from a full-scale wastewater treatment plant (WWTP) not adapted to low-DO nitrification, while a second reactor (JP_LowDO) was seeded with sludge from a full-scale WWTP already achieving low-DO nitrifiaction. The experimental evidence from quantitative PCR, rDNA tag pyrosequencing, and fluorescence in situ hybridization (FISH) suggested that ammonia-oxidizing bacteria (AOB) in the Nitrosomonas genus were responsible for low-DO nitrification in the NS_LowDO reactor, whereas in the JP_LowDO reactor nitrification was not associated with any known ammonia-oxidizing prokaryote. Neither reactor had a significant population of ammonia-oxidizing archaea (AOA) or anaerobic ammonium oxidation (anammox) organisms. Organisms isolated from JP_LowDO were capable of autotrophic and heterotrophic ammonia utilization, albeit without stoichiometric accumulation of nitrite or nitrate. Based on the experimental evidence we propose that Pseudomonas, Xanthomonadaceae, Rhodococcus, and Sphingomonas are involved in nitrification under low-DO conditions. PMID:25506762

  6. Isotopic signature of N(2)O produced by marine ammonia-oxidizing archaea.

    PubMed

    Santoro, Alyson E; Buchwald, Carolyn; McIlvin, Matthew R; Casciotti, Karen L

    2011-09-01

    The ocean is an important global source of nitrous oxide (N(2)O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N(2)O, but the isotopic signatures of N(2)O produced by these processes are not consistent with the marine contribution to the global N(2)O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N(2)O. Natural-abundance stable isotope measurements indicate that the produced N(2)O had bulk δ(15)N and δ(18)O values higher than observed for ammonia-oxidizing bacteria but similar to the δ(15)N and δ(18)O values attributed to the oceanic N(2)O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N(2)O source. PMID:21798895

  7. Moisture and temperature controls on nitrification differ among ammonia oxidizer communities from three alpine soil habitats

    USGS Publications Warehouse

    Osborne, Brooke B; Baron, Jill S.; Wallenstein, Matthew D.

    2015-01-01

    Climate change is altering the timing and magnitude of biogeochemical fluxes in many high elevation ecosystems. The consequent changes in alpine nitrification rates have the potential to influence ecosystem scale responses. In order to better understand how changing temperature and moisture conditions may influence ammonia oxidizers and nitrification activity, we conducted laboratory incubations on soils collected in a Colorado watershed from three alpine habitats (glacial outwash, talus, and meadow). We found that bacteria, not archaea, dominated all ammonia oxidizer communities. Nitrification increased with moisture in all soils and under all temperature treatments. However, temperature was not correlated with nitrification rates in all soils. Site-specific temperature trends suggest the development of generalist ammonia oxidizer communities in soils with greater in situ temperature fluctuations and specialists in soils with more steady temperature regimes. Rapidly increasing temperatures and changing soil moisture conditions could explain recent observations of increased nitrate production in some alpine soils.

  8. Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota.

    PubMed

    Kozlowski, Jessica A; Stieglmeier, Michaela; Schleper, Christa; Klotz, Martin G; Stein, Lisa Y

    2016-08-01

    Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76(T) exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196(T). In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions. PMID:26882267

  9. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta.

    PubMed

    Damashek, Julian; Smith, Jason M; Mosier, Annika C; Francis, Christopher A

    2014-01-01

    Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic

  10. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta

    PubMed Central

    Damashek, Julian; Smith, Jason M.; Mosier, Annika C.; Francis, Christopher A.

    2015-01-01

    Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic

  11. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    NASA Astrophysics Data System (ADS)

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-11-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g-1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  12. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    PubMed Central

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  13. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

    PubMed

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  14. In-vitro activity of newer quinolones against aerobic bacteria.

    PubMed

    Auckenthaler, R; Michéa-Hamzehpour, M; Pechère, J C

    1986-04-01

    Nalidixic and five newer 4-quinolones, ciprofloxacin, enoxacin, norfloxacin, ofloxacin and pefloxacin were tested against 576 recent clinical aerobic bacterial isolates. The 4-quinolones were regularly active (MIC90 less than 4 mg/l) against the following bacteria: Staphylococcus aureus, S. epidermidis, S. saprophyticus, different Enterobacteriaceae, Haemophilus influenzae, Campylobacter jejuni, Pseudomonas aeruginosa, Agrobacter spp., Aeromonas spp., Plesiomonas spp., Neisseria meningitidis. Other bacteria were usually intermediately susceptible or resistant: different streptococci, Listeria monocytogenes, Nocardia asteroides, P. maltophilia, Achromobacter xylosoxydans and Alcaligenes denitrificans. Ciprofloxacin was the most potent compound, followed by ofloxacin and pefloxacin, norfloxacin and enoxacin being less active. All the 4-quinolones were much more active than nalidixic acid. The MBC/MIC ratios of the 4-quinolones were between 1 and 2 with a majority of strains, and between 2 and 3 with Streptococcus agalactiae, Str. faecalis and L. monocytogenes. A two- to eight-fold increase of MIC was observed by increasing the inoculum 10,000-fold with most of the strains tested. Susceptible bacterial population of Klebsiella pneumoniae, Enterobacter cloacae, Serratia marcescens and P. aeruginosa contained more clones resistant to nalidixic acid (10(4) to 10(8) at four times the MIC) than to 4-quinolones (10(5) to 10(9) at four times the MIC). Supplementing the media with MgSO4 produced smaller inhibition zone diameters with a disc diffusion method than those obtained with non-supplemented agar, with all quinolone or strains. Less regular effect, or no effect was obtained after supplementation with ZnSO4 or Ca(NO3)2. PMID:2940214

  15. D1FHS, the Type Strain of the Ammonia-Oxidizing Bacterium Nitrosococcus wardiae spec. nov.: Enrichment, Isolation, Phylogenetic, and Growth Physiological Characterization

    PubMed Central

    Wang, Lin; Lim, Chee Kent; Dang, Hongyue; Hanson, Thomas E.; Klotz, Martin G.

    2016-01-01

    An ammonia-oxidizing bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4T. The average nucleotide identity between the genomes of strain D1FHS and N. halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic ammonia-oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37°C in dark. Because pertinent conditions for other studied Nitrosococcus spp. are 100–200 mM ammonium and <700 mM NaCl at pH of 7.5 to 8.0 and at 28–32°C, D1FHS is physiologically distinct from other Nitrosococcus spp. in terms of substrate, salt, and thermal tolerance. PMID:27148201

  16. Prevalence of Nitrosomonas cluster 7 populations in the ammonia-oxidizing community of a submerged membrane bioreactor treating urban wastewater under different operation conditions.

    PubMed

    Cerrone, F; Poyatos, J M; Molina-Muñoz, M; Cortés-Lorenzo, C; González-López, J; Rodelas, B

    2013-07-01

    A pilot-scale ultrafiltration membrane bioreactor (MBR) was used for the aerobic treatment of urban wastewater in four experimental stages influenced by seasonal temperature and different sets of operation conditions. The structure of the ammonia-oxidizing bacteria (AOB) community was profiled by temperature gradient gel electrophoresis (TGGE), based on the amplification and separation of partial ammonia-monoxygenase subunit A (amoA) genes. Canonical correspondence analysis revealed that temperature, hydraulic retention time and percentage of ammonia removal had a significant effect on the fingerprints of AOB communities. Phylogenetic analysis conducted on amoA/AmoA sequences of reamplified TGGE bands showed, however, that closely related ammonia-oxidizing populations inhabited the sludge of the MBR in all experimental stages. Nitrosomonas cluster 7 populations (N. europaea-N. eutropha cluster) prevailed under all conditions tested, even when the MBR was operated under complete biomass retention or at low temperatures, suggesting that the high ammonia concentrations in the system were determinant to select r-strategist AOB. PMID:22976820

  17. Evaluation of the petrifilm aerobic count plate for enumeration of aerobic marine bacteria from seawater and Caulerpa lentillifera.

    PubMed

    Kudaka, Jun; Horii, Toru; Tamanaha, Koji; Itokazu, Kiyomasa; Nakamura, Masaji; Taira, Katsuya; Nidaira, Minoru; Okano, Sho; Kitahara, Akio

    2010-08-01

    The enumeration and evaluation of the activity of marine bacteria are important in the food industry. However, detection of marine bacteria in seawater or seafood has not been easy. The Petrifilm aerobic count plate (ACP) is a ready-to-use alternative to the traditional enumeration media used for bacteria associated with food. The purpose of this study was to evaluate the usefulness of a simple detection and enumeration method utilizing the Petrifilm ACP for enumeration of aerobic marine bacteria from seawater and an edible seaweed, Caulerpa lentillifera. The efficiency of enumeration of total aerobic marine bacteria on Petrifilm ACP was compared with that using the spread plate method on marine agar with 80 seawater and 64 C. lentillifera samples. With sterile seawater as the diluent, a close correlation was observed between the method utilizing Petrifilm ACP and that utilizing the conventional marine agar (r=0.98 for seawater and 0.91 for C. lentillifera). The Petrifilm ACP method was simpler and less time-consuming than the conventional method. These results indicate that Petrifilm ACP is a suitable alternative to conventional marine agar for enumeration of marine microorganisms in seawater and C. lentillifera samples. PMID:20819367

  18. Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis

    PubMed Central

    2016-01-01

    The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation. PMID:27046099

  19. Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae

    PubMed Central

    Trias, Rosalia; García-Lledó, Arantzazu; Sánchez, Noemí; López-Jurado, José Luis; Hallin, Sara

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for O. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions. PMID:22081571

  20. Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis.

    PubMed

    Men, Yujie; Han, Ping; Helbling, Damian E; Jehmlich, Nico; Herbold, Craig; Gulde, Rebekka; Onnis-Hayden, Annalisa; Gu, April Z; Johnson, David R; Wagner, Michael; Fenner, Kathrin

    2016-05-01

    The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation. PMID:27046099

  1. Abundance and diversity of ammonia-oxidizing microorganisms in the sediments of Jinshan Lake.

    PubMed

    Liu, Biao; Li, Yimin; Zhang, Jinping; Zhou, Xiaohong; Wu, Chundu

    2014-11-01

    Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH4-N, NO3-N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment. PMID:25008777

  2. Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea

    PubMed Central

    Lu, Lu; Han, Wenyan; Zhang, Jinbo; Wu, Yucheng; Wang, Baozhan; Lin, Xiangui; Zhu, Jianguo; Cai, Zucong; Jia, Zhongjun

    2012-01-01

    The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, 15N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and forest soil (pH 5.4) and was inhibited by acetylene. Nitrification activity was significantly stimulated by urea fertilization and coupled well with abundance changes in archaeal amoA genes in acidic soils. Pyrosequencing of 16S rRNA genes at whole microbial community level demonstrates the active growth of AOA in urea-amended soils. Molecular fingerprinting further shows that changes in denaturing gradient gel electrophoresis fingerprint patterns of archaeal amoA genes are paralleled by nitrification activity changes. However, bacterial amoA and 16S rRNA genes of AOB were not detected. The results strongly suggest that archaeal ammonia oxidation is supported by hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate nitrification in two acidic soils tested. PMID:22592820

  3. Multiple factors affect diversity and abundance of ammonia-oxidizing microorganisms in iron mine soil.

    PubMed

    Xing, Yi; Si, Yan-Xiao; Hong, Chen; Li, Yang

    2015-07-01

    Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. In this study, four soil samples collected from a desert zone in an iron-exploration area and others from farmland and planted forest soil in an iron mine surrounding area. We analyzed the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in iron-mining area near the Miyun reservoir using ammonia monooxygenase. A subunit gene (amoA) as molecular biomarker. Quantitative polymerase chain reaction was applied to explore the relationships between the abundance of AOA and AOB and soil physicochemical parameters. The results showed that AOA were more abundant than AOB and may play a more dominant role in the ammonia-oxidizing process in the whole region. PCR-denaturing gradient gel electrophoresis was used to analyze the structural changes of AOA and AOB. The results showed that AOB were much more diverse than AOA. Nitrosospira cluster three constitute the majority of AOB, and AOA were dominated by group 1.1b in the soil. Redundancy analysis was performed to explore the physicochemical parameters potentially important to AOA and AOB. Soil characteristics (i.e. water, ammonia, organic carbon, total nitrogen, available phosphorus, and soil type) were proposed to potentially contribute to the distributions of AOB, whereas Cd was also closely correlated to the distributions of AOB. The community of AOA correlated with ammonium and water contents. These results highlight the importance of multiple drivers in microbial niche formation as well as their affect on ammonia oxidizer composition, both which have significant consequences for ecosystem nitrogen functioning. PMID:25860433

  4. The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger.

    PubMed

    Martens-Habbena, Willm; Qin, Wei; Horak, Rachel E A; Urakawa, Hidetoshi; Schauer, Andrew J; Moffett, James W; Armbrust, E Virginia; Ingalls, Anitra E; Devol, Allan H; Stahl, David A

    2015-07-01

    Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia-oxidizing archaea (AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide (NO) by Nitrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi-steady state concentrations between 0.05 and 0.08 μM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea (ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub-micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism. PMID:25420929

  5. Antibiotic Susceptibility Pattern of Aerobic and Anaerobic Bacteria Isolated From Surgical Site Infection of Hospitalized Patients

    PubMed Central

    Akhi, Mohammad Taghi; Ghotaslou, Reza; Beheshtirouy, Samad; Asgharzadeh, Mohammad; Pirzadeh, Tahereh; Asghari, Babak; Alizadeh, Naser; Toloue Ostadgavahi, Ali; Sorayaei Somesaraei, Vida; Memar, Mohammad Yousef

    2015-01-01

    Background: Surgical Site Infections (SSIs) are infections of incision or deep tissue at operation sites. These infections prolong hospitalization, delay wound healing, and increase the overall cost and morbidity. Objectives: This study aimed to investigate anaerobic and aerobic bacteria prevalence in surgical site infections and determinate antibiotic susceptibility pattern in these isolates. Materials and Methods: One hundred SSIs specimens were obtained by needle aspiration from purulent material in depth of infected site. These specimens were cultured and incubated in both aerobic and anaerobic condition. For detection of antibiotic susceptibility pattern in aerobic and anaerobic bacteria, we used disk diffusion, agar dilution, and E-test methods. Results: A total of 194 bacterial strains were isolated from 100 samples of surgical sites. Predominant aerobic and facultative anaerobic bacteria isolated from these specimens were the members of Enterobacteriaceae family (66, 34.03%) followed by Pseudomonas aeruginosa (26, 13.4%), Staphylococcus aureus (24, 12.37%), Acinetobacter spp. (18, 9.28%), Enterococcus spp. (16, 8.24%), coagulase negative Staphylococcus spp. (14, 7.22%) and nonhemolytic streptococci (2, 1.03%). Bacteroides fragilis (26, 13.4%), and Clostridium perfringens (2, 1.03%) were isolated as anaerobic bacteria. The most resistant bacteria among anaerobic isolates were B. fragilis. All Gram-positive isolates were susceptible to vancomycin and linezolid while most of Enterobacteriaceae showed sensitivity to imipenem. Conclusions: Most SSIs specimens were polymicrobial and predominant anaerobic isolate was B. fragilis. Isolated aerobic and anaerobic strains showed high level of resistance to antibiotics. PMID:26421133

  6. Moisture and temperature controls on nitrification differ among ammonia oxidizer communities from three alpine soil habitats

    NASA Astrophysics Data System (ADS)

    Osborne, Brooke B.; Baron, Jill S.; Wallenstein, Matthew D.

    2016-03-01

    Climate change is altering the timing and magnitude of biogeochemical fluxes in many highelevation ecosystems. The consequent changes in alpine nitrification rates have the potential to influence ecosystem scale responses. In order to better understand how changing temperature and moisture conditions may influence ammonia oxidizers and nitrification activity, we conducted laboratory incubations on soils collected in a Colorado watershed from three alpine habitats (glacial outwash, talus, and meadow). We found that bacteria, not archaea, dominated all ammonia oxidizer communities. Nitrification increased with moisture in all soils and under all temperature treatments. However, temperature was not correlated with nitrification rates in all soils. Site-specific temperature trends suggest the development of generalist ammonia oxidzer communities in soils with greater in situ temperature fluctuations and specialists in soils with more steady temperature regimes. Rapidly increasing temperatures and changing soil moisture conditions could explain recent observations of increased nitrate production in some alpine soils.

  7. Velvet pad surface sampling of anaerobic and aerobic bacteria: an in vitro laboratory model.

    PubMed Central

    Raahave, D; Friis-Møller, A

    1982-01-01

    Velvet pads have been evaluated in an experimental, laboratory model, simulating intraoperative sampling of Staphylococcus epidermis, Escherichia coli and Bacteroides fragilis. After sampling, the pad was placed in a transport medium and kept in an anaerobic atmosphere, before being shaken and rinsed, followed by anaerobic and aerobic culture. This technique permitted quantitatively high recoveries of the test bacteria. Velvet pad sampling could be a measure to determine the density of aerobic and anaerobic bacteria during operation in an effort to predict the risk of postoperative wound sepsis. Images PMID:6757273

  8. Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

    PubMed Central

    Sonthiphand, Puntipar; Cejudo, Eduardo; Schiff, Sherry L.

    2013-01-01

    The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3− or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities. PMID:24056472

  9. Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada.

    PubMed

    Sonthiphand, Puntipar; Cejudo, Eduardo; Schiff, Sherry L; Neufeld, Josh D

    2013-12-01

    The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3- or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities. PMID:24056472

  10. Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean.

    PubMed

    Luo, Zhu-Hua; Xu, Wei; Li, Meng; Gu, Ji-Dong; Zhong, Tian-Hua

    2015-08-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean. PMID:26014493

  11. [Microbial diversity and ammonia-oxidizing microorganism of a soil sample near an acid mine drainage lake].

    PubMed

    Liu, Ying; Wang, Li-Hua; Hao, Chun-Bo; Li, Lu; Li, Si-Yuan; Feng, Chuan-Ping

    2014-06-01

    The main physicochemical parameters of the soil sample which was collected near an acid mine drainage reservoir in Anhui province was analyzed. The microbial diversity and community structure was studied through the construction of bacteria and archaea 16S rRNA gene clone libraries and ammonia monooxygenase gene clone library of archaea. The functional groups which were responsible for the process of ammonia oxidation were also discussed. The results indicated that the soil sample had extreme low pH value (pH < 3) and high ions concentration, which was influenced by the acid mine drainage (AMD). All the 16S rRNA gene sequences of bacteria clone library fell into 11 phyla, and Acidobacteria played the most significant role in the ecosystem followed by Verrucomicrobia. A great number of acidophilic bacteria existed in the soil sample, such as Candidatus Koribacter versatilis and Holophaga sp.. The archaea clone library consisted of 2 phyla (Thaumarchaeota and Euryarchaeota). The abundance of Thaumarchaeota was remarkably higher than Euryarchaeota. The ammonia oxidation in the soil environment was probably driven by ammonia-oxidizing archaea, and new species of ammonia-oxidizing archaea existed in the soil sample. PMID:25158511

  12. Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils.

    PubMed

    Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

    2015-10-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH. PMID:26257304

  13. Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

    NASA Astrophysics Data System (ADS)

    Fuchslueger, L.; Kastl, E.-M.; Bauer, F.; Kienzl, S.; Hasibeder, R.; Ladreiter-Knauss, T.; Schmitt, M.; Bahn, M.; Schloter, M.; Richter, A.; Szukics, U.

    2014-11-01

    Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammonia-oxidizer abundances in soil without drought history. To this end we conducted rain-exclusion experiments at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for potential gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia-oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Drought induced different responses at the two studied sites. At the managed meadow drought increased NH4+ immobilization rates and NH4+ concentrations in the soil water solution, but led to a reduction of AOA abundance compared to controls. At the abandoned site gross nitrification and NO3- immobilization rates decreased during drought, while AOB and AOA abundances remained stable. Rewetting had only minor, short-term effects on the parameters that had been affected by drought. Seven weeks after the end of drought no differences to control plots could be detected. Thus, our findings demonstrated that in mountain grasslands drought had distinct transient effects on soil nitrogen cycling and ammonia-oxidizers, which could have been related to a niche differentiation of AOB and AOA with increasing NH4+ levels. However, the effect strength of drought was modulated by grassland management.

  14. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

    PubMed Central

    Kim, Jong-Geol; Park, Soo-Je; Sinninghe Damsté, Jaap S.; Schouten, Stefan; Rijpstra, W. Irene C.; Jung, Man-Young; Kim, So-Jeong; Gwak, Joo-Han; Hong, Heeji; Si, Ok-Ja; Lee, SangHoon; Madsen, Eugene L.; Rhee, Sung-Keun

    2016-01-01

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes. PMID:27339136

  15. Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils.

    PubMed

    Jung, Man-Young; Well, Reinhard; Min, Deullae; Giesemann, Anette; Park, Soo-Je; Kim, Jong-Geol; Kim, So-Jeong; Rhee, Sung-Keun

    2014-05-01

    N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ(15)N(bulk) and δ(18)O -N2O of soil AOA strains were 13-30%, -13 to -35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A (15)N-NH4(+)-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA. PMID:24225887

  16. Ammonia-oxidizer communities in an agricultural soil treated with contrasting nitrogen sources

    PubMed Central

    Habteselassie, Mussie Y.; Xu, Li; Norton, Jeanette M.

    2013-01-01

    The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for six seasons with contrasting nitrogen (N) sources. Molecular tools based on the genes encoding ammonia monooxygenase were used to characterize the ammonia oxidizer (AO) communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control), dairy waste compost, liquid dairy waste (LW), and ammonium sulfate (AS) treatments at approximately 100 and 200 kg available N ha-1 over 6 years. The N treatment affected the quantity of AO based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 107, 2.5 × 107, and 2.1 × 107copies g-1 soil, respectively) than in the control (8.1 × 106 copies g-1 soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 107 copies g-1 soil, average). The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of 6 years of contrasting nitrogen sources applications caused changes in AO abundance while the community composition remained relatively stable for both AOB and AOA. PMID:24223575

  17. Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

    PubMed Central

    Jung, Man-Young; Well, Reinhard; Min, Deullae; Giesemann, Anette; Park, Soo-Je; Kim, Jong-Geol; Kim, So-Jeong; Rhee, Sung-Keun

    2014-01-01

    N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ15Nbulk and δ18O -N2O of soil AOA strains were 13–30%, −13 to −35% and 22–36%, respectively, and strains MY1–3 and other soil AOA strains had distinct isotopic signatures. A 15N-NH4+-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA. PMID:24225887

  18. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea.

    PubMed

    Kim, Jong-Geol; Park, Soo-Je; Sinninghe Damsté, Jaap S; Schouten, Stefan; Rijpstra, W Irene C; Jung, Man-Young; Kim, So-Jeong; Gwak, Joo-Han; Hong, Heeji; Si, Ok-Ja; Lee, SangHoon; Madsen, Eugene L; Rhee, Sung-Keun

    2016-07-12

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes. PMID:27339136

  19. Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

    NASA Astrophysics Data System (ADS)

    Fuchslueger, L.; Kastl, E.-M.; Bauer, F.; Kienzl, S.; Hasibeder, R.; Ladreiter-Knauss, T.; Schmitt, M.; Bahn, M.; Schloter, M.; Richter, A.; Szukics, U.

    2014-06-01

    Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammonia-oxidizer abundances. To this end we conducted a rain-exclusion experiment at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Our results showed that the response to drought differed between the two sites. Effects were stronger at the managed meadow, where NH4+ immobilization rates increased and AOA abundances decreased. At the abandoned site gross nitrification and NO3- immobilization rates decreased during drought, while neither AOB, nor AOA abundances were affected. The different responses of the two sites to drought were likely related to site specific differences, such as soil organic matter content, nitrogen pools and absolute soil water content, resulting from differences in land-management. At both sites rewetting after drought had only minor short-term effects on the parameters that had been affected by drought, and seven weeks after the drought no effects of drought were detectable anymore. Thus, our findings indicate that drought can have distinct transient effects on soil nitrogen cycling and ammonia-oxidizer abundances in mountain grasslands and that the effect strength could be modulated by grassland management.

  20. Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary

    PubMed Central

    Stegman, Monica R; Cottrell, Matthew T; Kirchman, David L

    2014-01-01

    Aerobic anoxygenic phototrophic (AAP) bacteria are well known to be abundant in estuaries, coastal regions and in the open ocean, but little is known about their activity in any aquatic ecosystem. To explore the activity of AAP bacteria in the Delaware estuary and coastal waters, single-cell 3H-leucine incorporation by these bacteria was examined with a new approach that combines infrared epifluorescence microscopy and microautoradiography. The approach was used on samples from the Delaware coast from August through December and on transects through the Delaware estuary in August and November 2011. The percent of active AAP bacteria was up to twofold higher than the percentage of active cells in the rest of the bacterial community in the estuary. Likewise, the silver grain area around active AAP bacteria in microautoradiography preparations was larger than the area around cells in the rest of the bacterial community, indicating higher rates of leucine consumption by AAP bacteria. The cell size of AAP bacteria was 50% bigger than the size of other bacteria, about the same difference on average as measured for activity. The abundance of AAP bacteria was negatively correlated and their activity positively correlated with light availability in the water column, although light did not affect 3H-leucine incorporation in light–dark experiments. Our results suggest that AAP bacteria are bigger and more active than other bacteria, and likely contribute more to organic carbon fluxes than indicated by their abundance. PMID:24824666

  1. Conversion of upland to paddy field specifically alters the community structure of archaeal ammonia oxidizers in an acid soil

    NASA Astrophysics Data System (ADS)

    Alam, M. S.; Ren, G. D.; Lu, L.; Zheng, Y.; Peng, X. H.; Jia, Z. J.

    2013-08-01

    The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the major energy-generating compounds (i.e., ammonia and oxygen). The diversification of AOA and AOB communities along ecological gradients of substrate availability in a complex environment have been much debated but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB upon conversion of an upland field to a paddy field and long-term field fertilization in an acid soil. Real-time quantitative polymerase chain reaction of ammonia monooxygenase (amoA) genes demonstrated that the abundance of AOA was significantly stimulated after conversion of upland to paddy soils for more than 100 yr, whereas a slight decline in AOB numbers was observed. Denaturing gradient gel electrophoresis fingerprints of amoA genes further revealed remarkable changes in the community compositions of AOA after conversion of aerobic upland to flooded paddy field. Sequencing analysis revealed that upland soil was dominated by AOA within the soil group 1.1b lineage, whereas the marine group 1.1a-associated lineage predominated in AOA communities in paddy soils. Irrespective of whether the soil was upland or paddy soil, long-term field fertilization led to increased abundance of amoA genes in AOA and AOB compared with control treatments (no fertilization), whereas archaeal amoA gene abundances outnumbered their bacterial counterparts in all samples. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster-3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization treatment. The results of this study suggest that the marine group 1.1a-associated AOA will be better adapted to the flooded paddy field than AOA ecotypes of the soil group 1.1b lineage, and indicate that long-term flooding is the dominant selective force driving the

  2. Stimulating accumulation of nitrifying bacteria in porous carrier by addition of inorganic carbon in a continuous-flow fluidized bed wastewater treatment reactor.

    PubMed

    Jun, B H; Tanji, Y; Unno, H

    2000-01-01

    Porous polyurethane carrier particles have been successfully applied for microbial immobilization to simultaneously remove carbonaceous and nitrogenous substances from wastewater by a fill-and-draw operation. This reactor system was extended to a continuous-flow operation mode, by which inorganic carbon (IC) was supplemented in order to stimulate the growth of autotrophic nitrifying bacteria. By addition of sodium bicarbonate, the ammonia oxidation reaction proceeded remarkably in the porous particle fluidized bed reactor, while a small increase in the nitrification was observed in a reactor with suspended microbes. Dissolved oxygen profile was obtained using an oxygen microelectrode to measure the microbial consumption of oxygen in the porous carrier. The size of ammonia-oxidizing bacterial populations in the carrier was proportional to the volume of the aerobic region of the carrier. The aerobic region decreased with the increase in sodium bicarbonate concentration, which improved the ammonia-oxidizing activity of retained nitrifiers in the carrier. The maximum ammonia oxidation rate was up to 55.6 gN/m3/h within the aerobic region of the carrier under the following feed conditions: 100 mg/l of total organic compound, 55 mg/l of ammonium concentration and 48 mg/l of inorganic carbon. PMID:16232755

  3. [The phylogenetic diversity of aerobic organotrophic bacteria from the Dagan high-temperature oil field].

    PubMed

    Nazina, T N; Sokolova, D Sh; Shestakova, N M; Grigor'ian, A A; Mikhaĭlova, E M; Babich, T L; Lysenko, A M; Turova, T P; Poltaraus, A B; Feng, Tsin'syan; Ni, Fangtian; Beliaev, S S

    2005-01-01

    The distribution and species diversity of aerobic organotrophic bacteria in the Dagan high-temperature oil field (China), which is exploited via flooding, have been studied. Twenty-two strains of the most characteristic thermophilic and mesophilic aerobic organotrophic bacteria have been isolated from the oil stratum. It has been found that, in a laboratory, the mesophilic and thermophilic isolates grow in the temperature, pH, and salinity ranges characteristic of the injection well near-bottom zones or of the oil stratum, respectively, and assimilate a wide range of hydrocarbons, fatty acids, lower alcohols, and crude oil, thus exhibiting adaptation to the environment. Using comparative phylogenetic 16S rRNA analysis, the taxonomic affiliation of the isolates has been established. The aerobic microbial community includes gram-positive bacteria with a high and low G+C content of DNA, and gamma and beta subclasses of Proteobacteria. The thermophilic bacteria belong to the genera Geobacillus and Thermoactinomyces, and the mesophilic strains belong to the genera Bacillus, Micrococcus, Cellulomonas, Pseudomonas, and Acinetobacter. The microbial community of the oil stratum is dominated by known species of the genus Geobacillus (G. subterraneus, G. stearothermophilus, and G. thermoglucosidasius) and a novel species "Geobacillus jurassicus." A number of novel thermophilic oil-oxidizing bacilli have been isolated. PMID:16119855

  4. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

    SciTech Connect

    Stein, Lisa Y; Arp, D J; Berube, PM; Chain, Patrick S. G.; Hauser, Loren John; Jetten, MSM; Klotz, Martin G; Larimer, Frank W; Norton, Jeanette M.; Op den Camp, HJM; Shin, M; Wei, Xueming

    2007-12-01

    Analysis of the structure and inventory of the genome of Nitrosomonas eutropha C91 revealed distinctive features that may explain the adaptation of N. eutropha-like bacteria to N-saturated ecosystems. Multiple gene-shuffling events are apparent, including mobilized and replicated transposition, as well as plasmid or phage integration events into the 2.66 Mbp chromosome and two plasmids (65 and 56 kbp) of N. eutropha C91. A 117 kbp genomic island encodes multiple genes for heavy metal resistance, including clusters for copper and mercury transport, which are absent from the genomes of other ammonia-oxidizing bacteria (AOB). Whereas the sequences of the two ammonia monooxygenase and three hydroxylamine oxidoreductase gene clusters in N. eutropha C91 are highly similar to those of Nitrosomonas europaea ATCC 19718, a break of synteny in the regions flanking these clusters in each genome is evident. Nitrosomonas eutropha C91 encodes four gene clusters for distinct classes of haem-copper oxidases, two of which are not found in other aerobic AOB. This diversity of terminal oxidases may explain the adaptation of N. eutropha to environments with variable O2 concentrations and/or high concentrations of nitrogen oxides. As with N. europaea, the N. eutropha genome lacks genes for urease metabolism, likely disadvantaging nitrosomonads in low-nitrogen or acidic ecosystems. Taken together, this analysis revealed significant genomic variation between N. eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization.

  5. Nitrosomonas stercoris sp. nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure

    PubMed Central

    Nakagawa, Tatsunori; Takahashi, Reiji

    2015-01-01

    Among ammonia-oxidizing bacteria, Nitrosomonas eutropha-like microbes are distributed in strongly eutrophic environments such as wastewater treatment plants and animal manure. In the present study, we isolated an ammonia-oxidizing bacterium tolerant of high ammonium levels, designated strain KYUHI-ST, from composted cattle manure. Unlike the other known Nitrosomonas species, this isolate grew at 1,000 mM ammonium. Phylogenetic analyses based on 16S rRNA and amoA genes indicated that the isolate belonged to the genus Nitrosomonas and formed a unique cluster with the uncultured ammonia oxidizers found in wastewater systems and animal manure composts, suggesting that these ammonia oxidizers contributed to removing higher concentrations of ammonia in strongly eutrophic environments. Based on the physiological and phylogenetic data presented here, we propose and call for the validation of the provisional taxonomic assignment Nitrosomonas stercoris, with strain KYUHI-S as the type strain (type strain KYUHI-ST = NBRC 110753T = ATCC BAA-2718T). PMID:26156554

  6. Spatial and temporal diversity and abundance of ammonia oxidizers in semi-arid and arid soils: indications for a differential seasonal effect on archaeal and bacterial ammonia oxidizers.

    PubMed

    Sher, Yonatan; Zaady, Eli; Nejidat, Ali

    2013-12-01

    Besides water, nitrogen is the limiting factor for biomass production in arid ecosystems. Global climatic changes are exacerbating aridity levels, and the response of nitrogen-transforming microorganisms to these changes is not clear yet. Using semi-arid and arid ecosystems as surrogates for conditions of increased aridity, we investigated the activity, abundance, and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in arid and semi-arid soils. Ammonia oxidation potentials were higher during the winter in both sites than in the summer, and higher nitrate concentrations were measured in the arid soil than in the semi-arid soil. Denaturing gradient gel electrophoresis (DGGE) patterns of AOB 16S rRNA gene fragments were similar for the arid and semi-arid soils with no seasonal variations. In contrast, the DGGE patterns of the AOA amoA gene fragments differed between the sites and a soil transfer experiment suggested that these differences are possibly associated with soil type. AOB numbers were higher during the winter than in the summer, while AOA numbers were higher during the summer. The results indicate the resistance of AOB and AOA community structure to arid conditions, albeit with seasonal variations in their abundance. Together, the results suggest the resilience of nitrification activity to increased aridity level. PMID:23855990

  7. Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre

    PubMed Central

    Cottrell, Matthew T.; Mannino, Antonio; Kirchman, David L.

    2006-01-01

    The abundance of aerobic anoxygenic phototrophic (AAP) bacteria, cyanobacteria, and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific Gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic Ocean but only 5% or less in the Pacific Ocean. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than that of Prochlorococcus spp. and 10-fold higher than that of Synechococcus spp. In contrast, Prochlorococcus spp. outnumbered AAP bacteria 5- to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP bacterial genera (Erythrobacter and Roseobacter spp.). Concentrations of bacteriochlorophyll a (BChl a) were low (∼1%) compared to those of chlorophyll a in the North Atlantic. Although the BChl a content of AAP bacteria per cell was typically 20- to 250-fold lower than the divinyl-chlorophyll a content of Prochlorococcus, the pigment content of AAP bacteria approached that of Prochlorococcus in shelf break water. Our results suggest that AAP bacteria can be quite abundant in some oceanic regimes and that their distribution in the water column is consistent with phototrophy. PMID:16391092

  8. Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre. Revised

    NASA Technical Reports Server (NTRS)

    Cottrell, Matthew T.; Mannino, Antonio; Kirchman, David L.

    2005-01-01

    The abundance of aerobic anoxygenic phototrophic (AM) bacteria, cyanobacteria and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic but only 5% or less in the Pacific. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than Prochlorococcus and 10-folder higher than Synechococcus. In contrast, Prochlorococcus outnumbered AAP bacteria 5- to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. Concentrations of bacteriochlorophyll a (BChl a) were low (approx.1%) compared to chlorophyll a. Although the BChl a content of AAP bacteria per cell was typically 20- to 250-fold lower than the divinyl-chlorophyll a content of Prochlorococcus, in shelf break water the pigment content of AAP bacteria approached that of Prochlorococcus. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP genera (Erythrobacter and Roseobacter spp.). The distribution of AAP bacteria in the water column, which was similar in the Atlantic and the Pacific, was consistent with phototrophy.

  9. Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan

    PubMed Central

    Hirose, Setsuko; Matsuura, Katsumi; Haruta, Shin

    2016-01-01

    The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms. PMID:27453124

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

    PubMed Central

    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. PMID:22787457

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

    PubMed

    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. PMID:22787457

  12. Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production.

    PubMed

    Garcia-Chaves, Maria C; Cottrell, Matthew T; Kirchman, David L; Ruiz-González, Clara; Del Giorgio, Paul A

    2016-07-01

    Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance. PMID:26771928

  13. Binary Interactions of Antagonistic Bacteria with Candida albicans Under Aerobic and Anaerobic Conditions.

    PubMed

    Benadé, Eliska; Stone, Wendy; Mouton, Marnel; Postma, Ferdinand; Wilsenach, Jac; Botha, Alfred

    2016-04-01

    We used both aerobic and anaerobic liquid co-cultures, prepared with Luria Bertani broth, to study the effect of bacteria on the survival of Candida albicans in the external environment, away from an animal host. The bacteria were represented by Aeromonas hydrophila, Bacillus cereus, Bacillus subtilis, Clostridium, Enterobacter, Klebsiella pneumoniae, Kluyvera ascorbata and Serratia marcescens. Under aerobic conditions, the yeast's growth was inhibited in the presence of bacterial growth; however, under anaerobic conditions, yeast and bacterial growth in co-cultures was similar to that observed for pure cultures. Subsequent assays revealed that the majority of bacterial strains aerobically produced extracellular hydrolytic enzymes capable of yeast cell wall hydrolysis, including chitinases and mannan-degrading enzymes. In contrast, except for the A. hydrophila strain, these enzymes were not detected in anaerobic bacterial cultures, nor was the antimicrobial compound prodigiosin found in anaerobic cultures of S. marcescens. When we suspended C. albicans cells in crude extracellular enzyme preparations from K. pneumoniae and S. marcescens, we detected no negative effect on yeast viability. However, we found that these preparations enhance the toxicity of prodigiosin towards the yeast, especially in combination with mannan-degrading enzymes. Analyses of the chitin and mannan content of yeast cell walls revealed that less chitin was produced under anaerobic than aerobic conditions; however, the levels of mannan, known for its low permeability, remained the same. The latter phenomenon, as well as reduced production of the bacterial enzymes and prodigiosin, may contribute to anaerobic growth and survival of C. albicans in the presence of bacteria. PMID:26566932

  14. Monochloramine Cometabolism by Ammonia-Oxidizing Bacteria. Report #4341

    EPA Science Inventory

    Chloramine use is widespread in United States (US) drinking water distribution systems as a secondary disinfectant. In a recent survey of water utilities, 30% of the respondents used chloramines to maintain distribution system residual (AWWA Water Quality and Technology Division...

  15. Role of phosphate solubilizing bacteria on rock phosphate solubility and growth of aerobic rice.

    PubMed

    Panhwar, Q A; Radziah, O; Zaharah, A R; Sariah, M; Razi, I Mohd

    2011-09-01

    Use of phosphate-solubilizing bacteria (PSB) as inoculants has concurrently increased phosphorous uptake in plants and improved yields in several crop species. The ability of PSB to improve growth of aerobic rice (Oryza sativa L.) through enhanced phosphorus (P) uptake from Christmas island rock phosphate (RP) was studied in glasshouse experiments. Two isolated PSB strains; Bacillus spp. PSB9 and PSB16, were evaluated with RP treatments at 0, 30 and 60 kg ha(-1). Surface sterilized seeds of aerobic rice were planted in plastic pots containing 3 kg soil and the effect of treatments incorporated at planting were observed over 60 days of growth. The isolated PSB strains (PSB9 and PSB16) solubilized significantly high amounts of P (20.05-24.08 mg kg(-1)) compared to non-inoculated (19-23.10 mg kg(-1)) treatments. Significantly higher P solubilization (24.08 mg kg(-1)) and plant P uptake (5.31 mg plant(-1)) was observed with the PSB16 strain at the highest P level of 60 kg ha(-1). The higher amounts of soluble P in the soil solution increased P uptake in plants and resulted in higher plant biomass (21.48 g plant(-1)). PSB strains also increased plant height (80 cm) and improved root morphology in aerobic rice. The results showed that inoculation of aerobic rice with PSB improved phosphate solubilizing activity of incorporated RP. PMID:22319876

  16. Biodegradation and cometabolic modeling of selected beta blockers during ammonia oxidation.

    PubMed

    Sathyamoorthy, Sandeep; Chandran, Kartik; Ramsburg, C Andrew

    2013-11-19

    Accurate prediction of pharmaceutical concentrations in wastewater effluents requires that the specific biochemical processes responsible for pharmaceutical biodegradation be elucidated and integrated within any modeling framework. The fate of three selected beta blockers-atenolol, metoprolol, and sotalol-was examined during nitrification using batch experiments to develop and evaluate a new cometabolic process-based (CPB) model. CPB model parameters describe biotransformation during and after ammonia oxidation for specific biomass populations and are designed to be integrated within the Activated Sludge Models framework. Metoprolol and sotalol were not biodegraded by the nitrification enrichment culture employed herein. Biodegradation of atenolol was observed and linked to the activity of ammonia-oxidizing bacteria (AOB) and heterotrophs but not nitrite-oxidizing bacteria. Results suggest that the role of AOB in atenolol degradation may be disproportionately more significant than is otherwise suggested by their lower relative abundance in typical biological treatment processes. Atenolol was observed to competitively inhibit AOB growth in our experiments, though model simulations suggest inhibition is most relevant at atenolol concentrations greater than approximately 200 ng·L(-1). CPB model parameters were found to be relatively insensitive to biokinetic parameter selection suggesting the model approach may hold utility for describing pharmaceutical biodegradation during biological wastewater treatment. PMID:24112027

  17. Survival of anaerobic and aerobic bacteria in a nonsupportive gassed transport system.

    PubMed Central

    Chow, A W; Cunningham, P J; Guze, L B

    1976-01-01

    Survival of anaerobic and aerobic bacteria in a commercially available, non-supportive, gassed (oxygen-free) transport container (Anaport) was evaluated quantitatively. Saline-suspended obligate anaerobes survived significantly better in the gassed container in aerobic control tubes (P less than 0.025, t test), and counts were virtually unchanged after 8 h of holding. Similarly, initial counts and relative proportions of a mixture of Bacteroides fragilis and Staphylococcus aureus were maintained for 72 h. The value of the gassed transport system was less apparent when microorganisms were suspended in nutrient broth. The major advantage of the gassed transport system appears to be for holding of specimens collected by saline irrigation. PMID:1254710

  18. Influence of bovine lactoferrin on the growth of selected probiotic bacteria under aerobic conditions.

    PubMed

    Chen, Po-Wen; Ku, Yu-We; Chu, Fang-Yi

    2014-10-01

    Bovine lactoferrin (bLf) is a natural glycoprotein, and it shows broad-spectrum antimicrobial activity. However, reports on the influences of bLf on probiotic bacteria have been mixed. We examined the effects of apo-bLf (between 0.25 and 128 mg/mL) on both aerobic and anaerobic cultures of probiotics. We found that bLf had similar effects on the growth of probiotics under aerobic or anaerobic conditions, and that it actively and significantly (at concentrations of >0.25 mg/mL) retarded the growth rate of Bifidobacterium bifidum (ATCC 29521), B. longum (ATCC 15707), B. lactis (BCRC 17394), B. infantis (ATCC 15697), Lactobacillus reuteri (ATCC 23272), L. rhamnosus (ATCC 53103), and L. coryniformis (ATCC 25602) in a dose-dependent manner. Otherwise, minimal inhibitory concentrations (MICs) were 128 or >128 mg/mL against B. bifidum, B. longum, B. lactis, L. reuteri, and L. rhamnosus (ATCC 53103). With regard to MICs, bLf showed at least four-fold lower inhibitory effect on probiotics than on pathogens. Intriguingly, bLf (>0.25 mg/mL) significantly enhanced the growth of Rhamnosus (ATCC 7469) and L. acidophilus (BCRC 14065) by approximately 40-200 %, during their late periods of growth. Supernatants produced from aerobic but not anaerobic cultures of L. acidophilus reduced the growth of Escherichia coli by about 20 %. Thus, bLf displayed a dose-dependent inhibitory effect on the growth of most probiotic strains under either aerobic or anaerobic conditions. An antibacterial supernatant prepared from the aerobic cultures may have significant practical use. PMID:24916115

  19. Recovery of anaerobic, facultative, and aerobic bacteria from clinical specimens in three anaerobic transport systems.

    PubMed Central

    Helstad, A G; Kimball, J L; Maki, D G

    1977-01-01

    With aspirated specimens from clinical infections, we evaluated the recovery of anaerobic, aerobic, and facultative bacteria in three widely used transport systems: (i) aspirated fluid in a gassed-out tube (FGT), (ii) swab in modified Cary and Blair transport medium (SCB), and (iii) swab in a gassed-out tube (SGT). Transport tubes were held at 25 degrees C and semiquantitatively sampled at 0, 2, 24, and 48 h. Twenty-five clinical specimens yielded 75 anaerobic strains and 43 isolates of facultative and 3 of aerobic bacteria. Only one anaerobic isolate was not recovered in the first 24 h, and then, only in the SGT. At 48 h, 73 anaerobic strains (97%) were recovered in the FGT, 69 (92%) in the SCB, and 64 (85%) in the SGT. Two problems hindered the recovery of anaerobes in the SCB and SGT systems: first die-off of organisms, as evidenced by a decrease in colony-forming units of 20 strains (27%) in the SCB and 25 strains (33%) in the SGT, as compared with 7 strains (9%) in the FGT, over 48 h; and second, overgrowth of facultative bacteria, more frequent with SCB and SGT. The FGT method was clearly superior at 48 h to the SCB and SGT systems in this study and is recommended as the preferred method for transporting specimens for anaerobic culture. PMID:328525

  20. Aerobic Mercury-resistant bacteria alter Mercury speciation and retention in the Tagus Estuary (Portugal).

    PubMed

    Figueiredo, Neusa L; Canário, João; O'Driscoll, Nelson J; Duarte, Aida; Carvalho, Cristina

    2016-02-01

    Aerobic mercury-resistant bacteria were isolated from the sediments of two highly mercury-polluted areas of the Tagus Estuary (Barreiro and Cala do Norte) and one natural reserve area (Alcochete) in order to test their capacity to transform mercury. Bacterial species were identified using 16S rRNA amplification and sequencing techniques and the results indicate the prevalence of Bacillus sp. Resistance patterns to mercurial compounds were established by the determination of minimal inhibitory concentrations. Representative Hg-resistant bacteria were further tested for transformation pathways (reduction, volatilization and methylation) in cultures containing mercury chloride. Bacterial Hg-methylation was carried out by Vibrio fluvialis, Bacillus megaterium and Serratia marcescens that transformed 2-8% of total mercury into methylmercury in 48h. In addition, most of the HgR bacterial isolates showed Hg(2+)-reduction andHg(0)-volatilization resulting 6-50% mercury loss from the culture media. In summary, the results obtained under controlled laboratory conditions indicate that aerobic Hg-resistant bacteria from the Tagus Estuary significantly affect both the methylation and reduction of mercury and may have a dual face by providing a pathway for pollution dispersion while forming methylmercury, which is highly toxic for living organisms. PMID:26461264

  1. The effect of bacteria, enzymes and inulin on fermentation and aerobic stability of corn silage

    PubMed Central

    Peymanfar, S; Kermanshahi, RK

    2012-01-01

    Background and Objectives Ensiling is a conservation method for forage crops. It is based on the fact that anaerobe lactic acid bacteria (LAB) convert watersoluble carbohydrates into organic acids. Therefore, pH decreases and the forage is preserved. The aim of this study was to isolate special kinds of lactic acid bacteria from silage and to study the effect of bacteria, inulin and enzymes as silage additives on the fermentation and aerobic stability of the silage. Materials and Methods The heterofermentative LAB were isolated from corn silages in Broujerd, Iran and biochemically characterized. Acid tolerance was studied by exposure to acidic PBS and growth in bile salt was measured by the spectrophotometric method. Results The results of molecular analysis using 16SrDNA sequences showed that the isolates belonged to Lactobacillus and Enterococcus genera. To enhance stability in acidic environment and against bile salts, microencapsulation with Alginate and Chitosan was used. The Lactobacillus plantarum strains were used as control. The inoculants (1 × 107 cfu/g) alone or in combination with inulin or in combination with enzymes were added to chopped forages and ensiled in 1.5-L anaerobic jars. Conclusion Combination of the isolates Lactobacillus and Enterococcus with inulin and enzymes can improve the aerobic stability of corn silage. PMID:23205249

  2. Phylogenetic and Kinetic Diversity of Aerobic Vinyl Chloride-Assimilating Bacteria from Contaminated Sites

    PubMed Central

    Coleman, Nicholas V.; Mattes, Timothy E.; Gossett, James M.; Spain, Jim C.

    2002-01-01

    Aerobic bacteria that grow on vinyl chloride (VC) have been isolated previously, but their diversity and distribution are largely unknown. It is also unclear whether such bacteria contribute to the natural attenuation of VC at chlorinated-ethene-contaminated sites. We detected aerobic VC biodegradation in 23 of 37 microcosms and enrichments inoculated with samples from various sites. Twelve different bacteria (11 Mycobacterium strains and 1 Nocardioides strain) capable of growth on VC as the sole carbon source were isolated, and 5 representative strains were examined further. All the isolates grew on ethene in addition to VC and contained VC-inducible ethene monooxygenase activity. The Mycobacterium strains (JS60, JS61, JS616, and JS617) all had similar growth yields (5.4 to 6.6 g of protein/mol), maximum specific growth rates (0.17 to 0.23 day−1), and maximum specific substrate utilization rates (9 to 16 nmol/min/mg of protein) with VC. The Nocardioides strain (JS614) had a higher growth yield (10.3 g of protein/mol), growth rate (0.71 day−1), and substrate utilization rate (43 nmol/min/mg of protein) with VC but was much more sensitive to VC starvation. Half-velocity constant (Ks) values for VC were between 0.5 and 3.2 μM, while Ks values for oxygen ranged from 0.03 to 0.3 mg/liter. Our results indicate that aerobic VC-degrading microorganisms (predominantly Mycobacterium strains) are widely distributed at sites contaminated with chlorinated solvents and are likely to be responsible for the natural attenuation of VC. PMID:12450841

  3. Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system.

    PubMed

    Brown, Monisha N; Briones, Aurelio; Diana, James; Raskin, Lutgarde

    2013-01-01

    This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system (RAS) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia-oxidizing populations were examined by targeting 16S rRNA and amoA genes of ammonia-oxidizing bacteria (AOB) and archaea (AOA). The nitrite-oxidizing bacteria (NOB) were investigated by targeting the 16S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to Nitrosomonas marina and Nitrosopumilus maritimus. The NOB detected were related to Nitrospira marina and Nitrospira moscoviensis, and Nitrospira marina-type NOB were more abundant than N. moscoviensis-type NOB. Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira marina-over N. moscoviensis-type NOB. PMID:22775980

  4. Inhibitory Effects of C2 to C10 1-Alkynes on Ammonia Oxidation in Two Nitrososphaera Species

    PubMed Central

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

    2015-01-01

    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. PMID:25576608

  5. Evaluation of the 3M™ Petrifilm™ Rapid Aerobic Count Plate for the Enumeration of Aerobic Bacteria: Collaborative Study, First Action 2015.13.

    PubMed

    Bird, Patrick; Flannery, Jonathan; Crowley, Erin; Agin, James; Goins, David; Jechorek, Robert

    2016-05-01

    The 3M™ Petrifilm™ Rapid Aerobic Count (RAC) Plate is a sample-ready culture medium system containing dual-sensor indicator technology for the rapid quantification of aerobic bacteria in food products. The 3M Petrifilm RAC Plate was compared to the U.S. Food and Drug Administration Bacteriological Analytical Manual (FDA BAM) Chapter 3 (Aerobic Plate Count) for the enumeration of aerobic bacteria in raw easy-peel shrimp and the Standard Methods for the Examination of Dairy Products (SMEDP) Chapter 6 (Standard Plate Count Method) for the enumeration of aerobic bacteria in pasteurized skim milk and instant nonfat dry milk (instant NFDM). The 3M Petrifilm RAC Plate was evaluated using a paired study design in a multilaboratory collaborative study following current AOAC validation guidelines. Three target contamination levels (low, 10-100 CFU/g; medium, 100-1000 CFU/g; and high 1000-10 000 CFU/g) were evaluated for naturally occurring aerobic microflora for each matrix. For raw easy-peel shrimp, duplicate 3M Petrifilm RAC Plates were enumerated after 24 ± 2 h incubation at both 32 and 35°C. Pasteurized skim milk 3M Petrifilm RAC Plates were enumerated after 24 ± 2 h incubation at 32°C, and instant NFDM 3M Petrifilm RAC Plates were enumerated after 48 ± 3 h incubation at 32°C. No statistical difference was observed between 3M Petrifilm RAC Plate and FDA BAM or SMEDP reference methods for each contamination level. PMID:27297837

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

    PubMed Central

    Hu, Ziye; Meng, Han; Shi, Jin-Huan; Bu, Nai-Shun; Fang, Chang-Ming; Quan, Zhe-Xue

    2014-01-01

    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. PMID:25101072

  7. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.

    PubMed

    Bouskill, Nicholas J; Eveillard, Damien; Chien, Diana; Jayakumar, Amal; Ward, Bess B

    2012-03-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution. PMID:22050634

  8. Community structure of ammonia-oxidizing microorganisms in the Grand Canal, Zhenjiang, of Jiangsu Province, China.

    PubMed

    Liu, Biao; Wu, Chundu; Zhou, Xiaohong

    2014-01-01

    In this study, we simultaneously investigated the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the Grand Canal (the Zhenjiang section). Both clone library and qPCR (quantitative polymerase chain reaction) indicated that the abundance and diversity of AOB were higher than AOA in the Grand Canal for all four seasons. Among the 109 archaeal amoA sequences retrieved, 62.39 and 37.61% fell within the Nitrosopumilus and Nitrososphaera clusters, respectively. The 128 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 81.25 and 18.75% of the AOB group, respectively. The AOA abundance was significantly and positively correlated with the NH4-N. The AOB abundance did not show significant correlations with the measured parameters. Obvious differences were observed for the AOA community compositions obtained from different seasons. The community structure of AOB changed slightly. It indicated that AOB seemed to play a more important role for the nitrification process than AOA in this environment, and was more adapted to this environment. PMID:25259486

  9. [Characteristics of soil ammonia-oxidation microbial communities in different subtropical forests, China].

    PubMed

    Li, Yong-Chun; Liu, Bu-Rong; Guo, Shuai; Wu, Qi-Feng; Qin, Hua; Wu, Jia-Sen; Xu, Qiu-Fang

    2014-01-01

    To investigate the effects of different forest stands in subtropical China on the communities of soil ammonia-oxidizing microorganisms, we characterized the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and the community structure of AOA in soils under stands of broad-leaved (BF) , Chinese fir (CF) , Pinus massoniana (PF) and moso bamboo (MB) forests using real-time quantitative PCR and denaturing gradient gel electrophoresis (DGGE). The results showed that the AOA gene copy numbers (1.62 x 10(6)-1.88 x 10(7) per gram of dry soil) were significantly higher than those of AOB genes (2.41 x 10(5)-4.36 x 10(5) per gram of dry soil). Significantly higher soil AOA abundance was detected in the MB than that in the CF (P < 0.05), and the latter was significantly higher than that in the BF and PF soils (P < 0.05). There were no significant differences in the soil AOB abundance among the four forest stands. As indicated by DGGE pattern, soil AOA species varied among the four forest stands. There was a difference in the soil AOA communities between the CF and MB stands. The AOA demonstrated a competitive advantage over the AOB in the soils under these major subtropical forests. Soil pH, concentrations of soil available potassium and organic carbon as well as the forest type were the main factors that influence the variation of AOA community structure and diversity. PMID:24765851

  10. Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils.

    PubMed

    Wang, Xiaoyan; Wang, Cui; Bao, Linlin; Xie, Shuguang

    2014-02-01

    Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson's correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems. PMID:23949998

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    Our understanding of nitrogen biogeochemical cycling in high temperature environments underwent a dramatic revision with the discovery of ammonia oxidizing archaea (AOA). The importance of AOA to the global nitrogen cycle came to light when recent studies of marine AOA demonstrated the dominance of these organisms in the ocean microbiome and their role as producers of the greenhouse gas nitrous oxide (N2O). Understanding how AOA respond to fluctuating environments is crucial to fully comprehending their contribution to global biogeochemical cycling and climate change. In this study we use the thermophilic AOA Nitrosocaldus yellowstonii strain HL72 to explore the physiological plasticity of energy metabolism in these organisms. Previous studies have shown that HL72 grows autotrophically by aerobically oxidizing ammonia (NH3) to nitrite (NO2-). Unlike studies of marine AOA, we find that HL72 can grow over a wide ammonia concentration range (0.25 - 10 mM NH4Cl) with comparable generation times when in the presence of 0.25 to 4 mM NH4Cl. However, preliminary data indicate that amoA, the alpha subunit of ammonia monooxygenase (AMO), is upregulated at low ammonia concentrations (<50 μM) compared to growth at 1 mM. Although the ammonia oxidation pathway has not been fully elucidated, we have shown that nitric oxide (NO) appears to be a key intermediate: exponentially growing HL72 produces significant NO and the removal of NO using a scavenger reversibly inhibits growth. In addition to AMO, the HL72 genome also contains sequences for a urease encoded by subunits ureABC and an active urea transporter. Urea ((NH2)2CO) is an organic compound ubiquitous to aquatic and soil habitats that, when hydrolyzed, forms NH3 and CO2. We examined urea as an alternate source of ammonia for the ammonia oxidation pathway. HL72 grows over a wide range of urea concentrations (0.25 - 10 mM) at rates comparable to growth on ammonia. In a substrate competition experiment HL72 preferentially

  12. Diverse Arrangement of Photosynthetic Gene Clusters in Aerobic Anoxygenic Phototrophic Bacteria

    PubMed Central

    Zheng, Qiang; Zhang, Rui; Koblížek, Michal; Boldareva, Ekaterina N.; Yurkov, Vladimir; Yan, Shi; Jiao, Nianzhi

    2011-01-01

    Background Aerobic anoxygenic photototrophic (AAP) bacteria represent an important group of marine microorganisms inhabiting the euphotic zone of the ocean. They harvest light using bacteriochlorophyll (BChl) a and are thought to be important players in carbon cycling in the ocean. Methodology/Principal Findings Aerobic anoxygenic phototrophic (AAP) bacteria represent an important part of marine microbial communities. Their photosynthetic apparatus is encoded by a number of genes organized in a so-called photosynthetic gene cluster (PGC). In this study, the organization of PGCs was analyzed in ten AAP species belonging to the orders Rhodobacterales, Sphingomonadales and the NOR5/OM60 clade. Sphingomonadales contained comparatively smaller PGCs with an approximately size of 39 kb whereas the average size of PGCs in Rhodobacterales and NOR5/OM60 clade was about 45 kb. The distribution of four arrangements, based on the permutation and combination of the two conserved regions bchFNBHLM-LhaA-puhABC and crtF-bchCXYZ, does not correspond to the phylogenetic affiliation of individual AAP bacterial species. While PGCs of all analyzed species contained the same set of genes for bacteriochlorophyll synthesis and assembly of photosynthetic centers, they differed largely in the carotenoid biosynthetic genes. Spheroidenone, spirilloxanthin, and zeaxanthin biosynthetic pathways were found in each clade respectively. All of the carotenoid biosynthetic genes were found in the PGCs of Rhodobacterales, however Sphingomonadales and NOR5/OM60 strains contained some of the carotenoid biosynthetic pathway genes outside of the PGC. Conclusions/Significance Our investigations shed light on the evolution and functional implications in PGCs of marine aerobic anoxygenic phototrophs, and support the notion that AAP are a heterogenous physiological group phylogenetically scattered among Proteobacteria. PMID:21949847

  13. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors

    PubMed Central

    Hu, Hang-Wei; Zhang, Li-Mei; Yuan, Chao-Lei; Zheng, Yong; Wang, Jun-Tao; Chen, Deli; He, Ji-Zheng

    2015-01-01

    Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75–1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray–Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors. PMID:26388866

  14. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors.

    PubMed

    Hu, Hang-Wei; Zhang, Li-Mei; Yuan, Chao-Lei; Zheng, Yong; Wang, Jun-Tao; Chen, Deli; He, Ji-Zheng

    2015-01-01

    Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75-1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray-Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors. PMID:26388866

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

    PubMed Central

    Daebeler, Anne; Abell, Guy C. J.; Bodelier, Paul L. E.; Bodrossy, Levente; Frampton, Dion M. F.; Hefting, Mariet M.; Laanbroek, Hendrikus 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 ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization. PMID:23060870

  16. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

    PubMed Central

    Reis, Mariana P.; Ávila, Marcelo P.; Keijzer, Rosalinde M.; Barbosa, Francisco A. R.; Chartone-Souza, Edmar; Nascimento, Andréa M. A.; Laanbroek, Hendrikus J.

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  17. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

    PubMed

    Reis, Mariana P; Ávila, Marcelo P; Keijzer, Rosalinde M; Barbosa, Francisco A R; Chartone-Souza, Edmar; Nascimento, Andréa M A; Laanbroek, Hendrikus J

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  18. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.

    PubMed

    Zhang, Yu; Tian, Zhe; Liu, Miaomiao; Shi, Zhou Jason; Hale, Lauren; Zhou, Jizhong; Yang, Min

    2015-08-01

    To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems. PMID:26125322

  19. Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater ▿

    PubMed Central

    Reed, David W.; Smith, Jason M.; Francis, Christopher A.; Fujita, Yoshiko

    2010-01-01

    To evaluate the potential for organic nitrogen addition to stimulate the in situ growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA amoA genes outnumbering AOB amoA genes in all of the samples. Following urea addition, nitrate levels rose and bacterial amoA copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial amoA diversity was limited to two Nitrosomonas phylotypes, whereas archaeal amoA analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis. PMID:20190081

  20. Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China.

    PubMed

    Liu, Shuai; Shen, Lidong; Lou, Liping; Tian, Guangming; Zheng, Ping; Hu, Baolan

    2013-07-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the current knowledge of the distribution, diversity, and relative abundance of these two microbial groups in freshwater sediments is insufficient. We examined the spatial distribution and analyzed the possible factors leading to the niche segregation of AOA and AOB in the sediments of the Qiantang River, using clone library construction and quantitative PCR for both archaeal and bacterial amoA genes. pH and NH4(+)-N content had a significant effect on AOA abundance and AOA operational taxonomy unit (OTU) numbers. pH and organic carbon content influenced the ratio of AOA/AOB OTU numbers significantly. The influence of these factors showed an obvious spatial trend along the Qiantang River. This result suggested that AOA may contribute more than AOB to the upstream reaches of the Qiantang River, where the pH is lower and the organic carbon and NH4(+)-N contents are higher, but AOB were the principal driver of nitrification downstream, where the opposite environmental conditions were present. PMID:23624482

  1. In vitro susceptibility tests for cationic peptides: comparison of broth microdilution methods for bacteria that grow aerobically.

    PubMed

    Giacometti, A; Cirioni, O; Barchiesi, F; Del Prete, M S; Fortuna, M; Caselli, F; Scalise, G

    2000-06-01

    The in vitro susceptibilities of 90 clinical isolates of gram-positive and gram-negative aerobic bacteria to six cationic peptides, buforin II, cecropin P1, indolicidin, magainin II, nisin, and ranalexin, were evaluated by two broth microdilution methods. The first method was performed according to the procedures outlined by the National Committee for Clinical Laboratory Standards for bacteria that grow aerobically, while the second was performed according to the procedures recently proposed by the R. E. W. Hancock laboratory for testing antimicrobial peptides. Overall, the first method produced MICs two- and fourfold higher than the second method. PMID:10817731

  2. Response of Ammonia-oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater

    SciTech Connect

    David W. Reed; Yoshiko Fujita; Jason M. Smith; Christopher A. Francis

    2010-02-01

    To better understand the fate of ammonia introduced into low-nutrient groundwater as a result of the application of a novel remediation approach for trace metal contaminants, the diversity and abundance of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) were examined in samples collected during a field trial of the approach. The ammonia is derived from microbial urea hydrolysis, which has the potential to induce the formation of calcite and remove contaminants by coprecipitation in the calcite. The in situ oxidation of the ammonia by AOB and AOA could, however, potentially destabilize the calcite and lead to elevated nitrate levels in the groundwater. To evaluate the potential for stimulating ammonia oxidation by addition of urea, samples were collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea, and subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. AOB and AOA were present in all of the samples tested, with the AOA amoA genes more numerous in all of the samples except those collected following urea addition, when AOB genes were slightly more abundant. Following urea addition, nitrate levels rose and ammonia-oxidizing microorganisms (AOB + AOA) increased relative to the total microbial population, evidence that nitrification was stimulated by urea hydrolysis. Bacterial amoA diversity was limited to two sequence types, whereas the archaeal amoA analyses revealed 20 unique operational taxonomic units (OTUs), including several that were significantly different from any reported previously from other environments. In view of the results from this study, the potential for stimulation of ammonia-oxidizing communities should be considered in field-scale engineering activities involving microbial urea hydrolysis in groundwater.

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

    NASA Astrophysics Data System (ADS)

    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.

  4. Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary.

    PubMed

    Cottrell, Matthew T; Ras, Josephine; Kirchman, David L

    2010-07-01

    Photoheterotrophic microbes use organic substrates and light energy to satisfy their demand for carbon and energy and seem to be well adapted to eutrophic estuarine and oligotrophic oceanic environments. One type of photoheterotroph, aerobic anoxygenic phototrophic (AAP) bacteria, is especially abundant in particle-rich, turbid estuaries. To explore questions regarding the controls of these photoheterotrophic bacteria, we examined their abundance by epifluorescence microscopy, concentrations of the light-harvesting pigment, bacteriochlorophyll a (BChl a) and the diversity of pufM and 16S ribosomal RNA (rRNA) genes in the Chesapeake Bay. Concentrations of BChl a varied substantially, much more so than AAP bacterial abundance, along the estuarine salinity gradient. The BChl a concentration was correlated with turbidity only when oceanic and estuarine waters were considered together. Concentrations of BChl a and BChl a quotas were higher in particle-associated than in free-living AAP bacterial communities and appear to reflect physiological adaptation, not different AAP bacterial communities; pufM genes did not differ between particle-associated and free-living communities. In contrast, particle-associated and free-living bacterial communities were significantly different, on the basis of the analysis of 16S rRNA genes. The BChl a quota of AAP bacteria was not correlated with turbidity, suggesting that pigment synthesis varies in direct response to particles, not light attenuation. The AAP bacteria seem to synthesize more BChl a when dissolved and particulate substrates are available than when only dissolved materials are accessible, which has implications for understanding the impact of substrates on the level of photoheterotrophy compared with heterotrophy in AAP bacteria. PMID:20182527

  5. Ammonium-oxidizing bacteria facilitate aerobic degradation of sulfanilic acid in activated sludge.

    PubMed

    Chen, Gang; Ginige, Maneesha P; Kaksonen, Anna H; Cheng, Ka Yu

    2014-01-01

    Sulfanilic acid (SA) is a toxic sulfonated aromatic amine commonly found in anaerobically treated azo dye contaminated effluents. Aerobic acclimatization of SA-degrading mixed microbial culture could lead to co-enrichment of ammonium-oxidizing bacteria (AOB) because of the concomitant release of ammonium from SA oxidation. To what extent the co-enriched AOB would affect SA oxidation at various ammonium concentrations was unclear. Here, a series of batch kinetic experiments were conducted to evaluate the effect of AOB on aerobic SA degradation in an acclimatized activated sludge culture capable of oxidizing SA and ammonium simultaneously. To account for the effect of AOB on SA degradation, allylthiourea was used to inhibit AOB activity in the culture. The results indicated that specific SA degradation rate of the mixed culture was negatively correlated with the initial ammonium concentration (0-93 mM, R²= 0.99). The presence of AOB accelerated SA degradation by reducing the inhibitory effect of ammonium (≥ 10 mM). The Haldane substrate inhibition model was used to correlate substrate concentration (SA and ammonium) and oxygen uptake rate. This study revealed, for the first time, that AOB could facilitate SA degradation at high concentration of ammonium (≥ 10 mM) in an enriched activated sludge culture. PMID:25259503

  6. Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters

    PubMed Central

    Sauder, Laura A.; Engel, Katja; Stearns, Jennifer C.; Masella, Andre P.; Pawliszyn, Richard; Neufeld, Josh D.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology. PMID:21858055

  7. Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters.

    PubMed

    Sauder, Laura A; Engel, Katja; Stearns, Jennifer C; Masella, Andre P; Pawliszyn, Richard; Neufeld, Josh D

    2011-01-01

    Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology. PMID:21858055

  8. Antimicrobial Resistance and Resistance Genes in Aerobic Bacteria Isolated from Pork at Slaughter.

    PubMed

    Li, Lili; Olsen, Rikke Heidemann; Ye, Lei; Yan, He; Nie, Qing; Meng, Hecheng; Shi, Lei

    2016-04-01

    The aim of this study was to investigate the phenotypic and genotypic antimicrobial resistance, integrons, and transferability of resistance markers in 243 aerobic bacteria recovered from pork at slaughter in the People's Republic of China. The organisms belonged to 22 genera of gram-negative bacteria (92.2%) and gram-positive bacteria (7.8%). High levels of resistance were detected to tetracycline, trimethoprim-sulfamethoxazole, and ampicillin (36.2 to 54.3%), and lower levels were detected to nitrofurantoin, cefotaxime, gentamicin, ciprofloxacin, and chloramphenicol (7.8 to 29.2%). Across species, genes conferring antimicrobial resistance were observed with the following frequencies: blaTEM, 40.7%; blaCMY-2, 15.2%; blaCTX-M, 11.5%; sul2, 27.2%; sul1, 14.4%; tet(A), 5.4%; tet(L), 5.4%; tet(M), 5.0%; tet(E), 3.7%; tet(C), 3.3%; tet(S), 2.5%; and tet(K), 0.8%. Various antimicrobial resistance genes were found in new carriers: blaTEM in Lactococcus garvieae, Myroides odoratimimus, Aeromonas hydrophila, Staphylococcus sciuri, Raoultella terrigena, Macrococcus caseolyticus, Acinetobacter ursingii, Sphingobacterium sp., and Oceanobacillus sp.; blaCMY-2 in Lactococcus lactis, Klebsiella oxytoca, Serratia marcescens, Acinetobacter baumannii, and Myroides phaeus; tet(L) in M. caseolyticus; sul1 in Vibrio cincinnatiensis; sul2 in Acinetobacter bereziniae, Acinetobacter johnsonii, and V. cincinnatiensis; and the class 1 integron and gene cassette aadA2 in V. cincinnatiensis. Approximately 6.6% of isolates contained class 1 integrons, and one isolate harbored class 2 integrons. Plasmid associated intI1 and androgen receptor- encoding genes were transferred into Escherichia coli J53 and E. coli DH5α by conjugation and transformation experiments, respectively. Our study highlights the importance of aerobic bacteria from pork as reservoirs for antimicrobial resistance genes and mobile genetic elements that can readily be transferred intra- and interspecies. PMID:27052863

  9. Comparison between rinse and crush-and-rub sampling for aerobic bacteria recovery from broiler hatching eggs after sanitization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study compared surface and deep eggshell aerobic bacteria recovered by rinse and crush-and-rub sampling methods for commercial hatching eggs after treatment with sanitizers. Eggs were arranged into 5 treatments consisting of No-treatment, Water, and three sanitizers. Sanitizers were Hydrogen ...

  10. Comparison between Rinse and Crush-and-Rub Sampling for Aerobic Bacteria Recovery from Hatching Eggs after Sanitization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study compared surface and deep eggshell aerobic bacteria recovered by rinse and crush-and-rub sampling methods for commercial hatching eggs after treatments with sanitizers. Eggs were arranged into 5 treatments consisting of three sanitizers, Water, and No-treatment. Sanitizers were Hydrogen...

  11. Growth of Aerobic Ripening Bacteria at the Cheese Surface Is Limited by the Availability of Iron

    PubMed Central

    Back, Alexandre; Irlinger, Françoise

    2012-01-01

    The microflora on the surface of smear-ripened cheeses is composed of various species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. The objective of the present study was to show that iron availability is a limiting factor in the growth of typical aerobic ripening bacteria in cheese. For that purpose, we investigated the effect of iron or siderophore addition in model cheeses that were coinoculated with a yeast and a ripening bacterium. Both iron and the siderophore desferrioxamine B stimulated the growth of ripening bacteria belonging to the genera Arthrobacter, Corynebacterium, and Brevibacterium. The extent of stimulation was strain dependent, and generally, the effect of desferrioxamine B was greater than that of iron. Measurements of the expression of genes related to the metabolism of iron by Arthrobacter arilaitensis Re117 by real-time reverse transcription-PCR showed that these genes were transcribed during growth in cheese. The addition of desferrioxamine B increased the expression of two genes encoding iron-siderophore ABC transport binding proteins. The addition of iron decreased the expression of siderophore biosynthesis genes and of part of the genes encoding iron-siderophore ABC transport components. It was concluded that iron availability is a limiting factor in the growth of typical cheese surface bacteria. The selection of strains with efficient iron acquisition systems may be useful for the development of defined-strain surface cultures. Furthermore, the importance of iron metabolism in the microbial ecology of cheeses should be investigated since it may result in positive or negative microbial interactions. PMID:22367081

  12. [Abundance and Community Composition of Ammonia-Oxidizing Archaea in Two Completely Autotrophic Nitrogen Removal over Nitrite Systems].

    PubMed

    Gao, Jing-feng; Li, Ting; Zhang, Shu-jun; Fan, Xiao-yan; Pan, Kai-ling; Ma, Qian; Yuan, Ya-lin

    2015-08-01

    Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite (CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction (PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2.42 x 10(6) copies x g(-1) dry sludge and 6.51 x 10(6) copies x g(-1) dry sludge, respectively. The abundance of AOA in biofilm was 10.1-14.1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1.8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5.2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8.1, subcluster 4.1, subcluster 1.1 and Nitrosopumilus subcluster 5.2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system. PMID:26592025

  13. An initial investigation into the ecology of culturable aerobic postmortem bacteria.

    PubMed

    Chun, Lauren P; Miguel, Marcus J; Junkins, Emily N; Forbes, Shari L; Carter, David O

    2015-12-01

    Postmortem microorganisms are increasingly recognized for their potential to serve as physical evidence. Yet, we still understand little about the ecology of postmortem microbes, particularly those associated with the skin and larval masses. We conducted an experiment to characterize microbiological and chemical properties of decomposing swine (Sus scrofa domesticus) carcasses on the island of Oahu, Hawaii, USA, during June 2013. Bacteria were collected from the head, limb, and larval mass during the initial 145h of decomposition. We also measured the pH, temperature, and oxidation-reduction potential of larval masses in situ. Bacteria were cultured aerobically on Standard Nutrient Agar at 22°C and identified using protein or genetic signals. Carcass decomposition followed a typical sigmoidal pattern and associated bacterial communities differed by sampling location and time since death, although all communities were dominated by phyla Actinobacteria, Firmicutes, and Proteobacteria. Larval masses were reducing environments (~-200mV) of neutral pH (6.5-7.5) and high temperature (35°C-40°C). We recommend that culturable postmortem and larval mass microbiology and chemistry be investigated in more detail, as it has potential to complement culture-independent studies and serve as a rapid estimate of PMI. PMID:26654073

  14. Distribution and Physiology of Aerobic Bacteria Containing Bacteriochlorophyll a on the East and West Coasts of Australia †

    PubMed Central

    Shiba, Tsuneo; Shioi, Yuzo; Takamiya, Ken-Ichiro; Sutton, David C.; Wilkinson, Clive R.

    1991-01-01

    Aerobic heterotrophic bacteria containing bacteriochlorophyll were isolated from specimens from a wide variety of marine environments on the west (Shark Bay, Lake Clifton, Lake Heyward, and Perth) and east (near Townsville and Brisbane) coasts of Australia. The bacteria were found in a high proportion (10 to 30%) of the total heterotrophic bacterial strains isolated from marine algae, seagrasses, stromatolites, the epiphytes on stromatolites, seawater, and sands; in some cases they constituted up to 49% of the total. This is much higher than the previous report of 6% from Japan. A high percentage, 13%, was also found in the seawater of Hamelin Pool, at Shark Bay, where the salinity was 66%. The number of these bacteria was generally low in seawater and sands, with a few exceptions. There were no aerobic bacteriochlorophyll-containing bacteria on sponges or corals. The isolated strains were orange or pink, and most had absorption maxima around 800 and 850 to 870 nm, the latter range being the absorption of bacteriochlorophyll a in vivo. The maximum bacteriochlorophyll content was 1 nmol/mg (dry weight) of bacterial cells. Most of the bacteria did not grow phototrophically under anaerobic conditions in a broth medium containing succinate. Cells and cell extracts grown under aerobic conditions had photochemical activities such as reversible photooxidations of the reaction center and cytochrome(s). Some strains showed denitrifying activity. The optimal salinity for bacterial growth varied between strains. PMID:16348398

  15. Plutonium Oxidation State Distribution under Aerobic and Anaerobic Subsurface Conditions for Metal-Reducing Bacteria

    NASA Astrophysics Data System (ADS)

    Reed, D. T.; Swanson, J.; Khaing, H.; Deo, R.; Rittmann, B.

    2009-12-01

    The fate and potential mobility of plutonium in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium is the near-surface contaminant of concern at several DOE sites and continues to be the contaminant of concern for the permanent disposal of nuclear waste. The mobility of plutonium is highly dependent on its redox distribution at its contamination source and along its potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. The redox distribution of plutonium in the presence of facultative metal reducing bacteria (specifically Shewanella and Geobacter species) was established in a concurrent experimental and modeling study under aerobic and anaerobic conditions. Pu(VI), although relatively soluble under oxidizing conditions at near-neutral pH, does not persist under a wide range of the oxic and anoxic conditions investigated in microbiologically active systems. Pu(V) complexes, which exhibit high chemical toxicity towards microorganisms, are relatively stable under oxic conditions but are reduced by metal reducing bacteria under anaerobic conditions. These facultative metal-reducing bacteria led to the rapid reduction of higher valent plutonium to form Pu(III/IV) species depending on nature of the starting plutonium species and chelating agents present in solution. Redox cycling of these lower oxidation states is likely a critical step in the formation of pseudo colloids that may lead to long-range subsurface transport. The CCBATCH biogeochemical model is used to explain the redox mechanisms and final speciation of the plutonium oxidation state distributions observed. These results for microbiologically active systems are interpreted in the context of their importance in defining the overall migration

  16. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  17. Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

    PubMed Central

    Zheng, Yanling; Newell, Silvia; Liu, Min; Zhou, Junliang; Zhao, Hui; You, Lili; Cheng, Xunliang

    2014-01-01

    Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments. PMID:24185847

  18. The influence of land use on the abundance and diversity of ammonia oxidizers.

    PubMed

    Zhao, Dayong; Luo, Juan; Wang, Jianqun; Huang, Rui; Guo, Kun; Li, Yi; Wu, Qinglong L

    2015-02-01

    Nitrification plays a significant role in soil nitrogen cycling, a process in which the first step can be catalyzed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In this study, six soil samples with distinct land-use regimes (forestland soil, paddy soil, wheat-planted soil, fruit-planted soil, grassland soil, and rape-planted soil) were collected from Chuzhou city in the Anhui province to elucidate the effects of land use on the abundance and diversity of AOA and AOB. The abundance of the archaeal amoA gene ranged from 2.12 × 10(4) copies per gram of dry soil to 2.57 × 10(5) copies per gram of dry soil, while the abundance of the bacterial amoA gene ranged from 5.58 × 10(4) copies per gram of dry soil to 1.59 × 10(8) copies per gram of dry soil. The grassland and the rape-planted soil samples maintained the highest abundance of the bacterial and archaeal amoA genes, respectively. The abundance of the archaeal amoA gene was positively correlated with the pH (P < 0.05). The ammonia concentrations exhibited a significantly positive relation with the abundance of the bacterial amoA gene (P < 0.01) and the number of OTUs of AOB (P < 0.05). The community composition of AOB was more sensitive to the land-use regimes than that of AOA. The data obtained in this study may be useful to better understand the nitrification process in soils with different land-use regimes. PMID:25331793

  19. Ecosystem-specific selection of microbial ammonia oxidizers in an acid soil

    NASA Astrophysics Data System (ADS)

    Saiful Alam, M.; Ren, G.; Lu, L.; Zheng, Y.; Peng, X.; Jia, Z.

    2013-01-01

    The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the availability of ammonia substrate and the supply of oxygen. The interactions and evolutions of AOA and AOB communities along ecological gradients of substrate availability in complex environment have been much debated, but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB in response to long-term field fertilization and flooding management in an acid soil. Real-time quantitative PCR of amoA genes demonstrated that the abundance of AOA was significantly stimulated after conversion of upland to paddy soils, while slight decline of AOB populations was observed. DGGE fingerprints of amoA genes further revealed remarkable changes in community compositions of AOA in paddy soil when compared to upland soil. Sequencing analysis revealed that upland soil was dominated by AOA within the soil group 1.1b lineage, while the marine group 1.1a lineage predominated AOA communities in paddy soils. Irrespective of upland and paddy soils, long-term field fertilizations led to higher abundance of amoA genes of AOA and AOB than control treatment that received no fertilization, whereas archaeal amoA gene abundances outnumbered their bacterial counterpart in all samples. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster 3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization treatments. The results of this study suggest that the marine group 1.1a AOA could be better adapted to low-oxygen environment than AOA ecotypes of the soil group 1.1b lineage, and implicate that long-term flooding as the dominant selective force driving the community diversification of AOA populations in the acid soil tested.

  20. Community dynamics and activity of ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze estuary.

    PubMed

    Zheng, Yanling; Hou, Lijun; Newell, Silvia; Liu, Min; Zhou, Junliang; Zhao, Hui; You, Lili; Cheng, Xunliang

    2014-01-01

    Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments. PMID:24185847

  1. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.

    PubMed

    Norton, Jeanette M; Klotz, Martin G; Stein, Lisa Y; Arp, Daniel J; Bottomley, Peter J; Chain, Patrick S G; Hauser, Loren J; Land, Miriam L; Larimer, Frank W; Shin, Maria W; Starkenburg, Shawn R

    2008-06-01

    The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196(T)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments. PMID:18390676

  2. Analyses of Spatial Distributions of Sulfate-Reducing Bacteria and Their Activity in Aerobic Wastewater Biofilms

    PubMed Central

    Okabe, Satoshi; Itoh, Tsukasa; Satoh, Hisashi; Watanabe, Yoshimasa

    1999-01-01

    The vertical distribution of sulfate-reducing bacteria (SRB) in aerobic wastewater biofilms grown on rotating disk reactors was investigated by fluorescent in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes. To correlate the vertical distribution of SRB populations with their activity, the microprofiles of O2, H2S, NO2−, NO3−, NH4+, and pH were measured with microelectrodes. In addition, a cross-evaluation of the FISH and microelectrode analyses was performed by comparing them with culture-based approaches and biogeochemical measurements. In situ hybridization revealed that a relatively high abundance of the probe SRB385-stained cells (approximately 109 to 1010 cells per cm3 of biofilm) were evenly distributed throughout the biofilm, even in the oxic surface. The probe SRB660-stained Desulfobulbus spp. were found to be numerically important members of SRB populations (approximately 108 to 109 cells per cm3). The result of microelectrode measurements showed that a high sulfate-reducing activity was found in a narrow anaerobic zone located about 150 to 300 μm below the biofilm surface and above which an intensive sulfide oxidation zone was found. The biogeochemical measurements showed that elemental sulfur (S0) was an important intermediate of the sulfide reoxidation in such thin wastewater biofilms (approximately 1,500 μm), which accounted for about 75% of the total S pool in the biofilm. The contribution of an internal Fe-sulfur cycle to the overall sulfur cycle in aerobic wastewater biofilms was insignificant (less than 1%) due to the relatively high sulfate reduction rate. PMID:10543829

  3. Rapid high-throughput assessment of aerobic bacteria in complex samples by fluorescence-based oxygen respirometry.

    PubMed

    O'Mahony, Fiach C; Papkovsky, Dmitri B

    2006-02-01

    A simple method has been developed for the analysis of aerobic bacteria in complex samples such as broth and food homogenates. It employs commercial phosphorescent oxygen-sensitive probes to monitor oxygen consumption of samples containing bacteria using standard microtiter plates and fluorescence plate readers. As bacteria grow in aqueous medium, at certain points they begin to deplete dissolved oxygen, which is seen as an increase in probe fluorescence above baseline signal. The time required to reach threshold signal is used to either enumerate bacteria based on a predetermined calibration or to assess the effects of various effectors on the growth of test bacteria by comparison with an untreated control. This method allows for the sensitive (down to a single cell), rapid (0.5 to 12 h) enumeration of aerobic bacteria without the need to conduct lengthy (48 to 72 h) and tedious colony counts on agar plates. It also allows for screening a wide range of chemical and environmental samples for their toxicity. These assays have been validated with different bacteria, including Escherichia coli, Micrococcus luteus, and Pseudomonas fluorescens, with the enumeration of total viable counts in broth and industrial food samples (packaged ham, chicken, and mince meat), and comparison with established agar plating and optical-density-at-600-nm assays has been given. PMID:16461677

  4. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

    PubMed Central

    Knief, Claudia

    2015-01-01

    Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities. PMID:26696968

  5. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker.

    PubMed

    Knief, Claudia

    2015-01-01

    Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities. PMID:26696968

  6. Space agriculture for habitation on Mars with hyper-thermophilic aerobic composting bacteria

    NASA Astrophysics Data System (ADS)

    Space Agriculture Task Force; Ishikawa, Y.; Tomita-Yokotani, K.; Hashimoto, H.; Kitaya, Y.; Yamashita, M.; Nagatomo, M.; Oshima, T.; Wada, H.

    Manned Mars exploration, especially for extended periods of time, will require recycle of materials to support human life. Here, a conceptual design is developed for a Martian agricultural system driven by biologically regenerative functions. One of the core biotechnologies function is the use of hyper-thermophilic aerobic composting bacterial ecology. These thermophilic bacteria can play an important role in increasing the effectiveness of the processing of human metabolic waste and inedible biomass and of converting them to fertilizer for the cultivation of plants. This microbial technology has been already well established for the purpose of processing sewage and waste materials for small local communities in Japan. One of the characteristics of the technology is that the metabolic heat release that occurs during bacterial fermentation raises the processing temperature sufficiently high at 80 100 °C to support hyper-thermophilic bacteria. Such a hyper-thermophilic system is found to have great capability of decomposing wastes including even their normally recalcitrant components, in a reasonably short period of time and of providing a better quality of fertilizer as an end-product. High quality compost has been shown to be a key element in creating a healthy regenerative food production system. In ground-based studies, the soil microbial ecology after the addition of high quality compost was shown to improve plant growth and promote a healthy symbiosis of arbuscular mycorrhizal fungi. Another advantage of such high processing temperature is the ability to sterilize the pathogenic organisms through the fermentation process and thus to secure the hygienic safety of the system. Plant cultivation is one of the other major systems. It should fully utilize solar energy received on the Martian surface for supplying energy for photosynthesis. Subsurface water and atmospheric carbon dioxide mined on Mars should be also used in the plant cultivation system. Oxygen and

  7. Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere

    PubMed Central

    Stiefel, Philipp; Zambelli, Tomaso

    2013-01-01

    In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria in situ, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources. PMID:23770907

  8. Enhanced abundance and diversity of ammonia-oxidizing Archaea in the Pearl River estuary

    NASA Astrophysics Data System (ADS)

    Xie, W.; Zhang, C. L.; Wang, P.; Zhou, X.; Guo, W.

    2014-12-01

    Thaumarchaeota are recently recognized as an important group of Archaea that can perform aerobic oxidation of ammonia in a wide range of environments. The goal of this study was to evaluate changes in abundance and diversity of planktonic ammonia-oxidizing Archaea (e.g., Thaumarchaeota) along a salinity gradient from the lower Pearl River to the northern South China Sea. Quantitative PCR and sequencing of total archaeal 16S rRNA gene and the archaeal amoA gene were performed on suspended particulate organic matter collected in different seasons from the freshwater to the ocean water. Total amoA gene copies and relative abundance of Thaumarchaeota all peaked in the estuary where salinity ranged between 4.5‰ and 26.7‰. The diversity of archaeal amoA gene was also highest in the estuary. Seasonality and SiO32- appear to be two major factors affecting the distribution of subclusters of archaeal amoA genes. For example, Nitrosopumilus subcluster 7.1 was most abundant in winter in fresh water, whereas Nitrososphaera were more abundant in summer. Samples collected from the area around Wanshan Island, which is located at the outermost part of the Pearl River estuary, had high abundance of unclassified archaeal amoA genes, suggesting some new groups of Thaumarchaeota might inhabit this water body. Overall, the high abundance and diversity of Thaumarchaeota in the Pearl River estuary may indicate enhanced role of AOA in nitrogen cycle in this dynamic ecosystem.

  9. Organic Osmolytes in Aerobic Bacteria from Mono Lake, an Alkaline, Moderately Hypersaline Environment

    PubMed Central

    Ciulla, R. A.; Diaz, M. R.; Taylor, B. F.; Roberts, M. F.

    1997-01-01

    The identity and concentrations of intracellular organic solutes were determined by nuclear magnetic resonance spectroscopy for two strains of aerobic, gram-negative bacteria isolated from Mono Lake, Calif., an alkaline, moderately hypersaline lake. Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was the major endogenous solute in both organisms. Concentrations of ectoine varied with external NaCl levels in strain ML-D but not in strain ML-G, where the level was high but invariant from 1.5 to 3.0 M NaCl. Hydroxyectoine also occurred in strain ML-D, especially at elevated NaCl concentrations (2.5 and 3.0 M), but at levels lower than those of ectoine. Exogenous organic solutes that might occur in Mono Lake were examined for their effects on the de novo synthesis of ectoine. Dimethylsulfoniopropionate (DMSP) (0.1 or 1 mM) did not significantly lower ectoine levels in either isolate, and only strain ML-G showed any capacity for DMSP accumulation. With nitrogen limitation, however, DMSP (0.1 mM) substituted for ectoine in strain ML-G and became the main organic solute. Glycine betaine (GB) was more effective than DMSP in affecting ectoine levels, principally in strain ML-D. Strain ML-D accumulated GB to 50 or 67% of its organic solute pool at 2.5 M NaCl, at an external level of 0.1 or 1 mM GB, respectively. Strain ML-D also accumulated arsenobetaine. The methylated zwitterionic compounds, probably metabolic products of phytoplankton (DMSP and GB) or brine shrimps (arsenobetaine) in Mono Lake, may function as osmolytes for indigenous bacteria when present at high concentrations or under conditions of nitrogen limitation or salt stress. PMID:16535487

  10. Cultivation of aerobic chemoorganotrophic proteobacteria and gram-positive bacteria from a hot spring microbial mat.

    PubMed Central

    Nold, S C; Kopczynski, E D; Ward, D M

    1996-01-01

    The diversity of aerobic chemoorganotrophic bacteria inhabiting the Octopus Spring cyanobacterial mat community (Yellowstone National Park) was examined by using serial-dilution enrichment culture and a variety of enrichment conditions to cultivate the numerically significant microbial populations. The most abundant bacterial populations cultivated from dilutions to extinction were obtained from enrichment flasks which contained 9.0 x 10(2) primary producer (Synechococcus spp.) cells in the inoculum. Two isolates exhibited 16S rRNA nucleotide sequences typical of beta-proteobacteria. One of these isolates contained a 16S rRNA sequence identical to a sequence type previously observed in the mat by molecular retrieval techniques. Both are distantly related to a new sequence directly retrieved from the mat and contributed by a beta-proteobacterial community member. Phenotypically diverse gram-positive isolates genetically similar to Bacillus flavothermus were obtained from a variety of dilutions and enrichment types. These isolates exhibited identical 16S rRNA nucleotide sequences through a variable region of the molecule. Of the three unique sequences observed, only one had been previously retrieved from the mat, illustrating both the inability of the cultivation methods to describe the composition of a microbial community and the limitations of the ability of molecular retrieval techniques to describe populations which may be less abundant in microbial communities. PMID:8899976

  11. Production of wax esters during aerobic growth of marine bacteria on isoprenoid compounds

    PubMed

    Rontani; Bonin; Volkman

    1999-01-01

    This paper describes the production of isoprenoid wax esters during the aerobic degradation of 6,10,14-trimethylpentadecan-2-one and phytol by four bacteria (Acinetobacter sp. strain PHY9, Pseudomonas nautica [IP85/617], Marinobacter sp. strain CAB [DSMZ 11874], and Marinobacter hydrocarbonoclasticus [ATCC 49840]) isolated from the marine environment. Different pathways are proposed to explain the formation of these compounds. In the case of 6,10, 14-trimethylpentadecan-2-one, these esters result from the condensation of some acidic and alcoholic metabolites produced during the biodegradation, while phytol constitutes the alcohol moiety of most of the esters produced during growth on this isoprenoid alcohol. The amount of these esters formed increased considerably in N-limited cultures, in which the ammonium concentration corresponds to conditions often found in marine sediments. This suggests that the bacterial formation of isoprenoid wax esters might be favored in such environments. Although conflicting evidence exists regarding the stability of these esters in sediments, it seems likely that, under some conditions, bacterial esterification can enhance the preservation potential of labile compounds such as phytol. PMID:9872783

  12. Effects of exogenous aerobic bacteria on methane production and biodegradation of municipal solid waste in bioreactors.

    PubMed

    Ge, Sai; Liu, Lei; Xue, Qiang; Yuan, Zhiming

    2016-09-01

    Landfill is the most common and efficient ways of municipal solid waste (MSW) disposal and the landfill biogas, mostly methane, is currently utilized to generate electricity and heat. The aim of this work is to study the effects and the role of exogenous aerobic bacteria mixture (EABM) on methane production and biodegradation of MSW in bioreactors. The results showed that the addition of EABM could effectively enhance hydrolysis and acidogenesis processes of MSW degradation, resulting in 63.95% reduction of volatile solid (VS), the highest methane production rate (89.83Lkg(-1) organic matter) ever recorded and a threefold increase in accumulative methane production (362.9L) than the control (127.1L). In addition, it is demonstrated that white-rot fungi (WRF) might further promote the methane production through highly decomposing lignin, but the lower pH value in leachate and longer acidogenesis duration may cause methane production reduced. The data demonstrated that methane production and biodegradation of MSW in bioreactors could be significantly enhanced by EABM via enhanced hydrolysis and acidogenesis processes, and the results are of great economic importance for the future design and management of landfill. PMID:26601890

  13. Halotolerant aerobic heterotrophic bacteria from the Great Salt Plains of Oklahoma.

    PubMed

    Caton, T M; Witte, L R; Ngyuen, H D; Buchheim, J A; Buchheim, M A; Schneegurt, M A

    2004-11-01

    The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus. PMID:15696379

  14. Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile.

    PubMed

    Hernández, Marcela; Dumont, Marc G; Calabi, Marcela; Basualto, Daniel; Conrad, Ralf

    2014-02-01

    Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification. PMID:24596264

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

    PubMed

    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. PMID:26904010

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

    PubMed

    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. PMID:27063014

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

    PubMed Central

    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 (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. PMID:26904010

  18. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.

    PubMed

    Blainey, Paul C; Mosier, Annika C; Potanina, Anastasia; Francis, Christopher A; Quake, Stephen R

    2011-01-01

    Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles. PMID

  19. Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

    PubMed Central

    Potanina, Anastasia; Francis, Christopher A.; Quake, Stephen R.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles. PMID

  20. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes.

    PubMed

    Zhang, Jinping; Zhou, Xiaohong; Chen, Lei; Chen, Zhigang; Chu, Jinyu; Li, Yimin

    2016-05-01

    The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (SChao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, SChao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (SChao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil. PMID:27038955

  1. Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718.

    PubMed

    Kozlowski, Jessica A; Price, Jennifer; Stein, Lisa Y

    2014-08-01

    Nitrite reductase (NirK) and nitric oxide reductase (NorB) have long been thought to play an essential role in nitrous oxide (N2O) production by ammonia-oxidizing bacteria. However, essential gaps remain in our understanding of how and when NirK and NorB are active and functional, putting into question their precise roles in N2O production by ammonia oxidizers. The growth phenotypes of the Nitrosomonas europaea ATCC 19718 wild-type and mutant strains deficient in expression of NirK, NorB, and both gene products were compared under atmospheric and reduced O2 tensions. Anoxic resting-cell assays and instantaneous nitrite (NO2 (-)) reduction experiments were done to assess the ability of the wild-type and mutant N. europaea strains to produce N2O through the nitrifier denitrification pathway. Results confirmed the role of NirK for efficient substrate oxidation of N. europaea and showed that NorB is involved in N2O production during growth at both atmospheric and reduced O2 tensions. Anoxic resting-cell assays and measurements of instantaneous NO2 (-) reduction using hydrazine as an electron donor revealed that an alternate nitrite reductase to NirK is present and active. These experiments also clearly demonstrated that NorB was the sole nitric oxide reductase for nitrifier denitrification. The results of this study expand the enzymology for nitrogen metabolism and N2O production by N. europaea and will be useful to interpret pathways in other ammonia oxidizers that lack NirK and/or NorB genes. PMID:24907318

  2. Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary.

    PubMed

    Xia, Fei; Zeleke, Jemaneh; Sheng, Qiang; Wu, Ji-Hua; Quan, Zhe-Xue

    2015-05-01

    Spartina alterniflora, an aggressive invasive plant species at the estuarine wetlands of China's coasts, has become a major threat to the natural ecosystems. To understand its potential influence on nitrification processes, the community structures and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated using 454-pyrosequencing and quantitative real-time PCR (qPCR) in S. alterniflora invading salt marsh sediments at the Yangtze River estuary in Chongming island, Shanghai, China. Copy numbers of archaeal and bacterial ammonia monooxygenase subunit A (amoA) genes did not show accordant shifts with S. alterniflora invasion in the two sampling sites. However, the copy numbers of archaeal amoA gene were higher in summer than in spring. Phylogenetic analysis indicated that more than 90% of the archaeal and 92% of the bacterial amoA gene sequences were closely related to marine group I.1a and the clusters 13 and 15 in Nitrosospira lineage, respectively. The effect of different seasons (spring and summer) was important for the abundance variation of AOA, while different stages of S. alterniflora invasion did not show significant effect for both AOA and AOB. Variation of AOA community was significantly related to total carbon (TC) and sulfate concentration (P < 0.05), whereas the AOB community was significantly related to sulfate concentration, total nitrogen (TN), TC and pH (P < 0.05). In conclusion, the abundance and diversity of ammonia oxidizing microbial communities were not strongly affected by S. alterniflora invasion. PMID:25935302

  3. Characterization of aerobic spore-forming bacteria associated with industrial dairy processing environments and product spoilage.

    PubMed

    Lücking, Genia; Stoeckel, Marina; Atamer, Zeynep; Hinrichs, Jörg; Ehling-Schulz, Monika

    2013-09-01

    Due to changes in the design of industrial food processing and increasing international trade, highly thermoresistant spore-forming bacteria are an emerging problem in food production. Minimally processed foods and products with extended shelf life, such as milk products, are at special risk for contamination and subsequent product damages, but information about origin and food quality related properties of highly heat-resistant spore-formers is still limited. Therefore, the aim of this study was to determine the biodiversity, heat resistance, and food quality and safety affecting characteristics of aerobic spore-formers in the dairy sector. Thus, a comprehensive panel of strains (n=467), which originated from dairy processing environments, raw materials and processed foods, was compiled. The set included isolates associated with recent food spoilage cases and product damages as well as isolates not linked to product spoilage. Identification of the isolates by means of Fourier-transform infrared spectroscopy and molecular methods revealed a large biodiversity of spore-formers, especially among the spoilage associated isolates. These could be assigned to 43 species, representing 11 genera, with Bacillus cereus s.l. and Bacillus licheniformis being predominant. A screening for isolates forming thermoresistant spores (TRS, surviving 100°C, 20 min) showed that about one third of the tested spore-formers was heat-resistant, with Bacillus subtilis and Geobacillus stearothermophilus being the prevalent species. Strains producing highly thermoresistant spores (HTRS, surviving 125°C, 30 min) were found among mesophilic as well as among thermophilic species. B. subtilis and Bacillus amyloliquefaciens were dominating the group of mesophilic HTRS, while Bacillus smithii and Geobacillus pallidus were dominating the group of thermophilic HTRS. Analysis of spoilage-related enzymes of the TRS isolates showed that mesophilic strains, belonging to the B. subtilis and B. cereus

  4. Ultrasonic Treatment Enhanced Ammonia-Oxidizing Bacterial (AOB) Activity for Nitritation Process.

    PubMed

    Zheng, Min; Liu, Yan-Chen; Xin, Jia; Zuo, Hao; Wang, Cheng-Wen; Wu, Wei-Min

    2016-01-19

    Oxidation of ammonia to nitrite rather than nitrate is critical for nitritation process for wastewater treatment. We proposed a promising approach by using controlled ultrasonic treatment to enhance the activity of ammonia-oxidizing bacteria (AOB) and suppress that of nitrite-oxidizing bacteria (NOB). Batch activity assays indicated that when ultrasound was applied, AOB activity reached a peak level and then declined but NOB activity deteriorated continuously as the power intensity of ultrasound increased. Kinetic analysis of relative microbial activity versus ultrasonic energy density was performed to investigate the effect of operational factors (power, sludge concentration, and aeration) on AOB and NOB activities and the test parameters were selected for reactor tests. Laboratory sequential batch reactor (SBR) was further used to test the ultrasonic stimulus with 8 h per day operational cycle and synthetic waste urine as influent. With specific ultrasonic energy density of 0.09 kJ/mg VSS and continuously fed influent containing above 200 mg NH3-N/L, high AOB reproductive activity was achieved and nearly complete conversion of ammonia-N to nitrite was maintained. Microbial structure analysis confirmed that the treatment changed community of AOB, NOB, and heterotrophs. Known AOB Nitrosomonas genus remained at similar level in the biomass while typical NOB Nitrospira genus disappeared in the SBR under ultrasonic treatment and after the treatment was off for 30 days. PMID:26678011

  5. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm.

    PubMed

    Foesel, Bärbel U; Gieseke, Armin; Schwermer, Carsten; Stief, Peter; Koch, Liat; Cytryn, Eddie; de la Torré, José R; van Rijn, Jaap; Minz, Dror; Drake, Harold L; Schramm, Andreas

    2008-02-01

    Zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. In these systems, water is purified and recycled via microbial biofilters. Here, quantitative data on nitrifier community structure of a trickling filter biofilm associated with a recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amoA) confirmed the results. The most abundant ammonia-oxidizing bacteria (AOB) were members of the Nitrosomonas sp. Nm143-lineage (6.7% of the bacterial biovolume), followed by Nitrosomonas marina-like AOB (2.2% of the bacterial biovolume). Both were outnumbered by nitrite-oxidizing bacteria of the Nitrospira marina-lineage (15.7% of the bacterial biovolume). Although more than eight other nitrifying populations were detected, including Crenarchaeota closely related to the ammonia-oxidizer 'Nitrosopumilus maritimus', their collective abundance was below 1% of the total biofilm volume; their contribution to nitrification in the biofilter is therefore likely to be negligible. PMID:18093145

  6. Diversity of Ammonia Oxidation (amoA) and Nitrogen Fixation (nifH) Genes in Lava Caves of Terceira, Azores, Portugal

    PubMed Central

    Hathaway, Jennifer J. Marshall; Sinsabaugh, Robert L.; Dapkevicius, Maria De Lurdes N. E.; Northup, Diana E.

    2015-01-01

    Lava caves are an understudied ecosystem in the subterranean world, particularly in regard to nitrogen cycling. The diversity of ammonia oxidation (amoA) and nitrogen fixation (nifH) genes in bacterial mats collected from lava cave walls on the island of Terceira (Azores, Portugal) was investigated using denaturing gradient gel electrophoresis (DGGE). A total of 55 samples were collected from 11 lava caves that were selected with regard to surface land use. Land use types above the lava caves were categorized into pasture, forested, and sea/urban, and used to determine if land use influenced the ammonia oxidizing and nitrogen fixing bacterial communities within the lava caves. The soil and water samples from each lava cave were analyzed for total organic carbon, inorganic carbon, total nitrogen, ammonium, nitrate, phosphate and sulfate, to determine if land use influences either the nutrient content entering the lava cave or the nitrogen cycling bacteria present within the cave. Nitrosospira-like sequences dominated the ammonia-oxidizing bacteria (AOB) community, and the majority of the diversity was found in lava caves under forested land. The nitrogen fixation community was dominated by Klebsiella pneumoniae-like sequences, and diversity was evenly distributed between pasture and forested land, but very little overlap in diversity was observed. The results suggest that land use is impacting both the AOB and the nitrogen fixing bacterial communities. PMID:26778867

  7. Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management

    SciTech Connect

    Wessen, E.; Nyberg, K.; Jansson, J.K.; Hallin, S.

    2010-05-01

    Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soil, but their relative distribution may vary depending on the environmental conditions. Effects of changes in soil organic matter and nutrient content on the AOB and AOA are poorly understood. Our aim was to compare effects of long-term soil organic matter depletion and amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without easily plant-available nitrogen, on the activities, abundances and community structures of AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances and the community structures of both groups based on T-RFLP of amoA genes were determined. Straw amendment during 50 years had not altered any of the measured soil parameters, while the addition of peat resulted in a significant increase of soil organic carbon as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil pH, organic carbon and total nitrogen, but an increase in primary production. Type and amount of organic matter had an impact on the AOB and AOA community structures and the AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that under certain conditions the AOB dominate, suggesting niche differentiation between the two groups at the field site. The large differences in potential rates between treatments correlated to the AOA community size, indicating that they were functionally more important in the nitrification process than the AOB. The AOA abundance was positively related to addition of labile organic carbon, which supports the idea that AOA could have alternative growth strategies using organic carbon. The AOB community size varied little in contrast to that of the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater ecophysiological diversity and

  8. Drug resistance and molecular epidemiology of aerobic bacteria isolated from puerperal infections in Bangladesh.

    PubMed

    Ahmed, Salma; Kawaguchiya, Mitsuyo; Ghosh, Souvik; Paul, Shyamal Kumar; Urushibara, Noriko; Mahmud, Chand; Nahar, Kamrun; Hossain, Mohammad Akram; Kobayashi, Nobumichi

    2015-06-01

    Puerperal infection is a common complication during postnatal period in developing countries. Bacterial species, drug resistance, and genetic characteristics were investigated for a total of 470 isolates from puerperal infections in Bangladesh for a 2-year period (2010-2012). The most common species was Escherichia coli (n=98), followed by Enterococcus faecalis (n=54), Staphylococcus haemolyticus (n=33), Proteus mirabilis (n=32), Staphylococcus aureus (n=27), Klebsiella pneumoniae (n=22), and Enterobacter cloacae (n=21). S. aureus and Acinetobacter baumannii were isolated at a higher frequency from wound infections after cesarean section, while E. coli, E. cloacae, and K. pneumoniae were isolated from community-acquired endometritis and urinary tract infections. Resistance to third-generation cephalosporins was frequent for Enterobacteriacae, and was mainly mediated by blaCTX-M-1 group beta-lactamases. The CTX-M gene in E. coli from the four phylogroups was identified as blaCTX-M-15, and phylogroup B2 isolates with blaCTX-M-15 were classified into ST131 with O25b allele, harboring aac(6')-Ib-cr and various virulence factors. Carbapenemase genes blaNDM-1 and blaNDM-7 were identified in one isolate each of phylogroup A E. coli. Methicillin-resistant S. aureus isolates had type IV or V SCCmec, including isolates of ST361 (CC672), which is related to an emerging ST672 clone in the Indian subcontinent. This study revealed the recent epidemiological status of aerobic bacteria causing puerperal infections in Bangladesh, providing useful information to improve clinical practice and infection control. PMID:25555043

  9. Functional Relationship Between Phytoplankton and Aerobic Anoxygenic Photosynthetic Bacteria: Modes of Coexistence

    NASA Astrophysics Data System (ADS)

    Kolber, Z. S.; Haffa, A.; Klimov, D.

    2006-12-01

    Aerobic Anoxygenic Photosynthetic Bacteria (AAPs) are ubiquitously distributed in the upper ocean. Although they contain bacteriochlorophyll a (BChla), the main absorption bands in the near UV (370 nm) and infrared (800-850 nm) make this pigment impractical in light harvesting below the first few meters of the water column. Instead, they utilize carotenoids as major light harvesting pigments. Since these carotenoids absorb in the 430-550 nm range, phytoplankton and AAPs utilize a similar portion of the available light spectrum. As AAPs cannot utilize water as the electron donor, they transfer electrons between a range of organic/inorganic electron donors and electron acceptors, thus significantly participating in the redox cycle in the upper ocean. We have measured the vertical distribution and photosynthetic properties of both phytoplankton and AAPs in a highly oligotrophic region 800 km SW of Monterey Bay (34N, 129W), and we have consistently observed the presence of a BChla maximum about 30 to 40 meters above the chlorophyll maximum, indicating that phytoplankton and AAPs occupy different ecological niches in the water column. However, the abundance of AAPs generally displayed a maximum at dawn and a minimum at the dusk, indicating a high level of mortality. This diel cycle was observed in 5 micron and 3 micron size fractions, indicating active grazing by small protists. Incubation experiments with natural, mixed population of AAPs and phytoplankton results in an unusually high accumulation of AAPs in DCMU-treated samples, indicating that pigmented protists do contribute significantly to AAP grazing in a tightly-controlled microbial loop. On the other hand, AAP incubations in pure cultures indicate that they biomineralize sulfur, thus affecting the sulfur cycle. All of these observations indicate that the role of AAPs in the upper ocean ecology is defined by their relationship with phototrophic and heterotrophic communities, rather than by their relative

  10. [Antimicrobial susceptibility of clinical isolates of aerobic Gram-positive cocci and anaerobic bacteria in 2006].

    PubMed

    Yamaguchi, Takahiro; Yoshida, Isamu; Itoh, Yoshihisa; Tachibana, Mineji; Takahashi, Choichiro; Kaku, Mitsuo; Kanemitsu, Keiji; Okada, Masahiko; Horikawa, Yoshinori; Shiotani, Joji; Kino, Hiroyoshi; Ono, Yuka; Baba, Hisashi; Matsuo, Shuji; Asari, Seishi; Toyokawa, Masahiro; Matsuoka, Kimiko; Kusano, Nobuchika; Nose, Motoko; Murase, Mitsuharu; Miyamoto, Hitoshi; Saikawa, Tetsunori; Hiramatsu, Kazufumi; Kohno, Shigeru; Yanagihara, Katsunori; Yamane, Nobuhisa; Nakasone, Isamu; Maki, Hideki; Yamano, Yoshinori

    2010-12-01

    The activity of antibacterial agents against aerobic Gram-positive cocci (26 species, 1022 strains) and anaerobic bacteria (23 species, 184 strains) isolated from clinical specimens in 2006 at 16 clinical facilities in Japan were studied using either broth microdilution or agar dilution method. The ratio of methicillin-resistant strains among Staphylococcus aureus and Staphylococcus epidermidis was 53.0% and 65.8%, suggesting that resistant strains were isolated at high frequency. Vancomycin (VCM) and quinupristin/dalfopristin (QPR/DPR) had good antibacterial activity against methicillin-resistant S. aureus and methicillin-resistant S. epidermidis, with MIC90s of < or = 2 micrcog/mL. The ratio of penicillin (PC) intermediate and resistant strains classified by mutations of PC-binding proteins among Streptococcus pneumoniae was 87.6%. Ceftriaxone, cefpirome, cefepime, carbapenem antibiotics, VCM, teicoplanin, linezolid(LZD) and QPR/DPR had MIC90s of < or = 1 microg/mL against PC-intermediate and resistant S. pneumoniae strains. Against all strains of Enterococcus faecalis and Enterococcus faecium, the MICs of VCM and TEIC were under 2 microg/mL, and no resistant strain was detected, suggesting that these agents had excellent activities against these species. 10.9% of E. faecalis strains or 3.5% of E. faecium strains showed intermediate or resistant to LZD. 24.4% of E. faecium strains showed intermediate or resistant to QPR/DPR. Against all strains of Clostridium difficile, the MIC of VCM were under 1 microg/mL, suggesting that VCM had excellent activity against C. difficile. Carbapenems showed good activity against Peptococcaceae, Bacteroides spp., and Prevotella spp. However since several strains of Bacteroides fragilis showed resistant to carbapenems and the susceptibility of this species should be well-focused in the future. PMID:21425596

  11. [Antimicrobial susceptibility of clinical isolates of aerobic gram-positive cocci and anaerobic bacteria in 2008].

    PubMed

    Yoshida, Isamu; Yamaguchi, Takahiro; Kudo, Reiko; Fuji, Rieko; Takahashi, Choichiro; Oota, Reiko; Kaku, Mitsuo; Kunishima, Hiroyuki; Okada, Masahiko; Horikawa, Yoshinori; Shiotani, Joji; Kino, Hiroyoshi; Ono, Yuka; Fujita, Shinichi; Matsuo, Shuji; Kono, Hisashi; Asari, Seishi; Toyokawa, Masahiro; Kusano, Nobuchika; Nose, Motoko; Horii, Toshinobu; Tanimoto, Ayako; Miyamoto, Hitoshi; Saikawa, Tetsunori; Hiramatsu, Kazufumi; Kohno, Shigeru; Yanagihara, Katsunori; Yamane, Nobuhisa; Nakasone, Isamu; Maki, Hideki; Yamano, Yoshinori

    2012-02-01

    The activity of antibacterial agents against aerobic Gram-positive cocci (25 genus or species, 1029 strains) and anaerobic bacteria (21 genus or species, 187 strains) isolated from clinical specimens in 2008 at 16 clinical facilities in Japan were studied using either broth microdilution or agar dilution method. The ratio of methicillin-resistant strains among Staphylococcus aureus and Staphylococcus epidermidis was 59.6% and 81.2%, suggesting that resistant strains were isolated at high frequency. Vancomycin (VCM), linezolid (LZD) and quinupristin/dalfopristin (QPR/DPR) had good antibacterial activity against methicillin-resistant S. aureus and methicillin-resistant S. epidermidis, with MIC90s of < or = 2 microg/mL. The ratio of penicillin (PC) intermediate and resistant strains classified by mutations of PC-binding proteins among Streptococcus pneumoniae was 92.0% that was highest among our previous reports. Cefpirome, carbapenems, VCM, teicoplanin (TEIC), LZD and QPR/DPR had MIC90s of < or = 1 microg/mL against PC-intermediate and resistant S. pneumoniae strains. Against all strains of Enterococcus faecalis and Enterococcus faecium, the MICs of VCM and TEIC were under 2 microg/mL, and no resistant strain was detected, suggesting that these agents had excellent activities against these species. 15.9% of E. faecalis strains and 1.2% of E. faecium strains showed intermediate to LZD. 17.1% of E. faecium strains showed intermediate or resistant to QPR/DPR. Against all strains of Clostridium difficile, the MIC of VCM was under 1 microg/mL, suggesting that VCM had excellent activity. Carbapenems showed good activity against Clostridiales, Bacteroides spp., and Prevotella spp., but one strain of Bacteroides fragilis showed resistant to carbapenems. And so, the susceptibility of this species should be well-focused in the future at detecting continuously. PMID:22808693

  12. Biodiversity and characterization of aerobic spore-forming bacteria in surimi seafood products.

    PubMed

    Coton, M; Denis, C; Cadot, P; Coton, E

    2011-04-01

    The microbial quality and safety of surimi seafood products was assessed by studying the prevalence and biodiversity of aerobic spore-forming bacteria at the beginning and end of shelf life in 100 surimi samples. Low levels of total flora and sporulated flora were numerated at the beginning of storage, however, residual spores were detected in the majority of samples during storage. Furthermore, for 34 samples, total flora counts>10(4) CFU/g were observed at the end of shelf life which could lead to non-compliance with good practice recommendations or product spoilage. In total, 460 strains were isolated, fingerprinted by M13-PCR and grouped into 98 different clusters. Representative strains were then identified at the species level via 16S rRNA gene sequencing. Overall, dominant species belonged to Bacillus simplex, Bacillus subtilis and Bacillus licheniformis; while B. simplex, B. subtilis as well as Sporosarcina aquimarina were clearly the dominant species found in samples with higher total flora counts. Amylolytic and proteolytic activities were very frequent amongst tested strains (80 and 92.5%, respectively). Heat resistance parameters of 4 strains in a surimi-based medium were determined. B. simplex and B. subtilis strains were the most heat resistant (δ(96 °C)= 27.6 and 23.3 min and z(T)=8.6 and 7.9, respectively) which can explain their dominance in surimi samples exhibiting higher microbial counts. The heat resistance data obtained can now be used to model thermal destruction of strains using predictive microbiology tools (Sym'Previus). PMID:21315981

  13. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

    NASA Astrophysics Data System (ADS)

    Frame, C. H.; Casciotti, K. L.

    2010-09-01

    Nitrous oxide (N2O) is a trace gas that contributes to the greenhouse effect and stratospheric ozone depletion. The N2O yield from nitrification (moles N2O-N produced per mole ammonium-N consumed) has been used to estimate marine N2O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O yield from nitrification is not constant. Previous culture-based measurements indicate that N2O yield increases as oxygen (O2) concentration decreases and as nitrite (NO2-) concentration increases. Here, we have measured yields of N2O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM) media. These yields, which were typically between 4 × 10-4 and 7 × 10-4 for cultures with cell densities between 2 × 102 and 2.1 × 104 cells ml-1, were lower than previous reports for ammonia-oxidizing bacteria. The observed impact of O2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5 × 106 cells ml-1), where 160-fold higher yields were observed at 0.5% O2 (5.1 μM dissolved O2) compared with 20% O2 (203 μM dissolved O2). At lower cell densities (2 × 102 and 2.1 × 104 cells ml-1), cultures grown under 0.5% O2 had yields that were only 1.25- to 1.73-fold higher than cultures grown under 20% O2. Thus, previously reported many-fold increases in N2O yield with dropping O2 could be reproduced only at cell densities that far exceeded those of ammonia oxidizers in the ocean. The presence of excess NO2- (up to 1 mM) in the growth medium also increased N2O yields by an average of 70% to 87% depending on O2 concentration. We made stable isotopic measurements on N2O from these cultures to identify the biochemical mechanisms behind variations in N2O yield. Based on measurements of δ15Nbulk, site preference (SP = δ15Nα-δ15Nβ), and δ18O of N2O (δ18O-N2O), we estimate that nitrifier

  14. MICROBIOLOGICAL CHARACTERIZATION OF BACTERIA INHABITING A WATER DISTRIBUTION SYSTEM SIMULATOR

    EPA Science Inventory

    The impact of chlorination and chloramination treatments on heterotrophic bacteria (HB) and ammonia oxidizing bacteria (AOB) inhabiting a water distribution system simulator was investigated. Notable changes in bacterial densities were observed during this monitoring study. For e...

  15. Preferential Use of Carbon Sources in Culturable Aerobic Mesophilic Bacteria of Coptotermes curvignathus's (Isoptera: Rhinotermitidae) Gut and Its Foraging Area.

    PubMed

    Wong, W Z; H'ng, P S; Chin, K L; Sajap, Ahmad Said; Tan, G H; Paridah, M T; Othman, Soni; Chai, E W; Go, W Z

    2015-10-01

    The lower termite, Coptotermes curvignathus, is one of the most prominent plantation pests that feed upon, digest, and receive nourishment from exclusive lignocellulose diets. The objective of this study was to examine the utilization of sole carbon sources by isolated culturable aerobic bacteria among communities from the gut and foraging pathway of C. curvignathus. We study the bacteria occurrence from the gut of C. curvignathus and its surrounding feeding area by comparing the obtained phenotypic fingerprint with Biolog's extensive species library. A total of 24 bacteria have been identified mainly from the family Enterobacteriaceae from the identification of Biolog Gen III. Overall, the bacteria species in the termite gut differ from those of foraging pathway within a location, except Acintobacter baumannii, which was the only bacteria species found in both habitats. Although termites from a different study area do not have the same species of bacteria in the gut, they do have a bacterial community with similar role in degrading certain carbon sources. Sugars were preferential in termite gut isolates, while nitrogen carbon sources were preferential in foraging pathway isolates. The preferential use of specific carbon sources by these two bacterial communities reflects the role of bacteria for regulation of carbon metabolism in the termite gut and foraging pathway. PMID:26314017

  16. Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant

    PubMed Central

    Sauder, Laura A; Peterse, Francien; Schouten, Stefan; Neufeld, Josh D

    2012-01-01

    The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidizing populations in nitrifying rotating biological contactors (RBCs) from a municipal wastewater treatment plant. Individual RBC stages are arranged in series, with nitrification at each stage creating an ammonia gradient along the flowpath. This RBC system provides a valuable experimental system for testing the hypothesis that ammonia concentration determines the relative abundance of AOA and AOB. The results demonstrate that AOA increased as ammonium decreased across the RBC flowpath, as indicated by qPCR for thaumarchaeal amoA and 16S rRNA genes, and core lipid (CL) and intact polar lipid (IPL) crenarchaeol abundances. Overall, there was a negative logarithmic relationship (R2 = 0.51) between ammonium concentration and the relative abundance of AOA amoA genes. A single AOA population was detected in the RBC biofilms; this phylotype shared low amoA and 16S rRNA gene homology with existing AOA cultures and enrichments. These results provide evidence that ammonia availability influences the relative abundances of AOA and AOB, and that AOA are abundant in some municipal wastewater treatment systems. PMID:22639927

  17. Effects of submerged macrophytes on the abundance and community composition of ammonia-oxidizing prokaryotes in a eutrophic lake.

    PubMed

    Zhao, Da-yong; Luo, Juan; Zeng, Jin; Wang, Meng; Yan, Wen-ming; Huang, Rui; Wu, Qinglong L

    2014-01-01

    Abundances and community compositions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in unvegetated sediment and the rhizosphere sediments of three submerged macrophytes (Ceratophyllum demersum, Vallisneria spinulosa, and Potamogeton crispus) were investigated in a large, eutrophic freshwater lake, Lake Taihu. Abundances of archaeal ammonia monooxygenase alpha-subunit (amoA) gene (from 6.56 × 10(6) copies to 1.06 × 10(7) copies per gram of dry sediment) were higher than those of bacterial amoA (from 6.13 × 10(5) to 3.21 × 10(6) copies per gram of dry sediment) in all samples. Submerged macrophytes exhibited no significant effect on the abundance and diversity of archaeal amoA gene. C. demersum and V. spinulosa increased the abundance and diversity of bacterial amoA gene in their rhizosphere sediment. However, the diversity of bacterial amoA gene in the rhizosphere sediments of P. crispus was decreased. The data obtained in this study would be helpful to elucidate the roles of submerged macrophytes involved in the nitrogen cycling of eutrophic lake ecosystems. PMID:23784056

  18. Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland.

    PubMed

    Liu, Yong; Zhang, Jingxu; Zhang, Xiaoling; Xie, Shuguang

    2014-06-01

    Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) might be the key microorganisms in ammonia conversion in ecosystems. However, the depth-related change of AOA and AOB in sediment ecosystem is still not clear. The relative contribution of AOA and AOB to nitrification in wetland sediment remains also unclear. Moreover, information about ammonia-oxidizing microorganisms in high-altitude freshwater wetland is still lacking. The present study investigated the relative abundances and community structures of AOA and AOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China). Variations of the relative abundances and community structures of AOA and AOB were found in the wetland sediments, dependent on both sampling site and sediment depth. The relative abundances of AOA and AOB (0.04-3.84 and 0.01-0.52 %) and the AOA/AOB ratio (0.12-4.65) showed different depth-related change patterns. AOB community size was usually larger than AOA community size. AOB diversity was usually higher than AOA diversity. AOA diversity decreased with the increase of sediment depth, while AOB diversity showed no obvious link with the sediment depth. Pearson's correlation analysis showed that AOA diversity had a positive significant correlation with available phosphorus. Nitrosospira-like sequences, with different compositions, predominated in the wetland sediment AOB communities. This work could provide some new insights toward nitrification in freshwater sediment ecosystems. PMID:24619246

  19. Spatial and temporal dynamics of ammonia oxidizers in the sediments of the Gulf of Finland, Baltic Sea.

    PubMed

    Vetterli, Adrien; Hietanen, Susanna; Leskinen, Elina

    2016-02-01

    The diversity and dynamics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) nitrifying communities in the sediments of the eutrophic Gulf of Finland (GoF) were investigated. Using clone libraries of ammonia monooxygenase (amoA) gene fragments and terminal restriction fragment length polymorphism (TRFLP), we found a low richness of both AOB and AOA. The AOB amoA phylogeny matched that of AOB 16S ribosomal genes from the same samples. AOA communities were characterized by strong spatial variation while AOB communities showed notable temporal patterns. At open sea sites, where transient anoxic conditions prevail, richness of both AOA and AOB was lowest and communities were dominated by organisms with gene signatures unique to the GoF. Given the importance of nitrification as a link between the fixation of nitrogen and its removal from aquatic environments, the low diversity of ammonia-oxidizing microbes across the GoF could be of relevance for ecosystem resilience in the face of rapid global environmental changes. PMID:26722795

  20. Effectiveness of Active Packaging on Control of Escherichia Coli O157:H7 and Total Aerobic Bacteria on Iceberg Lettuce.

    PubMed

    Lu, Haixia; Zhu, Junli; Li, Jianrong; Chen, Jinru

    2015-06-01

    Contaminated leafy green vegetables have been linked to several outbreaks of human gastrointestinal infections. Antimicrobial interventions that are adoptable by the fresh produce industry for control of pathogen contamination are in great demand. This study was undertaken to evaluate the efficacy of sustained active packaging on control of Escherichia coli O157:H7 and total aerobic bacteria on lettuce. Commercial Iceberg lettuce was inoculated with a 3-strain mixture of E. coli O157:H7 at 10(2) or 10(4) CFU/g. The contaminated lettuce and un-inoculated controls were placed respectively in 5 different active packaging structures. Traditional, nonactive packaging structure was included as controls. Packaged lettuce was stored at 4, 10, or 22 °C for 3 wk and sampled weekly for the population of E. coli O157:H7 and total aerobic bacteria. Results showed that packaging structures with ClO2 generator, CO2 generator, or one of the O2 scavengers effectively controlled the growth of E. coli O157:H7 and total aerobic bacteria under all storage conditions. Packaging structure with the ClO2 generator was most effective and no E. coli O157:H7 was detected in samples packaged in this structure except for those that were inoculated with 4 log CFU/g of E. coli O157:H7 and stored at 22 °C. Packaging structures with an oxygen scavenger and the allyl isothiocyanate generator were mostly ineffective in control of the growth of the bacteria on Iceberg lettuce. The research suggests that some of the packaging structures evaluated in the study can be used to control the presence of foodborne pathogens on leafy green vegetables. PMID:25974213

  1. Temperature Responses of Ammonia-Oxidizing Prokaryotes in Freshwater Sediment Microcosms

    PubMed Central

    Yu, Zhongbo; Huang, Rui; Wu, Qinglong L.

    2014-01-01

    In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups. PMID:24959960

  2. Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States.

    PubMed

    Yang, Yuyin; Zhang, Jingxu; Zhao, Qun; Zhou, Qiheng; Li, Ningning; Wang, Yilin; Xie, Shuguang; Liu, Yong

    2016-02-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state. PMID:26111964

  3. Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms.

    PubMed

    Zeng, Jin; Zhao, Dayong; Yu, Zhongbo; Huang, Rui; Wu, Qinglong L

    2014-01-01

    In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups. PMID:24959960

  4. Inhibition, Inactivation, and Recovery of Ammonia-Oxidizing Activity in Cometabolism of Trichloroethylene by Nitrosomonas europaea

    PubMed Central

    Hyman, M. R.; Russell, S. A.; Ely, R. L.; Williamson, K. J.; Arp, D. J.

    1995-01-01

    The kinetics of the cometabolism of trichloroethylene (TCE) by the ammonia-oxidizing soil bacterium Nitrosomonas europaea in short-term (<10-min) incubations were investigated. Three individual effects of TCE cometabolism on this bacterium were characterized. First, we observed that TCE is a potent competitive inhibitor of ammonia oxidation by N. europaea. The K(infi) value for TCE (30 (mu)M) is similar to the K(infm) for ammonia (40 (mu)M). Second, we examined the toxicity associated with TCE cometabolism by N. europaea. Stationary-phase cells of N. europaea oxidized approximately 60 nmol of TCE per mg of protein before ammonia-oxidizing activity was completely inactivated by reactive intermediates generated during TCE oxidation. At the TCE concentrations used in these experiments, ammonia did not provide significant protection against inactivation. Third, we have determined the ability of cells to recover ammonia-oxidizing activity after exposure to TCE. Cells recovering from TCE inactivation were compared with cells recovering from the specific inactivation of ammonia-oxidizing activity by light. The recovery kinetics were indistinguishable when 40% or less of the activity was inactivated. However, at increased levels of inactivation, TCE-inactivated cells did not recover as rapidly as light-inactivated cells. The kinetics of recovery appear to be dependent on both the extent of inactivation of ammonia-oxidizing activity and the degree of specificity of the inactivating treatment. PMID:16534997

  5. Survival, injury and inactivation of Escherichia coli 0157:H7, salmonella and aerobic mesophilic bacteria in apple juice and cider amended with nisin-edta

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For health reasons, people are consuming fresh juices or minimally processed fruit and vegetable juices, thereby, exposing themselves to the risk of foodborne illness if such juices are contaminated with bacteria pathogens. Behavior of aerobic mesophilic bacteria, Escherichia coli O157:H7 and Salmon...

  6. The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

    PubMed Central

    Hope Wilkinson, Katheryn; Strait, Jacqueline M.; Hozalski, Raymond M.; Sadowksy, Michael J.; Hamilton, Matthew J.

    2015-01-01

    The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

  7. The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms.

    PubMed

    LaPara, Timothy M; Hope Wilkinson, Katheryn; Strait, Jacqueline M; Hozalski, Raymond M; Sadowksy, Michael J; Hamilton, Matthew J

    2015-10-01

    The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

  8. Drivers of archaeal ammonia-oxidizing communities in soil.

    PubMed

    Zhalnina, Kateryna; de Quadros, Patrícia Dörr; Camargo, Flavio A O; Triplett, Eric W

    2012-01-01

    Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA. PMID:22715335

  9. Drivers of archaeal ammonia-oxidizing communities in soil

    PubMed Central

    Zhalnina, Kateryna; de Quadros, Patrícia Dörr; Camargo, Flavio A. O.; Triplett, Eric W.

    2012-01-01

    Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA. PMID:22715335

  10. Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China.

    PubMed

    Lee, Kwok-Ho; Wang, Yong-Feng; Li, Hui; Gu, Ji-Dong

    2014-12-01

    Ecophysiological differences between ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) enable them to adapt to different niches in complex freshwater wetland ecosystems. The community characters of AOA and AOB in the different niches in a freshwater wetland receiving municipal wastewater, as well as the physicochemical parameters of sediment/soil samples, were investigated in this study. AOA community structures varied and separated from each other among four different niches. Wetland vegetation including aquatic macrophytes and terrestrial plants affected the AOA community composition but less for AOB, whereas sediment depths might contribute to the AOB community shift. The diversity of AOA communities was higher than that of AOB across all four niches. Archaeal and bacterial amoA genes (encoding for the alpha-subunit of ammonia monooxygenases) were most diverse in the dry-land niche, indicating O2 availability might favor ammonia oxidation. The majority of AOA amoA sequences belonged to the Soil/sediment Cluster B in the freshwater wetland ecosystems, while the dominant AOB amoA sequences were affiliated with Nitrosospira-like cluster. In the Nitrosospira-like cluster, AOB amoA gene sequences affiliated with the uncultured ammonia-oxidizing beta-proteobacteria constituted the largest portion (99%). Moreover, independent methods for phylogenetic tree analysis supported high parsimony bootstrap values. As a consequence, it is proposed that Nitrosospira-like amoA gene sequences recovered in this study represent a potentially novel cluster, grouping with the sequences from Gulf of Mexico deposited in the public databases. PMID:25163821

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

    PubMed Central

    Jung, Man-Young; Park, Soo-Je; Min, Deullae; Kim, Jin-Seog; Rijpstra, W. Irene C.; Sinninghe Damsté, Jaap S.; Kim, Geun-Joong; Madsen, Eugene L.; Rhee, Sung-Keun

    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 MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [13C]bicarbonate assimilation assay showed stoichiometric incorporation of 13C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to “Candidatus Nitrosopumilus maritimus” revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N2O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated “Candidatus Nitrosoarchaeum koreensis.” PMID:22003023

  12. Application of potential phosphate-solubilizing bacteria and organic acids on phosphate solubilization from phosphate rock in aerobic rice.

    PubMed

    Panhwar, Qurban Ali; Jusop, Shamshuddin; Naher, Umme Aminun; Othman, Radziah; Razi, Mohd Ismail

    2013-01-01

    A study was conducted at Universiti Putra Malaysia to determine the effect of phosphate-solubilizing bacteria (PSB) and organic acids (oxalic & malic) on phosphate (P) solubilization from phosphate rock (PR) and growth of aerobic rice. Four rates of each organic acid (0, 10, 20, and 30 mM), and PSB strain (Bacillus sp.) were applied to aerobic rice. Total bacterial populations, amount of P solubilization, P uptake, soil pH, and root morphology were determined. The results of the study showed significantly high P solubilization in PSB with organic acid treatments. Among the two organic acids, oxalic acid was found more effective compared to malic acid. Application of oxalic acid at 20 mM along with PSB16 significantly increased soluble soil P (28.39 mg kg(-1)), plant P uptake (0.78 P pot(-1)), and plant biomass (33.26 mg). Addition of organic acids with PSB and PR had no influence on soil pH during the planting period. A higher bacterial population was found in rhizosphere (8.78 log10 cfu g(-1)) compared to the nonrhizosphere and endosphere regions. The application of organic acids along with PSB enhanced soluble P in the soil solution, improved root growth, and increased plant biomass of aerobic rice seedlings without affecting soil pH. PMID:24288473

  13. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.

    PubMed

    Ramond, Jean-Baptiste; Lako, Joseph D W; Stafford, William H L; Tuffin, Marla I; Cowan, Don A

    2015-08-01

    Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils. PMID:25721729

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

    PubMed Central

    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

  15. Nitrogen isotope fractionation during archaeal ammonia oxidation: Coupled estimates from isotopic measurements of ammonium and nitrite

    NASA Astrophysics Data System (ADS)

    Mooshammer, Maria; Stieglmeier, Michaela; Bayer, Barbara; Jochum, Lara; Melcher, Michael; Wanek, Wolfgang

    2014-05-01

    Ammonia-oxidizing archaea (AOA) are ubiquitous in marine and terrestrial environments and knowledge about the nitrogen (N) isotope effect associated with their ammonia oxidation activity will allow a better understanding of natural abundance isotope ratios, and therefore N transformation processes, in the environment. Here we examine the kinetic isotope effect for ammonia oxidation in a pure soil AOA culture (Ca. Nitrososphaera viennensis) and a marine AOA enrichment culture. We estimated the isotope effect from both isotopic signatures of ammonium and nitrite over the course of ammonia oxidation. Estimates of the isotope effect based on the change in the isotopic signature of ammonium give valuable insight, because these estimates are not subject to the same concerns (e.g., accumulation of an intermediate) as estimates based on isotopic measurements of nitrite. Our results show that both the pure soil AOA culture and a marine AOA enrichment culture have similar but substantial isotope effect during ammonia consumption (31-34 per mill; based on ammonium) and nitrite production (43-45 per mill; based on nitrite). The 15N fractionation factors of both cultures tested fell in the upper range of the reported isotope effects for archaeal and bacterial ammonia oxidation (10-41 per mill) or were even higher than those. The isotope fractionation for nitrite production was significantly larger than for ammonium consumption, indicating that (1) some intermediate (e.g., hydroxylamine) of ammonia oxidation accumulates, allowing for a second 15N fractionation step to be expressed, (2) a fraction of ammonia oxidized is lost via gaseous N forms (e.g., NO or N2O), which is 15N-enriched or (3) a fraction of ammonium is assimilated into AOA biomass, biomass becoming 15N-enriched. The significance of these mechanisms will be explored in more detail for the soil AOA culture, based on isotope modeling and isotopic measurements of biomass and N2O.

  16. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Jeanthon, C.; Boeuf, D.; Dahan, O.; Le Gall, F.; Garczarek, L.; Bendif, E. M.; Lehours, A.-C.

    2011-07-01

    Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivable fraction. In total, 54 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94 %) was affiliated to the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies between culture-based and molecular methods, this study highlights the existing gaps in the understanding

  17. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Jeanthon, C.; Boeuf, D.; Dahan, O.; Le Gall, F.; Garczarek, L.; Bendif, E. M.; Lehours, A.-C.

    2011-05-01

    Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivable fraction. In total, 52 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94%) was affiliated with the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies between culture-based and molecular methods, this study highlights the existing gaps in the understanding

  18. Validation of the Peel Plate™ AC for Detection of Total Aerobic Bacteria in Dairy and Nondairy Products.

    PubMed

    Salter, Robert S; Durbin, Gregory W; Bird, Patrick; Fisher, Kiel; Crowley, Erin; Hammack, Thomas; Chen, Yi; Clark, Dorn; Ziemer, Wayne

    2016-01-01

    Peel Plate™ AC (aerobic count) is a low-profile plastic 47 mm culture dish with adhesive top that contains a dried standard plate count medium with oxidation/reduction indicator triphenyl tetrazolium chloride (TTC) that turns red with dehydrogenase enzyme activity of growing aerobic bacteria. The method provides a conventional quantitative count with simple rehydration and incubation for 48 ± 3 h at 35 ± 1°C for most food matrixes and 32 ± 1°C for 48 ± 3 h for dairy products. Dairy matrixes claimed and supported with total aerobic count data are whole milk, skim milk, chocolate milk (2% fat), light cream (20% fat), pasteurized whole goat milk, ultra-high temperature pasteurized milk, nonfat dried milk, lactose-reduced milk, strawberry milk, raw cow milk, raw goat milk, raw sheep milk, condensed skim milk, and vanilla ice cream. Food matrixes claimed for aerobic count detection are raw ground beef, environmental sponge of stainless steel, raw ground turkey, dry dog food, liquid whole pasteurized eggs, milk chocolate, poultry carcass rinse, and large animal carcass sponge. The method has been independently evaluated for aerobic count in dairy products: whole milk, skim milk, chocolate milk, and light cream. The method was also independently evaluated for aerobic count in food matrixes: ground beef and sponge rinse from stainless steel surfaces. In the matrix study, each matrix was assessed separately at each contamination level in comparison to an appropriate reference method. Colony counts were determined for each level and then log10-transformed. The transformed data were evaluated for repeatability, mean comparison between methods with 95% confidence interval (CI), and r(2). A CI range of (-0.5, 0.5) on the mean difference was used as the acceptance criterion to establish significant statistical differences between methods. The evaluations demonstrate that the Peel Plate AC provides no statistical differences across most of the matrixes with r(2) > 0

  19. Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply.

    PubMed

    Simonin, Marie; Le Roux, Xavier; Poly, Franck; Lerondelle, Catherine; Hungate, Bruce A; Nunan, Naoise; Niboyet, Audrey

    2015-10-01

    Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira. AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements. PMID:25877793

  20. Inhibition of Salmonella Typhimurium by Cultures of Cecal Bacteria during Aerobic Incubation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two trials were conducted to examine the ability of cecal bacterial cultures from broilers to inhibit growth of Salmonella Typhimurium during aerobic incubation. Cecal broth media was inoculated with 10 µl of cecal contents from 6 week old broilers taken from 2 separate flocks. Cultures were incubat...

  1. [Element Sulfur Autotrophic Denitrification Combined Anaerobic Ammonia Oxidation].

    PubMed

    Zhou, Jian; Huang, Yong; Liu, Xin; Yuan, Yi; Li Xiang; Wangyan, De-qing; Ding, Liang; Shao, Jing-wei; Zhao, Rong

    2016-03-15

    A novel element sulfur autotrophic denitrification combined anaerobic ammonia oxidation process, reacted in CSTR, was used to investigate the sulfate production and alkalinity consumption during the whole process. The element sulfur dosage was 50 g · L⁻¹. The inoculation volume of ANAMMOX granular sludge was 100 g · L⁻¹. The agitation rate and environment reaction temperature of the CSTR were set to 120 r · min⁻¹ and 35°C ± 0.5°C, respectively. The pH of influent was maintained in range of 8. 0-8. 4. During the start-up stage of sulfur based autotrophic denitrification, the nitrogen removal loading rate could reach 0.56-0.71 kg · (m³ · d) ⁻¹ in the condition of 5.3 h hydrogen retention time and 200 mg · L⁻¹ nitrate nitrogen. After the addition of 60 mg · L⁻¹ ammonia nitrogen, Δn(SO₄²⁻):Δn(NO₃⁻) decreased from 1.21 ± 0.06 to 1.01 ± 0.10, Δ(IC): Δ(NO₃⁻-N) decreased from 0.72 ± 0.1 to 0.51 ± 0.11, and the effluent pH increased from 6.5 to 7.2. During the combined stage, the ammonia concentration of effluent was 10.1-19.2 mg · L⁻¹, and the nitrate-nitrogen removal loading rate could be maintained in range of 0.66-0.88 kg · (m³ · d)⁻¹. The Δn (NH₄⁺): Δn (NO₃⁻) ratio reached 0.43, and the NO₃⁻ removal rate was increased by 60% in the simultaneous ammonia and nitrate removal reaction under the condition of G(T) = 22-64 s⁻¹ and pH = 8.08, while improper conditions reduced the efficiency of simultaneous reaction. PMID:27337901

  2. Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System.

    PubMed

    Pinto, Ameet J; Marcus, Daniel N; Ijaz, Umer Zeeshan; Bautista-de Lose Santos, Quyen Melina; Dick, Gregory J; Raskin, Lutgarde

    2016-01-01

    We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation

  3. Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System

    PubMed Central

    Marcus, Daniel N.; Ijaz, Umer Zeeshan; Bautista-de lose Santos, Quyen Melina; Dick, Gregory J.; Raskin, Lutgarde

    2015-01-01

    ABSTRACT We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close

  4. Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota.

    PubMed

    Weber, Eva B; Lehtovirta-Morley, Laura E; Prosser, James I; Gubry-Rangin, Cécile

    2015-03-01

    Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. PMID:25764563

  5. Remediation of polychlorinated biphenyl impacted sediment by concurrent bioaugmentation with anaerobic halorespiring and aerobic degrading bacteria

    PubMed Central

    Payne, Rayford B.; Fagervold, Sonja K.; May, Harold D.; Sowers, Kevin R.

    2013-01-01

    Bioremediation of sediments contaminated with commercial PCBs is potentially achievable by the sequential activity of anaerobic halorespiration to convert higher chlorinated congeners to less chlorinated congeners that are susceptible to aerobic respiratory degradation. The efficacy of bioaugmentation with anaerobic halorespiring “Dehalobium chlorocoercia” DF1 and aerobic Burkholderia xenovorans LB400 added concurrently with GAC as a delivery system was determined in 2-liter laboratory mesocosms containing weathered Aroclor-contaminated sediment from Baltimore Harbor, MD. The greatest effect was seen in the mesocosm bioaugmented with both DF1 and LB400 together, which resulted in an 80% decrease by mass of PCBs, from 8 mg/kg to less than 2 mg/kg after 120 days. There was no significant increase in lesser-chlorinated congeners, indicating that both anaerobic dechlorination by DF1 and aerobic degradation by LB400 occurred. In contrast, non-bioaugmented controls containing filtered culture supernatant showed only 25% decrease in total levels of PCBs after 365 days, which was likely due to biostimulation of the indigenous population by the medium. Direct colony counts and molecular analysis targeting a putative reductive dehalogenase gene of D. chlorocoercia, or the bphA gene of LB400 showed the presence of viable DF1 and LB400 in bioaugmented mesocosms after 365 days, indicating that both non-indigenous strains were sustainable within the indigenous microbial community. These results suggest that an in situ treatment employing the simultaneous application of anaerobic and aerobic microorganisms could be an effective, environmentally sustainable strategy to reduce PCBs levels in contaminated sediment. PMID:23463900

  6. Effects of 30 Years of Crop Rotation and Tillage on Bacterial and Archaeal Ammonia Oxidizers.

    PubMed

    Munroe, Jake W; McCormick, Ian; Deen, William; Dunfield, Kari E

    2016-05-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) both mediate soil nitrification and may have specialized niches in the soil. Little is understood of how these microorganisms are affected by long-term crop rotation and tillage practices. In this study, we assessed abundance and gene expression of AOB and AOA under two contrasting crop rotations and tillage regimes at a 30-yr-old long-term experiment on a Canadian silt loam soil. Continuous corn ( L.) (CC) was compared with a corn-corn-soybean [ (L.) Merr.]-winter wheat ( L.) rotation under-seeded with red clover ( L.) (RC), with conventional tillage (CT) and no-till (NT) as subplot treatments. Soil sampling was performed during the first corn year at four time points throughout the 2010 season and at three discrete depths (0-5, 5-15, and 15-30 cm). Overall, AOA abundance was found to be more than 10 times that of AOB, although AOA transcriptional activity was below detectable levels across all treatments. Crop rotation had a marginally significant effect on AOB abundance, with 1.3 times as many gene copies under the simpler CC rotation than under the more diverse RC rotation. More pronounced effects of depth on AOB abundance and gene expression were observed under NT versus CT management, and NT supported higher abundances of total archaea and AOA than CT across the growing season. We suggest that AOB may be more functionally important than AOA in this high-input agricultural soil but that NT management can promote enhanced soil archaeal populations. PMID:27136161

  7. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

    PubMed Central

    Alves, Ricardo J Eloy; Wanek, Wolfgang; Zappe, Anna; Richter, Andreas; Svenning, Mette M; Schleper, Christa; Urich, Tim

    2013-01-01

    The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota–AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils. PMID:23466705

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Isolation of culturable aerobic bacteria and evidence of Kerstersia gyiorum from the blowhole of captive Yangtze finless porpoises.

    PubMed

    Wan, Xiaoling; McLaughlin, Richard William; Zhou, Junying; Hao, Yujiang; Zheng, Jinsong; Wang, Ding

    2016-08-01

    Bacterial respiratory illnesses are problematic in aquatic mammals such as the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP), which is now at a critically endangered status. Yet little is known about the bacteria inhabiting the respiratory tract of YFPs. In this study, we preliminarily characterized the culturable aerobic bacteria from blow samples of captive YFPs. The bacterial diversity was assessed through cultivation by direct exhalation onto Columbia blood agar plates and identification of representative isolates through 16S rRNA gene sequence analysis. In total, eleven bacterial species belonging to four phyla Proteobacteria (71 %), Firmicutes (25 %), Bacteroidetes (3 %) and Actinobacteria (1 %) were identified. Most of these isolates were opportunistic pathogens found in respiratory illnesses in humans and animals. We also reported the first case of Kerstersia gyiorum isolated from an animal. This work provides a preliminary assessment of the bacteria present in the respiratory tract of captive YFPs, which will be an important first step in elucidating the roles of normal microbiota in maintaining respiratory health of YFPs. This study also points out the necessity of future long-term monitoring of blowhole microorganisms in the YFPs and making emergency preparedness plans for respiratory tract infections. These measures can aid in assessing the pathogenic risk of the critically endangered YFP populations. PMID:27251558

  10. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray.

    PubMed

    Ward, Bess B; Eveillard, Damien; Kirshtein, Julie D; Nelson, Joshua D; Voytek, Mary A; Jackson, George A

    2007-10-01

    The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2's largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean. PMID:17803777

  11. Vertical distribution of ammonia-oxidizing archaea (AOA) in the hyporheic zone of a eutrophic river in North China.

    PubMed

    Wang, Zhixin; Wang, Ziyuan; Huang, Caihong; Pei, Yuansheng

    2014-04-01

    Nitrification plays a significant role in the global nitrogen cycle, and this concept has been challenged with the discovery of ammonia-oxidizing archaea (AOA) in the environment. In this paper, the vertical variations of the diversity and abundance of AOA in the hyporheic zone of the Fuyang River in North China were investigated by molecular techniques, including clone libraries, phylogenetic analysis and real-time polymerase chain reaction. The archaeal amoA gene was detected in all sediments along the profile, and all AOA fell within marine group 1.1a and soil group1.1b of the Thaumarchaeota phylum, with the latter being the dominant type. The diversity of AOA decreased with the sediment depth, and there was a shift in AOA community between top-sediments (0-5 cm) and sub-sediments (5-70 cm). The abundance of the archaeal amoA gene (1.48 × 10⁷ to 5.50 × 10⁷ copies g⁻¹ dry sediment) was higher than that of the bacterial amoA gene (4.01 × 10⁴ to 1.75 × 10⁵ copies g⁻¹ dry sediment) in sub-sediments, resulting in a log₁₀ ratio of AOA to ammonia-oxidizing bacteria (AOB) from 2.27 to 2.69, whereas AOB outnumbered AOA in top-sediments with a low log10 ratio of (-0.24). The variations in the AOA community were primarily attributed to the combined effect of the nutrients (ammonium-N, nitrate-N and total organic carbon) and oxygen in sediments. Ammonium-N was the major factor influencing the relative abundance of AOA and AOB, although other factors, such as total organic carbon, were involved. This study helps elucidate the roles of AOA and AOB in the nitrogen cycling of hyporheic zone. PMID:24242890

  12. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

    USGS Publications Warehouse

    Ward, B.B.; Eveillard, D.; Kirshtein, J.D.; Nelson, J.D.; Voytek, M.A.; Jackson, G.A.

    2007-01-01

    The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2???s largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean. ?? 2007 The Authors.

  13. Effects of maturity stage and lactic acid bacteria on the fermentation quality and aerobic stability of Siberian wildrye silage.

    PubMed

    Li, Ping; Bai, Shiqie; You, Minghong; Shen, Yixin

    2016-09-01

    It is difficult to make good quality of silage from alpine gramineous from the Qinghai Tibetan plateau. The effects of lactic acid bacteria (LAB) on the fermentation quality and aerobic stability of Siberian wildrye silage were studied in southeast of the Qinghai Tibetan plateau. Siberian wildrye materials were freshly cut at the sprouting stage, flowering stage, and milky stage. Silage was prepared by using a small-scale silage fermentation system (bag silos). Lactobacillus plantarum (LP, 5 × 10(8) cfu/kg FM), Lactobacillus buchneri (LB, 5 × 10(8) cfu/kg FM) and their mixture (LP+LB, 5 × 10(8) cfu/kg FM) as silage additives were separately added to ensiled forages, and no additive served as control (CK). These bag silos were kept at room temperature (<15°C), and the silage qualities were analyzed after 60 days of ensiling. The number of indigenous LAB on fresh materials was less than that of yeasts and molds, and LAB species showed specification adapted to low temperature. LAB inoculated silages had lower (P < 0.05) pH value, NH 3-N/TN and butyric acid content compared with control silage. Silage treated with LB had higher contents of acetic acid, propionic acid, WSC and CP. However, the aerobic stability of silages inoculated with LAB did not differ significantly between stages (P > 0.05). When fermentation characteristics, chemical composition, and aerobic stability were considered, treatment with L. plantarum resulted in high quality of Siberian wildrye silage harvested at the flowering stage in the alpine region. PMID:27625768

  14. Recalcitrance of 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE) to cometabolic degradation by pure cultures of aerobic and anaerobic bacteria.

    PubMed

    Megharaj, M; Jovcic, A; Boul, H L; Thiele, J H

    1997-08-01

    Pure cultures of aerobic and anaerobic bacteria capable of oxidation and reductive dehalogenation of chloroethylenes, and aerobic bacteria involved in biodegradation of polychlorinated biphenyls (PCBs) were screened for their ability to cometabolize the persistent pollutant 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE). Bacterial cultures expressing methane monooxygenase (Methylosinus trichosporium), propane monooxygenase (Mycobacterium vaccae) and biphenyl 2,3-dioxygenase enzymes (Pseudomonas fluorescens and Rhodococcus globerulus), as well as bacteria reductively dechlorinating chloroethylenes (Acetobacterium woodii and Clostridium butyricum) could not degrade DDE. Cell-free extracts of M. trichosporium, M. vaccae, P. fluorescens and R. globerulus were also unable to transform DDE, indicating that cell wall and membrane diffusion barriers were not biodegradation limiting. These studies suggest that these bacteria can not degrade DDE, even when provided with cosubstrates that induce chlorophenyl- and dichloroethylene-group transforming enzymes. PMID:9294241

  15. Radioassay for Hydrogenase Activity in Viable Cells and Documentation of Aerobic Hydrogen-Consuming Bacteria Living in Extreme Environments

    PubMed Central

    Schink, Bernhard; Lupton, F. S.; Zeikus, J. G.

    1983-01-01

    An isotopic tracer assay based on the hydrogenase-dependent formation of tritiated water from tritium gas was developed for in life analysis of microbial hydrogen transformation. This method allowed detection of bacterial hydrogen metabolism in pure cultures or in natural samples obtained from aquatic ecosystems. A differentiation between chemical-biological and aerobic-anaerobic hydrogen metabolism was established by variation of the experimental incubation temperature or by addition of selective inhibitors. Hydrogenase activity was shown to be proportional to the consumption or production of hydrogen by cultures of Desulfovibrio vulgaris, Clostridium pasteurianum, and Methanosarcina barkeri. This method was applied, in connection with measurements of free hydrogen and most-probable-number enumerations, in aerobic natural source waters to establish the activity and document the ecology of hydrogen-consuming bacteria in extreme acid, thermal, or saline environments. The utility of the assay is based in part on the ability to quantify bacterial hydrogen transformation at natural hydrogen partial pressures, without the use of artificial electron acceptors. PMID:16346288

  16. Isolation and Identification of Aerobic Bacteria Carrying Tetracycline and Sulfonamide Resistance Genes Obtained from a Meat Processing Plant.

    PubMed

    Li, Lili; Ye, Lei; Zhang, Sen; Meng, Hecheng

    2016-06-01

    Microbial contamination in food-processing plants can play a fundamental role in food quality and safety. The purpose of this study was to investigate aerobic bacteria carrying tetracycline and sulfonamide resistance genes from a meat processing plant as possible sources of meat contamination. One hundred swab samples from surfaces of conveyor belts, meat slicers, meat knives, benches, plastic trays, gloves, and aprons were analyzed. A total of 168 isolates belonging to 10 genera were obtained, including Pseudomonas sp. (n = 35), Acinetobacter sp. (n = 30), Aeromonas sp. (n = 20), Myroides sp. (n = 15), Serratia sp. (n = 15), Staphylococcus sp. (n = 14), Enterobacter sp. (n = 11), Escherichia coli (n = 10), Lactococcus sp. (n = 10), and Klebsiella sp. (n = 8). Of the 168 isolates investigated, 60.7% showed resistance to tetracycline and 57.7% to trimethoprim/sulfamethoxazole. The tetracycline resistance genes tetL, tetA, tetB, tetC, tetE, tetM, tetS, tetK, and tetX were found in the frequency of 7.7%, 6.0%, 4.8%, 4.8%, 3.6%, 3.6%, 3.6%, 1.2%, and 0.6%, respectively. Sulfonamide resistance genes sul1 and sul2 were observed in the frequency of 17.9% and 38.1%, respectively. The tetracycline resistance genes tetX was first found in Myroides sp. This investigation demonstrated that food contact surfaces in a meat processing plant may be sources of contamination of aerobic bacteria carrying tetracycline and sulfonamide antibiotic resistance genes. PMID:27100915

  17. Abundance, depth distribution, and composition of aerobic bacteriochlorophyll a-producing bacteria in four basins of the central Baltic Sea.

    PubMed

    Salka, Ivette; Moulisová, Vladimíra; Koblízek, Michal; Jost, Günter; Jürgens, Klaus; Labrenz, Matthias

    2008-07-01

    The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 x 10(5) cells ml(-1) (11% of total prokaryotes) or 1.0 x 10(3) CFU ml(-1) (9 to 10% of total CFU). Environmental pufM clone sequences were grouped into 11 operational taxonomic units phylogenetically related to cultivated members of the Alpha-, Beta-, and Gammaproteobacteria. In spite of varying pufM compositions, five clones were present in all libraries. Of these, Jannaschia-related clones were always found in relative abundances representing 25 to 30% of the total AAP clones. The abundances of the other clones varied. Clones potentially affiliated with typical freshwater Betaproteobacteria sequences were present at three Baltic Sea stations, whereas clones grouping with Loktanella represented 40% of the total cell numbers in the Gotland Basin. For three alphaproteobacterial clones, probable pufM phylogenetic relationships were supported by 16S rRNA gene analyses of Baltic AAP isolates, which showed nearly identical pufM sequences. Our data indicate that the studied AAP assemblages represented a mixture of marine and freshwater taxa, thus characterizing the Baltic Sea as a "melting pot" of abundant, polyphyletic aerobic photoheterotrophic bacteria. PMID:18502937

  18. Space agriculture for habitation on Mars with hyper-thermophilic aerobic composting bacteria

    NASA Astrophysics Data System (ADS)

    Kanazawa, S.; Ishikawa, Y.; Tomita-Yokotani, K.; Hashimoto, H.; Kitaya, Y.; Yamashita, M.; Nagatomo, M.; Oshima, T.; Wada, H.; Space Agriculture Task Force, J.

    Manned Mars exploration requires recycle of materials to support human life A conceptual design is developed for space agriculture which is driven by the biologically regenerative function Hyper-thermophilic aerobic composting bacterial ecology is the core of materials recycling system to process human metabolic waste and inedible biomass and convert them to fertilizer for plants cultivation A photosynthetic reaction of plants will be driven by solar energy Water will be recycled by cultivation of plants and passing it through plant bodies Sub-surface water and atmospheric carbon dioxide are the natural resource available on Mars and these resources will be converted to oxygen and foods We envision that the agricultural system will be scaled up by importing materials from Martian environment Excess oxygen will be obtained from growing trees for structural and other components Minor elements including N P K and other traces will be introduced as fertilizers or nutrients into the agricultural materials circulation Nitrogen will be collected from Martian atmosphere We will assess biological fixation of nitrogen using micro-organisms responsible in Earth biosphere Hyper-thermophilic aerobic bacterial ecology is effective to convert waste materials into useful forms to plants This microbial technology has been well established on ground for processing sewage and waste materials For instance the hyper-thermophilic bacterial system is applied to a composting machine in a size of a trash box in home kitchen Since such a home electronics

  19. Occurrence and activity of sulphate reducing bacteria in aerobic activated sludge systems.

    PubMed

    van den Brand, T P H; Roest, K; Chen, G H; Brdjanovic, D; van Loosdrecht, M C M

    2015-03-01

    In the sewage or wastewater treatment plant, biological sulphate reduction can occur spontaneously or be applied beneficially for its treatment. The results of this study can be applied to control SRB in the sewage and WWTP. Therefore, population diversity analyses of SRB for nine activated sludge wastewater treatment plants (WWTP) in the Netherlands and the effect of long-term (months) oxygen exposures on the SRB activity were carried out. T-RFLP and clone sequencing analyses of winter and summer samples revealed that (1) all WWTP have a similar SRB population, (2) there is no seasonal impact (10-20 °C) on the SRB population present in the WWTP and (3) Desulfobacter postgatei, Desulfovibrio desulfuricans and Desulfovibrio intestinalis were the most common and dominant SRB species observed in these samples, and origin from the sewage. Short term activity tests demonstrated that SRB were not active in the aerobic WWTP, but while flushed with N2-gas SRB became slightly active after 3 h. In a laboratory reactor at a dissolved oxygen concentration of <2 %, sulphate reduction occurred and 89 % COD removal was achieved. SRB grew in granules, in order to protect themselves for oxygen exposures. SRB are naturally present in aerobic WWTP, which is due to the formation of granules. PMID:25649202

  20. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

    NASA Astrophysics Data System (ADS)

    Frame, C. H.; Casciotti, K. L.

    2010-04-01

    grown under 20% O2 and 43% to 87% under 0.5% O2. We also demonstrate that a positive correlation between SP and δ18O-N2O is expected when nitrifying bacteria produce N2O. A positive relationship between SP and δ18O-N2O has been observed in environmental N2O datasets, but until now, explanations for the observation invoked only denitrification. Such interpretations may overestimate the role of heterotrophic denitrification and underestimate the role of ammonia oxidation in environmental N2O production.

  1. Isolation of Aerobic Anoxygenic Photosynthetic Bacteria from Black Smoker Plume Waters of the Juan de Fuca Ridge in the Pacific Ocean

    PubMed Central

    Yurkov, Vladimir; Beatty, J. Thomas

    1998-01-01

    A strain of the aerobic anoxygenic photosynthetic bacteria was isolated from a deep-ocean hydrothermal vent plume environment. The in vivo absorption spectra of cells indicate the presence of bacteriochlorophyll a incorporated into light-harvesting complex I and a reaction center. The general morphological and physiological characteristics of this new isolate are described. PMID:16349490

  2. Colonization by aerobic bacteria in karst: Laboratory and in situ experiments

    USGS Publications Warehouse

    Personne, J.-C.; Poty, F.; Mahler, B.J.; Drogue, C.

    2004-01-01

    Experiments were carried out to investigate the potential for bacterial colonization of different substrates in karst aquifers and the nature of the colonizing bacteria. Laboratory batch experiments were performed using limestone and PVC as substrates, a natural bacterial isolate and a known laboratory strain (Escherichia coli [E. coli]) as inocula, and karst ground water and a synthetic formula as growth media. In parallel, fragments of limestone and granite were submerged in boreholes penetrating two karst aquifers for more than one year; the boreholes are periodically contaminated by enteric bacteria from waste water. Once a month, rock samples were removed and the colonizing bacteria quantified and identified. The batch experiments demonstrated that the natural isolate and E. coli both readily colonized limestone surfaces using karst ground water as the growth medium. In contrast, bacterial colonization of both the limestone and granite substrates, when submerged in the karst, was less intense. More than 300 bacterial strains were isolated over the period sampled, but no temporal pattern in colonization was seen as far as strain, and colonization by E. coli was notably absent, although strains of Salmonella and Citrobacter were each observed once. Samples suspended in boreholes penetrating highly fractured zones were less densely colonized than those in the borehole penetrating a less fractured zone. The results suggest that contamination of karst aquifers by enteric bacteria is unlikely to be persistent. We hypothesize that this may be a result of the high flow velocities found in karst conduits, and of predation of colonizing bacteria by autochthonous zooplankton.

  3. Species distribution and antimicrobial susceptibility of gram-negative aerobic bacteria in hospitalized cancer patients

    PubMed Central

    Ashour, Hossam M; El-Sharif, Amany

    2009-01-01

    Background Nosocomial infections pose significant threats to hospitalized patients, especially the immunocompromised ones, such as cancer patients. Methods This study examined the microbial spectrum of gram-negative bacteria in various infection sites in patients with leukemia and solid tumors. The antimicrobial resistance patterns of the isolated bacteria were studied. Results The most frequently isolated gram-negative bacteria were Klebsiella pneumonia (31.2%) followed by Escherichia coli (22.2%). We report the isolation and identification of a number of less-frequent gram negative bacteria (Chromobacterium violacum, Burkholderia cepacia, Kluyvera ascorbata, Stenotrophomonas maltophilia, Yersinia pseudotuberculosis, and Salmonella arizona). Most of the gram-negative isolates from Respiratory Tract Infections (RTI), Gastro-intestinal Tract Infections (GITI), Urinary Tract Infections (UTI), and Bloodstream Infections (BSI) were obtained from leukemic patients. All gram-negative isolates from Skin Infections (SI) were obtained from solid-tumor patients. In both leukemic and solid-tumor patients, gram-negative bacteria causing UTI were mainly Escherichia coli and Klebsiella pneumoniae, while gram-negative bacteria causing RTI were mainly Klebsiella pneumoniae. Escherichia coli was the main gram-negative pathogen causing BSI in solid-tumor patients and GITI in leukemic patients. Isolates of Escherichia coli, Klebsiella, Enterobacter, Pseudomonas, and Acinetobacter species were resistant to most antibiotics tested. There was significant imipenem -resistance in Acinetobacter (40.9%), Pseudomonas (40%), and Enterobacter (22.2%) species, and noticeable imipinem-resistance in Klebsiella (13.9%) and Escherichia coli (8%). Conclusion This is the first study to report the evolution of imipenem-resistant gram-negative strains in Egypt. Mortality rates were higher in cancer patients with nosocomial Pseudomonas infections than any other bacterial infections. Policies restricting

  4. Plant pathogenic anaerobic bacteria use aromatic polyketides to access aerobic territory.

    PubMed

    Shabuer, Gulimila; Ishida, Keishi; Pidot, Sacha J; Roth, Martin; Dahse, Hans-Martin; Hertweck, Christian

    2015-11-01

    Around 25% of vegetable food is lost worldwide because of infectious plant diseases, including microbe-induced decay of harvested crops. In wet seasons and under humid storage conditions, potato tubers are readily infected and decomposed by anaerobic bacteria (Clostridium puniceum). We found that these anaerobic plant pathogens harbor a gene locus (type II polyketide synthase) to produce unusual polyketide metabolites (clostrubins) with dual functions. The clostrubins, which act as antibiotics against other microbial plant pathogens, enable the anaerobic bacteria to survive an oxygen-rich plant environment. PMID:26542569

  5. A Method for Cell Culture and Maintenance of Ammonia-Oxidizing Archaea in Agar Stab.

    PubMed

    Chu, Yeon-Jin; Lee, Jin-Young; Shin, So-Ra; Kim, Geun-Joong

    2015-12-01

    Ammonia oxidizing archaea (AOA) are predominantly found and closely linked with geochemical cycling of nitrogen in non-extreme habitats. However, these strains have mainly been investigated using liquid cultures of enriched cells. Here, we provide an agar stab as a simple and reliable means of cultivating and maintaining AOA. PMID:26543273

  6. Isolation and characterization of poly(3-hydroxybutyrate)-producing bacteria from aerobic sludge.

    PubMed

    Zheng, Bingxin; Lu, Jianjiang; Tong, Yanbin; Li, Hongling; Chen, Qianqian

    2015-01-01

    Polyhydroxyalkanoates (PHAs) are biodegradable and environmentally friendly natural polymers. In this study, we isolated a bacterium strain capable of synthesizing PHAs from the aerobic sludge of a sewage treatment plant. The bacterium was identified as Burkholderia cepacia via physiological and biochemical tests as well as 16S rDNA sequence analysis. Strain WN-H41 produced PHAs, which was identified as P3HB. These PHAs have a number average molecular weight of 2.6 × 10(4) Da, a polydispersity index (PDI) of 2.4, and its thermal properties include a glass transition temperature of 1 °C, a melting temperature of 171 °C, and a decomposition temperature of 280 °C. These properties indicate that P3HB produced by WN-H41 has a high purity and good thermal stability. PMID:25304488

  7. Effect of selected monoterpenes on methane oxidation, denitrification, and aerobic metabolism by bacteria in pure culture.

    PubMed

    Amaral, J A; Ekins, A; Richards, S R; Knowles, R

    1998-02-01

    Selected monoterpenes inhibited methane oxidation by methanotrophs (Methylosinus trichosporium OB3b, Methylobacter luteus), denitrification by environmental isolates, and aerobic metabolism by several heterotrophic pure cultures. Inhibition occurred to various extents and was transient. Complete inhibition of methane oxidation by Methylosinus trichosporium OB3b with 1.1 mM (-)-alpha-pinene lasted for more than 2 days with a culture of optical density of 0.05 before activity resumed. Inhibition was greater under conditions under which particulate methane monooxygenase was expressed. No apparent consumption or conversion of monoterpenes by methanotrophs was detected by gas chromatography, and the reason that transient inhibition occurs is not clear. Aerobic metabolism by several heterotrophs was much less sensitive than methanotrophy was; Escherichia coli (optical density, 0.01), for example, was not affected by up to 7.3 mM (-)-alpha-pinene. The degree of inhibition was monoterpene and species dependent. Denitrification by isolates from a polluted sediment was not inhibited by 3.7 mM (-)-alpha-pinene, gamma-terpinene, or beta-myrcene, whereas 50 to 100% inhibition was observed for isolates from a temperate swamp soil. The inhibitory effect of monoterpenes on methane oxidation was greatest with unsaturated, cyclic hydrocarbon forms [e.g., (-)-alpha-pinene, (S)-(-)-limonene, (R)-(+)-limonene, and gamma-terpinene]. Lower levels of inhibition occurred with oxide and alcohol derivatives [(R)-(+)-limonene oxide, alpha-pinene oxide, linalool, alpha-terpineol] and a noncyclic hydrocarbon (beta-myrcene). Isomers of pinene inhibited activity to different extents. Given their natural sources, monoterpenes may be significant factors affecting bacterial activities in nature. PMID:9464387

  8. Effects of Agronomic Treatments on Structure and Function of Ammonia-Oxidizing Communities

    PubMed Central

    Phillips, Carol J.; Harris, Dave; Dollhopf, Sherry L.; Gross, Katherine L.; Prosser, James I.; Paul, Eldor A.

    2000-01-01

    The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the β subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 μg of NH4+-N ml−1, to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function. PMID:11097922

  9. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes

    PubMed Central

    Fauteux, Lisa; Cottrell, Matthew T.; Kirchman, David L.; Borrego, Carles M.; Garcia-Chaves, Maria Carolina; del Giorgio, Paul A.

    2015-01-01

    There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex. PMID:25927833

  10. Effect of applying lactic acid bacteria and propionic acid on fermentation quality and aerobic stability of oats-common vetch mixed silage on the Tibetan plateau.

    PubMed

    Zhang, Jie; Guo, Gang; Chen, Lei; Li, Junfeng; Yuan, Xianjun; Yu, Chengqun; Shimojo, Masataka; Shao, Tao

    2015-06-01

    The objective of this study was to evaluate effects of lactic acid bacteria and propionic acid on the fermentation quality and aerobic stability of oats-common vetch mixed silage by using a small-scale fermentation system on the Tibetan plateau. (i) An inoculant (Lactobacillus plantarum) (L) or (ii) propionic acid (P) or (iii) inoculant + propionic acid (PL) were used as additives. After fermenting for 60 days, silos were opened and the aerobic stability was tested for the following 15 days. The results showed that all silages were well preserved with low pH and NH3 -N, and high lactic acid content and V-scores. L and PL silages showed higher (P < 0.05) lactic acid and crude protein content than the control silage. P silage inhibited lactic acid production. Under aerobic conditions, L silage had similar yeast counts as the control silage (> 10(5) cfu/g fresh matter (FM)); however, it numerically reduced aerobic stability for 6 h. P and PL silages showed fewer yeasts (< 10(5) cfu/g FM) (P < 0.05) and markedly improved the aerobic stability (> 360 h). The result suggested that PL is the best additive as it could not only improved fermentation quality, but also aerobic stability of oats-common vetch mixed silage on the Tibetan plateau. PMID:25494579

  11. Anaerobic and aerobic bacteriology of the saliva and gingiva from 16 captive Komodo dragons (Varanus komodoensis): new implications for the "bacteria as venom" model.

    PubMed

    Goldstein, Ellie J C; Tyrrell, Kerin L; Citron, Diane M; Cox, Cathleen R; Recchio, Ian M; Okimoto, Ben; Bryja, Judith; Fry, Bryan G

    2013-06-01

    It has been speculated that the oral flora of the Komodo dragon (Varanus komodoensis) exerts a lethal effect on its prey; yet, scant information about their specific oral flora bacteriology, especially anaerobes, exists. Consequently, the aerobic and anaerobic oral bacteriology of 16 captive Komodo dragons (10 adults and six neonates), aged 2-17 yr for adults and 7-10 days for neonates, from three U.S. zoos were studied. Saliva and gingival samples were collected by zoo personnel, inoculated into anaerobic transport media, and delivered by courier to a reference laboratory. Samples were cultured for aerobes and anaerobes. Strains were identified by standard methods and 16S rRNA gene sequencing when required. The oral flora consisted of 39 aerobic and 21 anaerobic species, with some variation by zoo. Adult dragons grew 128 isolates, including 37 aerobic gram-negative rods (one to eight per specimen), especially Enterobacteriaceae; 50 aerobic gram-positive bacteria (two to nine per specimen), especially Staphylococcus sciuri and Enterococcusfaecalis, present in eight of 10 and nine of 10 dragons, respectively; and 41 anaerobes (one to six per specimen), especially clostridia. All hatchlings grew aerobes but none grew anaerobes. No virulent species were isolated. As with other carnivores, captive Komodo oral flora is simply reflective of the gut and skin flora of their recent meals and environment and is unlikely to cause rapid fatal infection. PMID:23805543

  12. Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China.

    PubMed

    Zhang, Fang-Qiu; Pan, Wen; Gu, Ji-Dong; Xu, Bin; Zhang, Wei-Hua; Zhu, Bao-Zhu; Wang, Yu-Xia; Wang, Yong-Feng

    2016-08-01

    A considerable proportion of Masson pine forests have been converted into eucalypt plantations in the last 30 years in Guangdong Province, subtropical China, for economic reasons, which may affect the ammonia-oxidizing archaea (AOA) community and the process of ammonia transformation. In order to determine the effects of forest conversion on AOA community, AOA communities in a Masson pine (Pinus massoniana) plantation and a eucalypt (Eucalyptus urophylla) plantation, which was converted from the Masson pine, were compared. Results showed that the land use change from the Masson pine to the eucalypt plantation decreased soil nutrient levels. A significant decrease of the potential nitrification rates (PNR) was also observed after the forest conversion (p < 5 %, n = 6). AOA were the only ammonia oxidizers in both plantations (no ammonia-oxidizing bacteria were detected). The detected AOA are affiliated with the genera Nitrosotalea and Nitrososphaera. A decrease of AOA abundance and an increase of the diversity were evident with the plantation conversion in the surface layer. AOA amoA gene diversity was negatively correlated with organic C and total N, respectively (p < 0.05, n = 12). AOA amoA gene abundance was negatively correlated with NH4 (+) and available P, respectively (p < 0.05, n = 12). However, AOA abundance was positively correlated with PNR, but not significantly (p < 0.05, n = 6), indicating AOA community change was only a partial reason for the decrease of PNR. PMID:27094186

  13. Aerobic degradation of a mixture of azo dyes in a packed bed reactor having bacteria-coated laterite pebbles.

    PubMed

    Senan, Resmi C; Shaffiqu, T S; Roy, J Jegan; Abraham, T Emilia

    2003-01-01

    A microbial consortium capable of aerobic degradation of a mixture of azo dyes consisting of two isolated strains (RRL,TVM) and one known strain of Pseudomonas putida (MTCC 1194) was immobilized on laterite stones. The amount of bacterial biomass attached to the laterite stones was 8.64 g per 100 g of the stone on a dry weight basis. The packed bed reactor was filled with these stones and had a total capacity of 850 mL and a void volume of 210 mL. The feed consisted of an equal mixture of seven azo dyes both in water as well as in a simulated textile effluent, at a pH of 9.0 and a salinity of 900 mg/L. The dye concentrations of influent were 25, 50, and 100 microg/mL. The residence time was varied between 0.78 and 6.23 h. It was found that at the lowest residence time 23.55, 45.73, and 79.95 microg of dye was degraded per hour at an initial dye concentration of 25, 50, and 100 microg, respectively. The pH was reduced from 9.0 to 7.0. Simulated textile effluent containing 50 microg/mL dye was degraded by 61.7%. Analysis of degradation products by TLC and HPLC showed that the dye mixture was degraded to nontoxic smaller molecules. The bacteria-coated pebbles were stable, there was no washout even after 2 months, and the reactor was found to be suitable for the aerobic degradation of azo dyes. PMID:12675610

  14. Aerobic Vinyl Chloride Metabolism in Groundwater Microcosms by Methanotrophic and Etheneotrophic Bacteria.

    PubMed

    Findlay, Margaret; Smoler, Donna F; Fogel, Samuel; Mattes, Timothy E

    2016-04-01

    Vinyl chloride (VC) is a carcinogen generated in groundwater by reductive dechlorination of chloroethenes. Under aerobic conditions, etheneotrophs oxidize ethene and VC, while VC-assimilators can use VC as their sole source of carbon and energy. Methanotrophs utilize only methane but can oxidize ethene to epoxyethane and VC to chlorooxirane. Microcosms were constructed with groundwater from the Carver site in MA containing these three native microbial types. Methane, ethene, and VC were added to the microcosms singly or as mixtures. In the absence of VC, ethene degraded faster when methane was also present. We hypothesized that methanotroph oxidation of ethene to epoxyethane competed with their use of methane, and that epoxyethane stimulated the activity of starved etheneotrophs by inducing the enzyme alkene monooxygenase. We then developed separate enrichment cultures of Carver methanotrophs and etheneotrophs, and demonstrated that Carver methanotrophs can oxidize ethene to epoxyethane, and that starved Carver etheneotrophs exhibit significantly reduced lag time for ethene utilization when epoxyethane is added. In our groundwater microcosm tests, when all three substrates were present, the rate of VC removal was faster than with either methane or ethene alone, consistent with the idea that methanotrophs stimulate etheneotroph destruction of VC. PMID:26918370

  15. Population Changes in Enteric Bacteria and Other Microorganisms During Aerobic Thermophilic Windrow Composting1

    PubMed Central

    Savage, Jacob; Chase, Theodore; Macmillan, James D.

    1973-01-01

    Composting of wastes from swine feeding operations was studied. The effects of the frequency of turning the wastes and addition of straw to improve the physical structure were studied to determine the most effective technique to rapidly increase the temperature and, consequently, destroy coliforms and Salmonella. Four different treatments were studied; the results showed that, with addition of 5% (wt/wt) straw and mechanical turning of the compost 20 times per week, the temperature reached 60 C within 3 days and enteric bacteria were destroyed within 14 days. Images PMID:4203338

  16. Temperature and moisture effects on ammonia oxidizer communities in cryoturbated Arctic soils

    NASA Astrophysics Data System (ADS)

    Aiglsdorfer, Stefanie; Alves, Ricardo J. E.; Bárta, Jiří; Kohoutová, Iva; Bošková, Hana; Diáková, Katerina; Čapek, Petr; Schnecker, Jörg; Wild, Birgit; Mooshammer, Maria; Urich, Tim; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Mikutta, Robert; Lashchinskiy, Nikolay; Richter, Andreas; Šantrůčková, Hana; Shibistova, Olga; Schleper, Christa

    2014-05-01

    Arctic permafrost-affected soils contain large amounts of soil organic carbon (SOC) and are expected to experience drastic changes in environmental conditions, such as moisture and temperature, due to the high surface temperature increase predicted for these regions. Although the SOC decomposition processes driven by the microbiota are considered to be nitrogen (N) limited, little information about the microbial groups involved in N cycle is currently available, including their reactions to environmental changes. Here, we investigate the presence of ammonia oxidizing archaea (AOA) and bacteria (AOB) in distinct soil horizons from the Taymyr peninsula (Siberia, Russia), and investigate their activities under changing temperature and moisture regimes. These two groups of organisms perform the first step in nitrification, an important and rate limiting process in the global N cycle, which involves the oxidation of ammonia to nitrate via nitrite. The soil samples were separated into different horizons: organic topsoil (O) and subducted organic topsoil (Ajj). The samples were incubated for 18 weeks at 4, 12 and 20° C and 50, 80 and 100 % water holding capacity (WHC). AOA and AOB abundances were quantified by quantitative PCR targeting genes of the key metabolic enzyme, ammonia monooxygenase. AOA diversity was analyzed in-depth by high-throughput amplicon sequencing of the same gene. Additionally, gross and net nitrification and mineralization rates were determined in order to investigate potential relationships between AOA and AOB populations and these processes, in response to the incubation treatments. We found higher abundances of AOA than AOB in the organic topsoil, whereas AOB dominated in the subducted organic topsoil. Increased temperature resulted in higher numbers of both groups at low WHC %, with AOB showing a more pronounced response. However, these effects were not observed under anaerobic conditions (100 % WHC). Deep sequencing of AOA amoA genes revealed

  17. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

    NASA Astrophysics Data System (ADS)

    Alves, Ricardo J. E.; Wanek, Wolfgang; Zappe, Anna; Richter, Andreas; Svenning, Mette M.; Schleper, Christa; Urich, Tim

    2014-05-01

    The functioning of Arctic soil ecosystems is crucially important for global climate, although basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and therefore it is particularly important to gain a better understanding of the microbial populations catalyzing transformations that influence N bioavailability. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils from Svalbard were analyzed through a polyphasic approach, including determination of gross nitrification rates through a 15N pool dilution method, qualitative and quantitative analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) populations based on the functional marker gene amoA (encoding the ammonia monooxygenase subunit A), and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils, and outnumbered AOB by 1 to 3 orders of magnitude in most others. AOA showed a great overall phylogenetic diversity that was differentially distributed across soil ecosystems, and exhibited an uneven population composition that reflected the dominance of a single AOA phylotype in each population. Moreover, AOA populations showed a multifactorial association with the soil properties, which reflected an overall distribution associated with tundra type and with several physico-chemical parameters combined, namely pH and soil moisture and N contents (i.e., NO3- and dissolved organic N). Remarkably, the different gross in situ and potential nitrification rates between soils were associated with distinct AOA phylogenetic clades, suggesting differences in their nitrifying potential, both under the native NH3 conditions and as a response to higher NH3 availability. This was further supported by the selective enrichment of two AOA clades that exhibited

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

    SciTech Connect

    Bollmann, Annette; Sedlacek, Christopher J; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Klotz, Martin G; Arp, D J; Sayavedra-Soto, LA; Lu, Megan; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, James; Woyke, Tanja; Lucas, Susan; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L; Huntemann, Marcel; Deshpande, Shweta; Han, Cliff; Chen, Amy; Kyrpides, Nikos C; Mavromatis, K; Markowitz, Victor; Szeto, Ernest; Ivanova, N; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Peters, Lin; Ovchinnikova, Galina; Goodwin, Lynne A.

    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.

  19. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils.

    PubMed

    Woo, Hannah L; Hazen, Terry C; Simmons, Blake A; DeAngelis, Kristen M

    2014-02-01

    Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal-Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts. PMID:24238986

  20. Formation of Polyhydroxyalkanoate in Aerobic Anoxygenic Phototrophic Bacteria and Its Relationship to Carbon Source and Light Availability▿

    PubMed Central

    Xiao, Na; Jiao, Nianzhi

    2011-01-01

    Aerobic anoxygenic phototrophic bacteria (AAPB) are unique players in carbon cycling in the ocean. Cellular carbon storage is an important mechanism regulating the nutrition status of AAPB but is not yet well understood. In this paper, six AAPB species (Dinoroseobacter sp. JL1447, Roseobacter denitrificans OCh 114, Roseobacter litoralis OCh 149, Dinoroseobacter shibae DFL 12T, Labrenzia alexandrii DFL 11T, and Erythrobacter longus DSMZ 6997) were examined, and all of them demonstrated the ability to form the carbon polymer polyhydroxyalkanoate (PHA) in the cell. The PHA in Dinoroseobacter sp. JL1447 was identified as poly-beta-hydroxybutyrate (PHB) according to evidence from Fourier transform infrared spectroscopy, differential scanning calorimetry, and 1H nuclear magnetic resonance spectroscopy examinations. Carbon sources turned out to be critical for PHA production in AAPB. Among the eight media tested with Dinoroseobacter sp. JL1447, sodium acetate, giving a PHA production rate of 72%, was the most productive carbon source, followed by glucose, with a 68% PHA production rate. Such PHA production rates are among the highest recorded for all bacteria. The C/N ratio of substrates was verified by the experiments as another key factor in PHA production. In the case of R. denitrificans OCh 114, PHA was not detected when the organism was cultured at C/N ratios of <2 but became apparent at C/N ratios of >3. Light is also important for the formation of PHA in AAPB. In the case of Dinoroseobacter sp. JL1447, up to a one-quarter increase in PHB production was observed when the culture underwent growth in a light-dark cycle compared to growth completely in the dark. PMID:21908634

  1. Development and characterization of the partial nitrification aerobic granules in a sequencing batch airlift reactor.

    PubMed

    Song, Yanjun; Ishii, Satoshi; Rathnayake, Lashitha; Ito, Tsukasa; Satoh, Hisashi; Okabe, Satoshi

    2013-07-01

    In this study, partial nitrifying (PN) aerobic granules were developed in a sequencing batch airlift reactor by controlling the airflow rate and NH4(+) loading rate. The PN reactor produced an effluent with a NO2(-)/NH4(+) ratio of approximately one and with an NH4(+) conversion rate of 1.22 kg N m(-3)day(-1). More than 95% of the total organic carbon was removed during the process. On the basis of clone library analysis and fluorescence in situ hybridization, ammonia-oxidizing bacteria (AOB) closely related to Nitrosomonas eutropha and putative heterotrophic denitrifiers were mainly present near the surface of the PN aerobic granules. Microelectrode measurements revealed that both NH4(+) and NO2(-) were consumed near the surface (<200 μm), whereas no nitrate (NO3(-)) accumulation was observed throughout the granules. These results indicate that PN by AOB and nitrite denitrification by heterotrophs, but not nitrite oxidation, simultaneously occurred near the surface of the PN aerobic granules. PMID:23665689

  2. Microbiologically influenced corrosion of 304 stainless steel by aerobic Pseudomonas NCIMB 2021 bacteria: AFM and XPS study.

    PubMed

    Yuan, S J; Pehkonen, S O

    2007-09-01

    Microbiologically influenced corrosion (MIC) of stainless steel 304 by a marine aerobic Pseudomonas bacterium in a seawater-based medium was investigated by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). AFM was used to observe in situ the proliferation of a sessile Pseudomonas cell by binary fission. The development of a biofilm on the coupon surface and the extent of corrosion damage beneath the biofilm after various exposure times were also characterized by AFM. Results showed that the biofilm formed on the coupon surface increased in thickness and heterogeneity with time, and thus resulting in the occurrence of extensive micro-pitting corrosion; whilst the depth of pits increased linearly with time. The XPS results confirmed that the colonization of Pseudomonas bacteria on the coupon surface induced subtle changes in the alloy elemental composition in the outermost layer of surface films. The most significant feature resulting from microbial colonization on the coupon surface was the depletion of iron (Fe) and the enrichment of chromium (Cr) content as compared to a control coupon exposed to the sterile medium, and the enrichment of Cr increased with time. These compositional changes in the main alloying elements may be correlated with the occurrence of extensive micropitting corrosion on the surface. PMID:17582747

  3. Production of autoinducer-2 by aerobic endospore-forming bacteria isolated from the West African fermented foods.

    PubMed

    Qian, Yang; Kando, Christine Kere; Thorsen, Line; Larsen, Nadja; Jespersen, Lene

    2015-11-01

    Autoinducer-2 (AI-2) is a quorum-sensing (QS) molecule which mediates interspecies signaling and affects various bacterial behaviors in food fermentation. Biosynthesis of AI-2 is controlled by S-ribosylhomocysteine lyase encoded by the luxS gene. The objective of this study was to investigate production of AI-2 by aerobic endospore-forming bacteria (AEB) isolated from the West African alkaline fermented seed products Mantchoua and Maari. The study included 13 AEB strains of Bacillus subtilis, B. cereus, B. altitudinis, B. amyloliquefaciens, B. licheniformis, B. aryabhattai, B. safensis, Lysinibacillus macroides and Paenibacillus polymyxa. All the tested strains harbored the luxS gene and all strains except for P. polymyxa B314 were able to produce AI-2 during incubation in laboratory medium. Production of AI-2 by AEB was growth phase dependent, showing maximum activity at the late exponential phase. AI-2 was depleted from the culture medium at the beginning of the stationary growth phase, indicating that the tested AEB possess a functional AI-2 receptor that internalizes AI-2. This study provides the evidences of QS system in Bacillus spp. and L. macroides and new knowledge of AI-2 production by AEB. This knowledge contributes to the development of QS-based strategies for better control of alkaline fermentation. PMID:26449556

  4. Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica.

    PubMed

    Pinheiro, Guilherme L; Correa, Raquel F; Cunha, Raquel S; Cardoso, Alexander M; Chaia, Catia; Clementino, Maysa M; Garcia, Eloi S; de Souza, Wanderley; Frasés, Susana

    2015-01-01

    The enzymatic hydrolysis of cellulose by cellulases is one of the major limiting steps in the conversion of lignocellulosic biomass to yield bioethanol. To overcome this hindrance, significant efforts are underway to identify novel cellulases. The snail Achatina fulica is a gastropod with high cellulolytic activity, mainly due to the abundance of glycoside hydrolases produced by both the animal and its resident microbiota. In this study, we partially assessed the cellulolytic aerobic bacterial diversity inside the gastrointestinal tract of A. fulica by culture-dependent methods and evaluated the hydrolytic repertoire of the isolates. Forty bacterial isolates were recovered from distinct segments of the snail gut and identified to the genus level by 16S rRNA gene sequence analysis. Additional phenotypic characterization was performed using biochemical tests provided by the Vitek2 identification system. The overall enzymatic repertoire of the isolated strains was investigated by enzymatic plate assays, containing the following substrates: powdered sugarcane bagasse, carboxymethylcellulose (CMC), p-nitrophenyl-β-D-glucopyranoside (pNPG), p-nitrophenyl-β-D-cellobioside (pNPC), 4-methylumbelliferyl-β-D-glucopyranoside (MUG), 4-methylumbelliferyl-β-D-cellobioside (MUC), and 4-methylumbelliferyl-β-D-xylopyranoside (MUX). Our results indicate that the snail A. fulica is an attractive source of cultivable bacteria that showed to be valuable resources for the production of different types of biomass-degrading enzymes. PMID:26347735

  5. Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica

    PubMed Central

    Pinheiro, Guilherme L.; Correa, Raquel F.; Cunha, Raquel S.; Cardoso, Alexander M.; Chaia, Catia; Clementino, Maysa M.; Garcia, Eloi S.; de Souza, Wanderley; Frasés, Susana

    2015-01-01

    The enzymatic hydrolysis of cellulose by cellulases is one of the major limiting steps in the conversion of lignocellulosic biomass to yield bioethanol. To overcome this hindrance, significant efforts are underway to identify novel cellulases. The snail Achatina fulica is a gastropod with high cellulolytic activity, mainly due to the abundance of glycoside hydrolases produced by both the animal and its resident microbiota. In this study, we partially assessed the cellulolytic aerobic bacterial diversity inside the gastrointestinal tract of A. fulica by culture-dependent methods and evaluated the hydrolytic repertoire of the isolates. Forty bacterial isolates were recovered from distinct segments of the snail gut and identified to the genus level by 16S rRNA gene sequence analysis. Additional phenotypic characterization was performed using biochemical tests provided by the Vitek2 identification system. The overall enzymatic repertoire of the isolated strains was investigated by enzymatic plate assays, containing the following substrates: powdered sugarcane bagasse, carboxymethylcellulose (CMC), p-nitrophenyl-β-D-glucopyranoside (pNPG), p-nitrophenyl-β-D-cellobioside (pNPC), 4-methylumbelliferyl-β-D-glucopyranoside (MUG), 4-methylumbelliferyl-β-D-cellobioside (MUC), and 4-methylumbelliferyl-β-D-xylopyranoside (MUX). Our results indicate that the snail A. fulica is an attractive source of cultivable bacteria that showed to be valuable resources for the production of different types of biomass-degrading enzymes. PMID:26347735

  6. Distribution and Abundance of Archaeal and Bacterial Ammonia Oxidizers in the Sediments of the Dongjiang River, a Drinking Water Supply for Hong Kong

    PubMed Central

    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. PMID:24256973

  7. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany.

    PubMed

    Opitz, Sebastian; Küsel, Kirsten; Spott, Oliver; Totsche, Kai Uwe; Herrmann, Martina

    2014-10-01

    We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics. PMID:24953994

  8. Molecular analysis of enrichment cultures of ammonia oxidizers from the Salar de Huasco, a high altitude saline wetland in northern Chile.

    PubMed

    Dorador, Cristina; Busekow, Annika; Vila, Irma; Imhoff, Johannes F; Witzel, Karl-Paul

    2008-05-01

    We analyzed enrichment cultures of ammonia-oxidizing bacteria (AOB) collected from different areas of Salar de Huasco, a high altitude, saline, pH-neutral water body in the Chilean Altiplano. Samples were inoculated into mineral media with 10 mM NH4+ at five different salt concentrations (10, 200, 400, 800 and 1,400 mM NaCl). Low diversity (up to three phylotypes per enrichment) of beta-AOB was detected using 16S rDNA and amoA clone libraries. Growth of beta-AOB was only recorded in a few enrichment cultures and varied according to site or media salinity. In total, five 16S rDNA and amoA phylotypes were found which were related to Nitrosomonas europaea/Nitrosococcus mobilis, N. marina and N. communis clusters. Phylotype 1-16S was 97% similar with N. halophila, previously isolated from Mongolian soda lakes, and phylotypes from amoA sequences were similar with yet uncultured beta-AOB from different biofilms. Sequences related to N. halophila were frequently found at all salinities. Neither gamma-AOB nor ammonia-oxidizing Archaea were recorded in these enrichment cultures. PMID:18305895

  9. Hexavalent chromium reduction by aerobic heterotrophic bacteria indigenous to chromite mine overburden

    PubMed Central

    Dey, Satarupa; Paul, A.K.

    2013-01-01

    Microbiological analysis of overburden samples collected from chromite mining areas of Orissa, India revealed that they are rich in microbial density as well as diversity and dominated by Gram-negative (58%) bacteria. The phenotypically distinguishable bacterial isolates (130) showed wide degree of tolerance to chromium (2–8 mM) when tested in peptone yeast extract glucose agar medium. Isolates (92) tolerating 2 mM chromium exhibited different degrees of Cr+6 reducing activity in chemically defined Vogel Bonner (VB) broth and complex KSC medium. Three potent isolates, two belonging to Arthrobacter spp. and one to Pseudomonas sp. were able to reduce more than 50 and 80% of 2 mM chromium in defined and complex media respectively. Along with Cr+6 (MIC 8.6–17.8 mM), the isolates showed tolerance to Ni+2, Fe+3, Cu+2 and Co+2 but were extremely sensitive to Hg+2 followed by Cd+2, Mn+2 and Zn+2. In addition, they were resistant to antibiotics like penicillin, methicillin, ampicillin, neomycin and polymyxin B. During growth under shake-flask conditions, Arthrobacter SUK 1201 and SUK 1205 showed 100% reduction of 2 mM Cr+6 in KSC medium with simultaneous formation of insoluble precipitates of chromium salts. Both the isolates were also equally capable of completely reducing the Cr+6 present in mine seepage when grown in mine seepage supplemented with VB concentrate. PMID:24159321

  10. Alleviation of toxic hexavalent chromium using indigenous aerobic bacteria isolated from contaminated tannery industry sites.

    PubMed

    Pandey, Siddhartha; Singh, Nitin Kumar; Bansal, Ankur Kumar; Arutchelvan, V; Sarkar, Sudipta

    2016-07-01

    In the last decade, much attention has been paid to bioremediation of Cr(VI) using various bacterial species. Cr(VI) remediation by indegeneous bacteria isolated from contaminated sites of a tannery industry located in Tamil Nadu, India, was investigated in this study. Three Cr(VI) resistant bacterial strains (TES-1, TEf-1, and TES-2) were isolated and selected based on their Cr(VI) reduction ability in minimal salt medium. Among these three bacterial strains, TES-1 was found to be most efficient in bioreduction, while TES-2 was only found to be Cr(VI) resistant and showed negligible bioreduction, whereas TEf-1 was observed to be most Cr(VI) tolerant. Potential for bioremediation of TES-1 and TEf-1 was further investigated at different concentrations of Cr(VI) in the range of 50 to 350 mg L(-1). TEf-1 showed prominent synchronous growth throughout the experiment, whereas TES-1 took a longer acclimatization time. Minimum inhibitory concentrations (MIC) of Cr(VI) for TES-1 and TEf-1 were approximated as 600 mg L(-1) and 750 mg L(-1), respectively. The kinetic behavior of Cr(VI) reduction by TES-1 and TEf-1 exhibited zero- and first-order removal kinetics for Cr(VI), respectively. The most efficient strain TES-1 was identified as Streptomyces sp. by gene sequencing of 16S rRNA. PMID:26458110

  11. Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy.

    PubMed

    Hurley, Sarah J; Elling, Felix J; Könneke, Martin; Buchwald, Carolyn; Wankel, Scott D; Santoro, Alyson E; Lipp, Julius Sebastian; Hinrichs, Kai-Uwe; Pearson, Ann

    2016-07-12

    Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate. We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R(2) = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol·cell(-1)·d(-1) increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86 Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86-SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature. PMID:27357675

  12. Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean

    PubMed Central

    Sintes, Eva; De Corte, Daniele; Haberleitner, Elisabeth; Herndl, Gerhard J.

    2016-01-01

    In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization. PMID:26903961

  13. Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean.

    PubMed

    Sintes, Eva; De Corte, Daniele; Haberleitner, Elisabeth; Herndl, Gerhard J

    2016-01-01

    In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization. PMID:26903961

  14. A Reference Broth Microdilution Method for Dalbavancin In Vitro Susceptibility Testing of Bacteria that Grow Aerobically.

    PubMed

    Koeth, Laura M; DiFranco-Fisher, Jeanna M; McCurdy, Sandra

    2015-01-01

    Antimicrobial susceptibility testing (AST) is performed to assess the in vitro activity of antimicrobial agents against various bacteria. The AST results, which are expressed as minimum inhibitory concentrations (MICs) are used in research for antimicrobial development and monitoring of resistance development and in the clinical setting for antimicrobial therapy guidance. Dalbavancin is a semi-synthetic lipoglycopeptide antimicrobial agent that was approved in May 2014 by the Food and Drug Administration (FDA) for the treatment of acute bacterial skin and skin structure infections caused by Gram-positive organisms. The advantage of dalbavancin over current anti-staphylococcal therapies is its long half-life, which allows for once-weekly dosing. Dalbavancin has activity against Staphylococcus aureus (including both methicillin-susceptible S. aureus [MSSA] and methicillin-resistant S. aureus [MRSA]), coagulase-negative staphylococci, Streptococcus pneumoniae, Streptococcus anginosus group, β-hemolytic streptococci and vancomycin susceptible enterococci. Similar to other recent lipoglycopeptide agents, optimization of CLSI and ISO broth susceptibility test methods includes the use of dimethyl sulfoxide (DMSO) as a solvent when preparing stock solutions and polysorbate 80 (P80) to alleviate adherence of the agent to plastic. Prior to the clinical studies and during the initial development of dalbavancin, susceptibility studies were not performed with the use of P-80 and MIC results tended to be 2-4 fold higher and similarly higher MIC results were obtained with the agar dilution susceptibility method. Dalbavancin was first included in CLSI broth microdilution methodology tables in 2005 and amended in 2006 to clarify use of DMSO and P-80. The broth microdilution (BMD) procedure shown here is specific to dalbavancin and is in accordance with the CLSI and ISO methods, with step-by-step detail and focus on the critical steps added for clarity. PMID:26381422

  15. Performance of aerobic granular sludge in a sequencing batch bioreactor for slaughterhouse wastewater treatment.

    PubMed

    Liu, Yali; Kang, Xiaorong; Li, Xin; Yuan, Yixing

    2015-08-01

    Lab-scale experiment was conducted to investigate the formation and characteristics of aerobic granular sludge for biological nutrient removal of slaughterhouse wastewater. Experimental results showed that removal performances of chemical oxygen demand (COD), ammonia and phosphate were enhanced with sludge granulation, and their removal efficiencies reached 95.1%, 99.3% and 83.5%, respectively. The aerobic granular sludge was matured after 90days cultivation, and protein-like substances were the main components. Simultaneously, the mass ratio of proteins and polysaccharides (PN/PS) was enhanced to 2.5 from 1.7. The granules with particle sizes of 0.6-1.2 and 1.2-1.8mm, accounting for 69.6%, were benefit for the growth of ammonia oxidizing bacteria (AOB) and nitrate oxidizing bacteria (NOB), and corresponding specific oxygen demand rates (SOUR) of AOB and NOB were 31.4 and 23.3mgO2/gMLSSh, respectively. PMID:25777064

  16. Relating the Diversity, Abundance, and Activity of Ammonia-Oxidizing Archaeal Communities to Nitrification Rates in the Coastal Ocean

    NASA Astrophysics Data System (ADS)

    Tolar, B. B.; Smith, J. M.; Chavez, F.; Francis, C.

    2015-12-01

    Ammonia oxidation, the rate-limiting first step of nitrification, is an important link between reduced (ammonia) and oxidized (nitrate) nitrogen, and controls the relative distribution of these forms of inorganic nitrogen. This process is catalyzed via the ammonia monooxygenase enzyme of both ammonia-oxidizing Bacteria (AOB) and Archaea (AOA); the α subunit of this enzyme is encoded by the amoA gene and has been used as the molecular marker to detect this process. In the ocean, AOA are typically 10-1000 times more and are likely more active than AOB, and thus are key players in the marine nitrogen cycle. Monterey Bay is a dynamic site to study nitrification, as seasonal upwelling brings deep water and nutrients into surface waters, which can promote phytoplankton blooms and impact biogeochemical processes such as the nitrogen cycle. We have sampled two sites within Monterey Bay bimonthly for two years as part of the ongoing Monterey Bay Time Series (MBTS) to quantify AOA genes, transcripts, and nitrification rates. Two ecotypes of AOA are routinely found in Monterey Bay - the 'shallow' water column A (WCA) and 'deep' water column B (WCB) clades, which are thought to have distinct physiological properties and can be distinguished based on the amoA gene sequence. Previous work has shown a strong relationship between nitrification rates in Monterey Bay with the abundance of WCA amoA genes and transcripts. Additionally, we found a correlation between the relative abundance of Marine Group I (MGI) Thaumarchaeota 16S rRNA reads (as % of total) and the absolute abundance of AOA amoA genes (determined via qPCR) in Monterey Bay and the California Current System. AOA 16S rRNA gene abundances in turn correlated significantly with changes in nitrification rate with depth, while the relative abundance of genes and transcripts binned to a single AOA (Nitrosopumilus maritimus) was not significantly correlated to nitrification rate. Further analysis of the sequenced AOA

  17. Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in mediterranean urban stream biofilms.

    PubMed

    Merbt, Stephanie N; Auguet, Jean-Christophe; Blesa, Alba; Martí, Eugènia; Casamayor, Emilio O

    2015-01-01

    Streams affected by wastewater treatment plant (WWTP) effluents are hotspots of nitrification. We analyzed the influence of WWTP inputs on the abundance, distribution, and composition of epilithic ammonia-oxidizing (AO) assemblages in five Mediterranean urban streams by qPCR and amoA gene cloning and sequencing of both archaea (AOA) and bacteria (AOB). The effluents significantly modified stream chemical parameters, and changes in longitudinal profiles of both NH(4)(+) and NO(3)(-) indicated stimulated nitrification activity. WWTP effluents were an allocthonous source of both AOA, essentially from the Nitrosotalea cluster, and mostly of AOB, mainly Nitrosomonas oligotropha, Nitrosomonas communis, and Nitrosospira spp. changing the relative abundance and the natural composition of AO assemblages. Under natural conditions, Nitrososphaera and Nitrosopumilus AOA dominated AO assemblages, and AOB were barely detected. After the WWTP perturbation, epilithic AOB increased by orders of magnitude whereas AOA did not show quantitative changes but a shift in population composition to dominance of Nitrosotalea spp. The foraneous AOB successfully settled in downstream biofilms and probably carried out most of the nitrification activity. Nitrosotalea were only observed downstream and only in biofilms exposed to either darkness or low irradiance. In addition to other potential environmental limitations for AOA distribution, this result suggests in situ photosensitivity as previously reported for Nitrosotalea under laboratory conditions. PMID:25062836

  18. Impact of inocula and growth mode on the molecular microbial ecology of anaerobic ammonia oxidation (anammox) bioreactor communities.

    PubMed

    Park, Hongkeun; Rosenthal, Alex; Jezek, Roland; Ramalingam, Krish; Fillos, John; Chandran, Kartik

    2010-09-01

    The composition of distinctly inoculated granular anammox and biofilm-based completely autotrophic nitrogen removal over nitrite (CANON) bioreactors was investigated from start-up through continuous long-term operation via denaturing gradient gel electrophoresis (DGGE) and sequencing. The granular anammox reactor was seeded with sludge from an operational anammox reactor in Strass, Austria. The CANON reactor was seeded with activated sludge from a local wastewater treatment plant in New York City. The principal anammox bacteria (AMX) shifted from members related to Kuenenia stuttgartiensis present in the initial inoculum to members related to Candidatus Brocadia fulgida during pre-enrichment (before this study) and to members related to Candidatus Brocadia sp. 40 (during this study) in the granular reactor. AMX related to C. Brocadia sp. 40 were also enriched from activated sludge in the CANON reactor. The estimated doubling times of AMX in the granular and CANON reactors were 5.3 and 8.9 days, respectively, which are lower than the value of 11 days, reported previously. Both the granular anammox and CANON reactors also fostered significant amounts of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). The fractions of AMX and two groups of NOB were generally similar in the granular anammox and CANON reactors. However, the diversity and fractions of AOB in the two reactors was markedly different. Therefore, it is suggested that the composition of the feed and extant substrate concentrations in the reactor likely select for the microbial community composition more than the inocula and reactor configuration. Further, such selection is not equivalent for all resident communities. PMID:20684970

  19. The determination of the real nano-scale sizes of bacteria in chernozem during microbial succession by means of hatching of a soil in aerobic and anaerobic conditions

    NASA Astrophysics Data System (ADS)

    Gorbacheva, M.

    2012-04-01

    M.A. Gorbacheva,L.M. Polyanskaya The Faculty of Soil Science, Moscow State University, Leninskie Gory, GSP-1, Moscow,119991,Russia In recent years there's been particular attention paid to the smallest life's forms- bacteria which size can be measured in nanometer. These are the forms of bacteria with diameter of 5-200 nm. Theoretical calculations based on the content of the minimum number of DNA, enzyme, lipids in and ribosome in cells indicates impossibility of existence of a living cells within diameter less than 300 nm. It is theoretically possible for a living cell to exist within possible diameter of approximately 140 nm. Using a fluorescence microscope there's been indicated in a number of samples from lakes, rivers, soil, snow and rain water that 200 nm is the smallest diameter of a living cell. Supposingly, such a small size of bacteria in soil is determined by natural conditions which limit their development by nutritious substances and stress-factors. Rejuvenescence of nanobacteria under unfavourable natural conditions and stress-factors is studied in laboratory environment. The object of the current study has become the samples of typical arable chernozem of the Central Chernozem State Biosphere Reserve in Kursk. The detailed morphological description of the soil profile and its basic analytical characteristics are widely represented in scientific publications. The soil is characterized by a high carbon content which makes up 3,96% ,3,8% , and 2,9% for the upper layers of the A horizon, and 0,79% for the layer of the B horizon. A microbial succession was studied under aerobic and anaerobic conditions by means of experiments with microcosms in upper A horizons and B horizon of a chernozem. The final aim is to identify the cells size of bacteria in aerobic and anaerobic soil conditions in chernozem during the microbial succession, by dampening and application of chitin by means of «cascade filtration» method. The study of the microcosms is important for

  20. Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers.

    PubMed

    Avrahami, Sharon; Liesack, Werner; Conrad, Ralf

    2003-08-01

    We investigated the effect of temperature on the activity of soil ammonia oxidizers caused by changes in the availability of ammonium and in the microbial community structure. Both short (5 days) and long (6.5, 16 and 20 weeks) incubation of an agricultural soil resulted in a decrease in ammonium concentration that was more pronounced at temperatures between 10 and 25 degrees C than at either 4 degrees C or 30-37 degrees C. Consistently, potential nitrification was higher between 10 and 25 degrees C than at either 4 degrees C or 37 degrees C. However, as long as ammonium was not limiting, release rates of N2O increased monotonously between 4 and 37 degrees C after short-term temperature adaptation, with nitrification accounting for about 35-50% of the N2O production between 4 and 25 degrees C. In order to see whether temperature may also affect the community structure of ammonia oxidizers, we studied moist soil during long incubation at low and high concentrations of commercial fertilizer. The soil was also incubated in buffered (pH 7) slurry amended with urea. Communities of ammonia oxidizers were assayed by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the alpha subunit of ammonia monooxygenase. We found that a polymerase chain reaction (PCR) system using a non-degenerated reverse primer (amoAR1) gave the best results. Community shifts occurred in all soil treatments after 16 weeks of incubation. The community shifts were obviously influenced by the different fertilizer treatments, indicating that ammonium was a selective factor for different ammonia oxidizer populations. Temperature was also a selective factor, in particular as community shifts were also observed in the soil slurries, in which ammonium concentrations and pH were better controlled. Cloning and sequencing of selected DGGE bands indicated that amoA sequences belonging to Nitrosospira cluster 1 were dominant at low temperatures (4-10 degrees C), but were absent after

  1. Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

    PubMed Central

    Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B.

    2013-01-01

    Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition. PMID:23847601

  2. The Impact of Monochloramine on Ammonia-Oxidizing Bacteria in Lab-Scale Annular Reactors

    EPA Science Inventory

    Drinking water utilities typically use chlorine or monochloramine (NH2Cl) as secondary disinfectants. In general, disinfectants react with natural organic matter, producing disinfection by-products (DBP), which are a health concern. As a result, the stage 1 & 2 disin...

  3. The Impact of Monochloramine on Ammonia-Oxidizing Bacteria in Lab-Scale Annular Reactors - abstract

    EPA Science Inventory

    Drinking water utilities use free chlorine or monochloramine (NH2Cl) as secondary disinfectants, which react with natural organic matter to form disinfection by-products (DBP). To reduce DBP concentrations and comply with the USEPA Stage 1 & 2 Disinfectant and DBP rul...

  4. The Impact of Monochloramine on Ammonia-Oxidizing Bacteria in Lab-Scale Annular Reactors - Poster

    EPA Science Inventory

    Drinking water utilities typically use chlorine or monochloramine (NH2Cl) as secondary disinfectants. In general, disinfectants react with natural organic matter, producing disinfection by-products (DBP), which are a health concern. As a result, the stage 1 & 2 disinfectant and...

  5. Growth parameters of Escherichia coli O157:H7, Salmonella spp., Listeria monocytogenes, and aerobic mesophilic bacteria of apple cider amended with nisin-EDTA.

    PubMed

    Ukuku, Dike O; Zhang, Howard; Huang, Lihan

    2009-05-01

    The effect of nisin (0 or 300 IU/mL), ethylenediamine tetraacetic acid (EDTA, 20 mM), and nisin (300 IU)-EDTA (20 mM) on growth parameters, including lag period (LP) and generation time, of Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella spp. in the presence or absence of aerobic mesophilic bacteria of apple cider during storage at 5 degrees C for up to 16 days or 23 degrees C for 16 h was investigated. The growth data were analyzed and fitted to the modified Gompertz model. The LP values for aerobic mesophilic bacteria of apple cider (control) and those amended with EDTA and nisin during storage at 5 degrees C were 1.61, 1.76, and 5.45 days, respectively. In apple cider stored at 23 degrees C for 16 h, the LP values for the same bacteria and treatment were 3.24, 3.56, and 5.85 h, respectively. The LP values for E. coli O157:H7 determined in the presence of aerobic mesophilic bacteria of apple cider stored at 23 degrees C for 16 h was 1.48 h, while populations for L. monocytogenes and Salmonella in the same cider declined. In sterile apple cider left at 23 degrees C for 16 h, the LP values for E. coli O157:H7, Salmonella, and L. monocytogenes averaged 2.74, 2.37, and 3.16 h, respectively. The generation time for these pathogens were 0.402, 0.260, and 0.187 log (CFU/mL)/h, respectively. Addition of nisin and EDTA combination caused a decline in lag phase duration and the populations for all pathogens tested, suggesting possible addition of this additive to freshly prepared apple cider to enhance its microbial safety and prevent costly recalls. PMID:19415973

  6. A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

    PubMed Central

    Jung, Man-Young; Park, Soo-Je; Kim, So-Jeong; Kim, Jong-Geol; Sinninghe Damsté, Jaap S.

    2014-01-01

    Soil nitrification plays an important role in the reduction of soil fertility and in nitrate enrichment of groundwater. Various ammonia-oxidizing archaea (AOA) are considered to be members of the pool of ammonia-oxidizing microorganisms in soil. This study reports the discovery of a chemolithoautotrophic ammonia oxidizer that belongs to a distinct clade of nonmarine thaumarchaeal group I.1a, which is widespread in terrestrial environments. The archaeal strain MY2 was cultivated from a deep oligotrophic soil horizon. The similarity of the 16S rRNA gene sequence of strain MY2 to those of other cultivated group I.1a thaumarchaeota members, i.e., Nitrosopumilus maritimus and “Candidatus Nitrosoarchaeum koreensis,” is 92.9% for both species. Extensive growth assays showed that strain MY2 is chemolithoautotrophic, mesophilic (optimum temperature, 30°C), and neutrophilic (optimum pH, 7 to 7.5). The accumulation of nitrite above 1 mM inhibited ammonia oxidation, while ammonia oxidation itself was not inhibited in the presence of up to 5 mM ammonia. The genome size of strain MY2 was 1.76 Mb, similar to those of N. maritimus and “Ca. Nitrosoarchaeum koreensis,” and the repertoire of genes required for ammonia oxidation and carbon fixation in thaumarchaeal group I.1a was conserved. A high level of representation of conserved orthologous genes for signal transduction and motility in the noncore genome might be implicated in niche adaptation by strain MY2. On the basis of phenotypic, phylogenetic, and genomic characteristics, we propose the name “Candidatus Nitrosotenuis chungbukensis” for the ammonia-oxidizing archaeal strain MY2. PMID:24705324

  7. Segregation of biomass in cyclic anaerobic/aerobic granular sludge allows the enrichment of anaerobic ammonium oxidizing bacteria at low temperatures.

    PubMed

    Winkler, Mari K H; Kleerebezem, Robbert; Kuenen, J Gijs; Yang, Jingjing; van Loosdrecht, Mark C M

    2011-09-01

    A cyclic anaerobic/aerobic bubble column reactor was run for 420 days to study the competition for nitrite between nitrite oxidizing bacteria (NOB) and anaerobic ammonium oxidizing bacteria (Anammox) at low temperatures. An anaerobic feeding period with nitrite and ammonium in the influent followed by an aerated period was applied resulting in a biomass specific conversion rate of 0.18 ± 0.02 [gN(2) - N · gVSS(-1)· day(-1)] when the dissolved oxygen concentration was maintained at 1.0 mgO(2) · L(-1). An increase in white granules was observed in the reactor which were mainly located at the top of the settled sludge bed, whereas red granules were located at the bottom. FISH, activity tests, and qPCR techniques revealed that red biomass was dominated by Anammox bacteria and white granules by NOB. Granules from the top of the sludge bed were smaller and therefore had a higher aerobic volume fraction, a lower density, and consequently a slower settling rate. Sludge was manually removed from the top of the settled sludge bed to selectively remove NOB which resulted in an increased overall biomass specific N-conversion rate of 0.32 ± 0.02 [gN(2) - N · gVSS(-1) · day(-1)]. Biomass segregation in granular sludge reactors gives an extra opportunity to select for specific microbial groups by applying a different SRT for different microbial groups. PMID:21744798

  8. Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota

    PubMed Central

    Weber, Eva B.; Lehtovirta-Morley, Laura E.; Prosser, James I.; Gubry-Rangin, Cécile

    2015-01-01

    Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. PMID:25764563

  9. Presence of Ammonia-oxidizing Archaea and Their Influence on Nitrogen Cycling in Ilica Bay, Turkey

    NASA Astrophysics Data System (ADS)

    Gulecal, Y.; Temel, M.

    2011-12-01

    Recenlty, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. The distribution and ubiquity of marine Archaea an important role in global carbon and nitrogen cycling (Ingalls et al., 2006; Leininger et al., 2006; Wuchter et al.,2006a). However, our knowledge on archaeal distribution in aquatic ecosystem was largely confined to the extreme environments for a long time until DeLong (1992, 1998) revealed the ubiquity of archaea in common marine environments. Despite the great progress, more efforts need to be given to the study of archaeal diversity in the vast oceans and of the variations in the ecological environment from coastal to oceanic waters (Massana et al.,2000). Our studying area which Ilica Bay in Izmir (Turkey) has a lot of thermal springs. The aim of study was to investigate the presence of ammonia-oxidizing Archaea and their roles of nitrogen cycling in marine enviroments.We have not only used the geochemical analyses but also genetic tools. This study will supply knowledge for marine nitrogen cycling to understanding very well, in addition how Archea genes players in the process of anammox in shallow coastal marine environments.

  10. Ammonia-oxidizing archaea in the low-oxygen water column of the Gulf of California

    NASA Astrophysics Data System (ADS)

    Beman, J.; Popp, B. N.; Francis, C. A.

    2006-12-01

    Archaea constitute a ubiquitous and exceptionally abundant component of marine microbial assemblages, yet their role in ocean biogeochemistry has remained elusive. Several recent lines of evidence suggest that many mesophilic Crenarchaeota are capable of performing ammonia oxidation, the first and rate-limiting step of chemoautotrophic nitrification. However, associations between these organisms and ammonia oxidation in the marine water column have yet to be explored--as has their means of survival under low oxygen conditions, where, paradoxically, they appear to be remarkably successful. In this study, we examined AOA diversity and abundance throughout the water column of the Gulf of California, which is characterized by highly productive near-surface waters and a pronounced oxygen minimum layer (OML) at depths below about 300 meters. We examined AOA both in the near surface and the OML of the Gulf of California, comparing across the transition to low oxygen conditions in two separate basins. Our results suggest that these organisms may play a key role in oxidizing ammonia in the Gulf of California water column, yet their presence and abundance under low oxygen conditions remains unresolved.

  11. Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers.

    PubMed

    Courtens, Emilie N P; Vandekerckhove, Tom; Prat, Delphine; Vilchez-Vargas, Ramiro; Vital, Marius; Pieper, Dietmar H; Meerbergen, Ken; Lievens, Bart; Boon, Nico; Vlaeminck, Siegfried E

    2016-04-01

    Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process. PMID:26841233

  12. Lactic Acid Bacteria in Total Mixed Ration Silage Containing Soybean Curd Residue: Their Isolation, Identification and Ability to Inhibit Aerobic Deterioration

    PubMed Central

    Li, Y.; Wang, F.; Nishino, N.

    2016-01-01

    We investigated the effects of the predominant lactic acid bacteria (LAB) on the fermentation characteristics and aerobic stability of total mixed ration (TMR) silage containing soybean curd residue (SC-TMR silage). The SC-TMR materials were ensiled in laboratory silos for 14 or 56 days. LAB predominant in SC-TMR silage were identified (Exp. 1). Lactobacillus fermentum (L. fermentum) and Streptococcus bovis (S. bovis) were found in the untreated materials, Leuconostoc pseudomesenteroides (L. pseudomesenteroides) in 14-day silage and Lactobacillus plantarum (L. plantarum) in all silages. Pediococcus acidilactici (P. acidilactici), Lactobacillus paracasei (L. paracasei), and Lactobacillus brevis (L. brevis) formed more than 90% of the isolates in 56-day silage. Italian ryegrass and whole crop maize were inoculated with P. acidilactici and L. brevis isolates and the fermentation and aerobic stability determined (Exp. 2). Inoculation with P. acidilactici and L. brevis alone or combined improved the fermentation products in ryegrass silage and markedly enhanced its aerobic stability. In maize silage, P. acidilactici and L. brevis inoculation caused no changes and suppressed deterioration when combined with increases in acetic acid content. The results indicate that P. acidilactici and L. brevis may produce a synergistic effect to inhibit SC-TMR silage deterioration. Further studies are needed to identify the inhibitory substances, which may be useful for developing potential antifungal agents. PMID:26949952

  13. Lactic Acid Bacteria in Total Mixed Ration Silage Containing Soybean Curd Residue: Their Isolation, Identification and Ability to Inhibit Aerobic Deterioration.

    PubMed

    Li, Y; Wang, F; Nishino, N

    2016-04-01

    We investigated the effects of the predominant lactic acid bacteria (LAB) on the fermentation characteristics and aerobic stability of total mixed ration (TMR) silage containing soybean curd residue (SC-TMR silage). The SC-TMR materials were ensiled in laboratory silos for 14 or 56 days. LAB predominant in SC-TMR silage were identified (Exp. 1). Lactobacillus fermentum (L. fermentum) and Streptococcus bovis (S. bovis) were found in the untreated materials, Leuconostoc pseudomesenteroides (L. pseudomesenteroides) in 14-day silage and Lactobacillus plantarum (L. plantarum) in all silages. Pediococcus acidilactici (P. acidilactici), Lactobacillus paracasei (L. paracasei), and Lactobacillus brevis (L. brevis) formed more than 90% of the isolates in 56-day silage. Italian ryegrass and whole crop maize were inoculated with P. acidilactici and L. brevis isolates and the fermentation and aerobic stability determined (Exp. 2). Inoculation with P. acidilactici and L. brevis alone or combined improved the fermentation products in ryegrass silage and markedly enhanced its aerobic stability. In maize silage, P. acidilactici and L. brevis inoculation caused no changes and suppressed deterioration when combined with increases in acetic acid content. The results indicate that P. acidilactici and L. brevis may produce a synergistic effect to inhibit SC-TMR silage deterioration. Further studies are needed to identify the inhibitory substances, which may be useful for developing potential antifungal agents. PMID:26949952

  14. Dynamics of development of aerobic and anaerobic bacteria during aeration of an oil-bearing stratum to enhance oil recovery

    SciTech Connect

    Belyaev, S.S.

    1983-03-01

    The distribution and activity of microorganisms in ground formations has been studied in order to assess their use and regulation during oil field exploitation. Experiments were performed on water-flooded oil fields of the Tatar ASSR and revealed some regularity in the distribution of aerobic and anaerobic microflora. Wells were opened after 3, 28 and 68 days after flooding with aerated water supplemented with nitrogen and phosphate salts. Activation of aerobes results in oxidation of residual oil (not released over 3 years of exploitation). The products (CO/sub 2/ fatty acids) of oxidation promote oil recovery. In the longer experiments anaerobic processes, especially methanogenesis from CO/sub 2/ were enhanced.

  15. Extent of copper tolerance and consequences for functional stability of the ammonia-oxidizing community in long-term copper-contaminated soils.

    PubMed

    Mertens, Jelle; Wakelin, Steven A; Broos, Kris; McLaughlin, Mike J; Smolders, Erik

    2010-01-01

    Adaptation of soil microbial communities to elevated copper (Cu) concentrations has been well documented. However, effects of long-term Cu exposure on adaptation responses associated with functional stability and structural composition within the nitrifying community are still unknown. Soils were sampled in three field sites (Denmark, Thailand, and Australia) where Cu gradients had been established from 3 to 80 years prior to sampling. In each field site, the potential nitrification rate (PNR) decreased by over 50% with increasing soil Cu, irrespective of a 20 to >200-fold increase in Cu tolerance (at the highest soil Cu) among the nitrifying communities. This increased tolerance was associated with decreasing numbers (15-120-fold) of ammonia-oxidizing bacteria (AOB), except in the oldest contaminated field site, decreasing numbers of ammonia-oxidizing archaea (AOA; 10-130-fold) and differences in the operational taxonomic unit (OTU) composition of the AOB and, to a lesser extent, AOA communities. The sensitivity of nitrifying communities, previously under long-term Cu exposure, to additional stresses was assessed. Nitrification in soils from the three field sites was measured following acidification, pesticide addition, freeze-thaw cycles, and dry-rewetting cycles. Functional stability of the nitrification process was assessed immediately after stress application (resistance) and after an additional three weeks of incubation (resilience). No indications were found that long-term Cu exposure affected the sensitivity to the selected stressors, suggesting that resistance and resilience were unaffected. It was concluded that the nitrifying community changed structurally in all long-term Cu-exposed field sites and that these changes were associated with increased Cu tolerance but not with a loss of functional stability. PMID:20821416

  16. Land Spreading of Wastewaters from the Fruit-Packaging Industry and Potential Effects on Soil Microbes: Effects of the Antioxidant Ethoxyquin and Its Metabolites on Ammonia Oxidizers

    PubMed Central

    Papadopoulou, Evangelia S.; Tsachidou, Bella; Sułowicz, Sławomir; Menkissoglu-Spiroudi, Urania

    2015-01-01

    Thiabendazole (TBZ), imazalil (IMZ), ortho-phenylphenol (OPP), diphenylamine (DPA), and ethoxyquin (EQ) are used in fruit-packaging plants (FPP) with the stipulation that wastewaters produced by their application would be depurated on site. However, no such treatment systems are currently in place, leading FPP to dispose of their effluents in agricultural land. We investigated the dissipation of those pesticides and their impact on soil microbes known to have a key role on ecosystem functioning. OPP and DPA showed limited persistence (50% dissipation time [DT50], 0.6 and 1.3 days) compared to TBZ and IMZ (DT50, 47.0 and 150.8 days). EQ was rapidly transformed to the short-lived quinone imine (QI) (major metabolite) and the more persistent 2,4-dimethyl-6-ethoxyquinoline (EQNL) (minor metabolite). EQ and OPP exerted significant inhibition of potential nitrification, with the effect of the former being more persistent. This was not reflected in the abundance (determined by quantitative PCR [qPCR]) of the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Considering the above discrepancy and the metabolic pattern of EQ, we further investigated the hypothesis that its metabolites and not only EQ were toxic to ammonia oxidizers. Potential nitrification, amoA gene abundance, and amoA gene transcripts of AOB and AOA showed that QI was probably responsible for the inhibition of nitrification. Our findings have serious ecological and practical implications for soil productivity and N conservation in agriculturally impacted ecosystems and stress the need to include metabolites and RNA-based methods when the soil microbial toxicity of pesticides is assessed. PMID:26590271

  17. Nitrospina-like bacteria are the main drivers of nitrite oxidation in the seasonal upwelling area of the Eastern South Pacific (Central Chile ∼36°S).

    PubMed

    Levipan, Héctor A; Molina, Verónica; Fernandez, Camila

    2014-12-01

    Aerobic nitrite oxidation in marine environments plays a key role in the nitrification process. Marine bacteria involved in this nitrate-producing process have however been seldom studied compared with the ammonia-oxidizing community. Here, we report for the first time the community structure of aerobic nitrite-oxidizing bacteria (NOB) in the seasonal upwelling and oxygen-deficient area off Central Chile. Analysis of 16S rRNA by tag pyrosequencing was combined with specific quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR in summer and wintertime. Nitrospina-like bacteria were the only known NOB detected by means of pyrosequencing between 30 and 80 m depth, accounting for up to 5% of total bacteria. This guild was represented by 11 and 7 operational taxonomic units (97% cut-off) in winter and summertime respectively. Nitrospina-like bacteria were phylogenetically related to sequences retrieved from coastal upwelling, oxygen minimum zones and deep-sea environments. This group was also detected by qPCR with abundances that increased with depth throughout the water column. Importantly, Nitrospina from surface layers showed low abundances but high 16S rRNA : rDNA ratios and mainly in summertime. Overall, our results highlight the seasonal variability between the structure and physiological state of this community and suggest a significant role of Nitrospina in the nitrogen cycle of seasonal upwelling areas. PMID:25756109

  18. Influence of Partial Denitrification and Mixotrophic Growth of NOB on Microbial Distribution in Aerobic Granular Sludge.

    PubMed

    Winkler, Mari-K H; Le, Quan H; Volcke, Eveline I P

    2015-09-15

    In aerobic granular sludge (AGS), the growth of nitrite oxidizing bacteria (NOB) can be uncoupled from the nitrite supply of ammonia oxidizing bacteria (AOB). Besides, unlike for conventional activated sludge, Nitrobacter was found to be the dominant NOB and not Nitrospira. To explain these experimental observations, two possible pathways have been put forward in literature. The first one involves the availability of additional nitrite from partial denitrification (nitrite-loop) and the second one consists of mixotrophic growth of Nitrobacter in the presence of acetate (ping-pong). In this contribution, mathematical models were set up to assess the possibility of these pathways to explain the reported observations. Simulation results revealed that both pathways influenced the nitrifier distribution in the granules. The nitrite-loop pathway led to an elevated NOB/AOB ratio, while mixotrophic growth of Nitrobacter guaranteed their predominance among the NOB population. Besides, mixotrophic growth of Nitrobacter could lead to NO emission from AGS. An increasing temperature and/or a decreasing oxygen concentration led to an elevated NOB/AOB ratio and increased NO emissions. PMID:26248168

  19. Stable partial nitritation for low-strength wastewater at low temperature in an aerobic granular reactor.

    PubMed

    Isanta, Eduardo; Reino, Clara; Carrera, Julián; Pérez, Julio

    2015-09-01

    Partial nitritation for a low-strength wastewater at low temperature was stably achieved in an aerobic granular reactor. A bench-scale granular sludge bioreactor was operated in continuous mode treating an influent of 70 mg N-NH4(+) L(-1) to mimic pretreated municipal nitrogenous wastewater and the temperature was progressively decreased from 30 to 12.5 °C. A suitable effluent nitrite to ammonium concentrations ratio to a subsequent anammox reactor was maintained stable during 300 days at 12.5 °C. The average applied nitrogen loading rate at 12.5 °C was 0.7 ± 0.3 g N L(-1) d(-1), with an effluent nitrate concentration of only 2.5 ± 0.7 mg N-NO3(-) L(-1). The biomass fraction of nitrite-oxidizing bacteria (NOB) in the granular sludge decreased from 19% to only 1% in 6 months of reactor operation at 12.5 °C. Nitrobacter spp. where found as the dominant NOB population, whereas Nitrospira spp. were not detected. Simulations indicated that: (i) NOB would only be effectively repressed when their oxygen half-saturation coefficient was higher than that of ammonia-oxidizing bacteria; and (ii) a lower specific growth rate of NOB was maintained at any point in the biofilm (even at 12.5 °C) due to the bulk ammonium concentration imposed through the control strategy. PMID:26001281

  20. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Valois, Frederica; Bollmann, Annette; Bottomley, Peter J; Klotz, Martin G; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Sayavedra-Soto, Luis; Woyke, Tanja; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Kyrpides, Nikos; Varghese, Neha; Mikhailova, Natalia; Markowitz, Victor; Palaniappan, Krishna; Ivanova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris

    2016-01-01

    Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments. PMID:27471578

  1. Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

    PubMed Central

    Auguet, Jean-Christophe; Triadó-Margarit, Xavier; Nomokonova, Natalya; Camarero, Lluís; Casamayor, Emilio O

    2012-01-01

    Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter–spring (that is, the 0 oC slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer—autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC−1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC−1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC−1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments. PMID:22495069

  2. Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake.

    PubMed

    Auguet, Jean-Christophe; Triadó-Margarit, Xavier; Nomokonova, Natalya; Camarero, Lluís; Casamayor, Emilio O

    2012-09-01

    Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter-spring (that is, the 0 (o)C slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer-autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC-1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC-1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC-1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments. PMID:22495069

  3. pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils.

    PubMed

    Stempfhuber, Barbara; Engel, Marion; Fischer, Doreen; Neskovic-Prit, Ganna; Wubet, Tesfaye; Schöning, Ingo; Gubry-Rangin, Cécile; Kublik, Susanne; Schloter-Hai, Brigitte; Rattei, Thomas; Welzl, Gerhard; Nicol, Graeme W; Schrumpf, Marion; Buscot, Francois; Prosser, James I; Schloter, Michael

    2015-05-01

    In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH. PMID:25501889

  4. The hydrological context determines the beta-diversity of aerobic anoxygenic phototrophic bacteria in European Arctic seas but does not favor endemism

    PubMed Central

    Lehours, Anne-Catherine; Jeanthon, Christian

    2015-01-01

    Despite an increasing number of studies over the last 15 years, aerobic anoxygenic photoheterotrophic (AAP) bacteria remain a puzzling functional group in terms of physiology, metabolism, and ecology. To contribute to a better knowledge of their environmental distribution, the present study aims at analyzing their diversity and structure at the boundary between the Norwegian, Greenland, and Barents Seas. The polymorphism of a marker gene encoding a sub-unit of the photosynthetic apparatus (pufM gene) was analyzed and attempted to be related to environmental parameters. The Atlantic or Arctic origin of water masses had a strong impact on the AAP bacterial community structure whose populations mostly belonged to the Alpha- and Gammaproteobacteria. A majority (>60%) of pufM sequences were affiliated to the Gammaproteobacteria reasserting that this class often represents the major component of the AAP bacterial community in oceanic regions. Two alphaproteobacterial groups dominate locally suggesting that they can constitute key players in this marine system transiently. We found that temperature is a major determinant of alpha diversity of AAP bacteria in this marine biome with specific clades emerging locally according to the partitioning of water masses. Whereas we expected specific AAP bacterial populations in this peculiar and newly explored ecosystem, most pufM sequences were highly related to sequences retrieved elsewhere. This observation highlights that the studied area does not favor AAP bacteria endemism but also opens new questions about the truthfulness of biogeographical patterns and on the extent of AAP bacterial diversity. PMID:26191046

  5. Nitritation and denitritation of domestic wastewater using a continuous anaerobic-anoxic-aerobic (A(2)O) process at ambient temperatures.

    PubMed

    Zeng, Wei; Li, Lei; Yang, Yingying; Wang, Shuying; Peng, Yongzhen

    2010-11-01

    In a continuous anaerobic-anoxic-aerobic (A(2)O) process treating domestic wastewater at ambient temperatures, nitritation was achieved through a combination of short aerobic actual hydraulic retention time (AHRT) and low dissolved oxygen (DO) levels (0.3-0.5mg/L). The nitrite accumulation rate was about 90% and ammonia removal efficiency was over 95%. With respect to total nitrogen removal, nitritation-denitritation at low DO levels of 0.3-0.5mg/L was essentially equal to the complete nitrification-denitrification at DO levels of 1.5-2.5mg/L with the addition of external carbon sources. Regardless of low DO operation, sludge bulking did not occur since the sludge volume index was below 150ml/g. Real-time PCR assays showed that in response to complete and partial nitrification modes, the numbers of ammonia oxidizing bacteria population were 5.28x10(9)cells/g MLVSS and 3.95x10(10)cells/g MLVSS, respectively. Achievement of nitritation-denitritation is highly beneficial to the treatment of domestic wastewater in terms of lower carbon requirements and reduced aeration costs. PMID:20579871

  6. Iodide Accumulation by Aerobic Bacteria Isolated from Subsurface Sediments of a 129I-Contaminated Aquifer at the Savannah River Site, South Carolina ▿

    PubMed Central

    Li, Hsiu-Ping; Brinkmeyer, Robin; Jones, Whitney L.; Zhang, Saijin; Xu, Chen; Schwehr, Kathy A.; Santschi, Peter H.; Kaplan, Daniel I.; Yeager, Chris M.

    2011-01-01

    129I is of major concern because of its mobility in the environment, excessive inventory, toxicity (it accumulates in the thyroid), and long half-life (∼16 million years). The aim of this study was to determine if bacteria from a 129I-contaminated oxic aquifer at the F area of the U.S. Department of Energy's Savannah River Site, SC, could accumulate iodide at environmentally relevant concentrations (0.1 μM I−). Iodide accumulation capability was found in 3 out of 136 aerobic bacterial strains isolated from the F area that were closely related to Streptomyces/Kitasatospora spp., Bacillus mycoides, and Ralstonia/Cupriavidus spp. Two previously described iodide-accumulating marine strains, a Flexibacter aggregans strain and an Arenibacter troitsensis strain, accumulated 2 to 50% total iodide (0.1 μM), whereas the F-area strains accumulated just 0.2 to 2.0%. Iodide accumulation by FA-30 was stimulated by the addition of H2O2, was not inhibited by chloride ions (27 mM), did not exhibit substrate saturation kinetics with regard to I− concentration (up to 10 μM I−), and increased at pH values of <6. Overall, the data indicate that I− accumulation likely results from electrophilic substitution of cellular organic molecules. This study demonstrates that readily culturable, aerobic bacteria of the F-area aquifer do not accumulate significant amounts of iodide; however, this mechanism may contribute to the long-term fate and transport of 129I and to the biogeochemical cycling of iodine over geologic time. PMID:21278282

  7. Multicenter Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Gram-Positive Aerobic Bacteria

    PubMed Central

    Burnham, Carey-Ann D.; Bythrow, Maureen; Garner, Omai B.; Ginocchio, Christine C.; Jennemann, Rebecca; Lewinski, Michael A.; Manji, Ryhana; Mochon, A. Brian; Procop, Gary W.; Richter, Sandra S.; Sercia, Linda; Westblade, Lars F.; Ferraro, Mary Jane; Branda, John A.

    2013-01-01

    Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting. PMID:23658261

  8. Abundance, Depth Distribution, and Composition of Aerobic Bacteriochlorophyll a-Producing Bacteria in Four Basins of the Central Baltic Sea▿ †

    PubMed Central

    Salka, Ivette; Moulisová, Vladimíra; Koblížek, Michal; Jost, Günter; Jürgens, Klaus; Labrenz, Matthias

    2008-01-01

    The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 × 105 cells ml−1 (11% of total prokaryotes) or 1.0 × 103 CFU ml−1 (9 to 10% of total CFU). Environmental pufM clone sequences were grouped into 11 operational taxonomic units phylogenetically related to cultivated members of the Alpha-, Beta-, and Gammaproteobacteria. In spite of varying pufM compositions, five clones were present in all libraries. Of these, Jannaschia-related clones were always found in relative abundances representing 25 to 30% of the total AAP clones. The abundances of the other clones varied. Clones potentially affiliated with typical freshwater Betaproteobacteria sequences were present at three Baltic Sea stations, whereas clones grouping with Loktanella represented 40% of the total cell numbers in the Gotland Basin. For three alphaproteobacterial clones, probable pufM phylogenetic relationships were supported by 16S rRNA gene analyses of Baltic AAP isolates, which showed nearly identical pufM sequences. Our data indicate that the studied AAP assemblages represented a mixture of marine and freshwater taxa, thus characterizing the Baltic Sea as a “melting pot” of abundant, polyphyletic aerobic photoheterotrophic bacteria. PMID:18502937

  9. Fluctuations in Ammonia Oxidizing Communities Across Agricultural Soils are Driven by Soil Structure and pH

    PubMed Central

    Pereira e Silva, Michele C.; Poly, Franck; Guillaumaud, Nadine; van Elsas, Jan Dirk; Salles, Joana Falcão

    2012-01-01

    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 toward defining a NOR for soil nitrification. The sensitivity of the process and organisms to impacts from the milieu support their use as proxies in the

  10. Novel pod for chlorine dioxide generation and delivery to control aerobic bacteria on the inner surface of floor drains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Floor drains in poultry processing and further processing plants are a harborage site for bacteria both free swimming and in biofilms. This population can include Listeria monocytogenes which has been shown to have potential for airborne spreading from mishandled open drains. Chlorine dioxide (ClO...

  11. Management of aerobic vaginitis.

    PubMed

    Tempera, Gianna; Furneri, Pio Maria

    2010-01-01

    Aerobic vaginitis is a new nonclassifiable pathology that is neither specific vaginitis nor bacterial vaginosis. The diversity of this microbiological peculiarity could also explain several therapeutic failures when patients were treated for infections identified as bacterial vaginosis. The diagnosis 'aerobic vaginitis' is essentially based on microscopic examinations using a phase-contrast microscope (at ×400 magnification). The therapeutic choice for 'aerobic vaginitis' should take into consideration an antibiotic characterized by an intrinsic activity against the majority of bacteria of fecal origin, bactericidal effect and poor/absent interference with the vaginal microbiota. Regarding the therapy for aerobic vaginitis when antimicrobial agents are prescribed, not only the antimicrobial spectrum but also the presumed ecological disturbance on the anaerobic and aerobic vaginal and rectal microbiota should be taken into a consideration. Because of their very low impact on the vaginal microbiota, kanamycin or quinolones are to be considered a good choice for therapy. PMID:21051843

  12. Comparison of two transport systems available in Japan (TERUMO kenkiporter II and BBL Port-A-Cul) for maintenance of aerobic and anaerobic bacteria.

    PubMed

    Fujimoto, Daichi; Takegawa, Hiroshi; Doi, Asako; Sakizono, Kenji; Kotani, Yoko; Miki, Kanji; Naito, Takuya; Niki, Marie; Miyamoto, Junko; Tamai, Koji; Nagata, Kazuma; Nakagawa, Atsushi; Tachikawa, Ryo; Otsuka, Kojiro; Katakami, Nobuyuki; Tomii, Keisuke

    2014-01-01

    The kenkiporter II (KP II) transport system is commonly used in many hospitals in Japan for transporting bacterial specimens to microbiology laboratories. Recently, the BBL Port-A-Cul (PAC) fluid vial became available. However, no reports thus far have compared the effectiveness of these two transport systems. We chose 4 aerobic and facultative anaerobic bacteria as well as 8 anaerobic organisms, and prepared three strains of each bacterium in culture media for placement into PAC and KP II containers. We compared the effectiveness of each transport system for preserving each organism at 6, 24, and 48 h after inoculation at room temperature. Thirty-six strains out of 12 bacteria were used in this study. The PAC system yielded better recovery in quantity of organisms than the KP II system at 6, 24 and 48 h. More strains were significantly recovered with the PAC system than with the KP II at 24 h (36/36 vs. 23/36, P < 0.001) and 48 h (30/36 vs. 12/36, P < 0.001). The PAC system was better in the recovery of viable organisms counted at 24 and 48 h after inoculation compared with the KP II system. The PAC system may be recommended for the transfer of bacterial specimens in clinical settings. PMID:24462420

  13. Abundance and Diversity of Archaeal Ammonia Oxidizers in a Coastal Groundwater System ▿ †

    PubMed Central

    Rogers, Daniel R.; Casciotti, Karen L.

    2010-01-01

    Nitrification, the microbially catalyzed oxidation of ammonia to nitrate, is a key process in the nitrogen cycle. Archaea have been implicated in the first part of the nitrification pathway (oxidation of ammonia to nitrite), but the ecology and physiology of these organisms remain largely unknown. This work describes two different populations of sediment-associated ammonia-oxidizing archaea (AOA) in a coastal groundwater system in Cape Cod, MA. Sequence analysis of the ammonia monooxygenase subunit A gene (amoA) shows that one population of putative AOA inhabits the upper meter of the sediment, where they may experience frequent ventilation, with tidally driven overtopping and infiltration of bay water supplying dissolved oxygen, ammonium, and perhaps organic carbon. A genetically distinct population occurs deeper in the sediment, in a mixing zone between a nitrate- and oxygen-rich freshwater zone and a reduced, ammonium-bearing saltwater wedge. Both of these AOA populations are coincident with increases in the abundance of group I crenarchaeota 16S rRNA gene copies. PMID:20971859

  14. Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.

    PubMed

    Park, Soo-Je; Ghai, Rohit; Martín-Cuadrado, Ana-Belén; Rodríguez-Valera, Francisco; Chung, Won-Hyong; Kwon, KaeKyoung; Lee, Jung-Hyun; Madsen, Eugene L; Rhee, Sung-Keun

    2014-01-01

    Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA. PMID:24798206

  15. The role of ammonia oxide in the reaction of hydroxylamine with carboxylic esters.

    PubMed

    Silva, Carlos M; Dias, Isabela C; Pliego, Josefredo R

    2015-06-14

    Theoretical calculations indicate that hydroxylamine can exist in both neutral and zwitterionic (ammonia oxide) forms in aqueous solution, the former being 3.5 kcal mol(-1) more stable. In this report, we have studied the reaction mechanism of hydroxylamine with phenyl acetate and analyzed the role of the zwitterionic isomer. We have observed that the main reaction pathway takes place through the zwitterionic form with a concerted mechanism, not involving the classical tetrahedral intermediate. Attack by the nitrogen atom (via neutral isomer) has a minor contribution and it is also a concerted process. The activation free energy barriers in aqueous solution were calculated at the MP4/TZVPP + diff level for gas phase energies, CPCM for optimization and frequencies, and through single point calculation of the solvation free energy using the SM8 method. Our theoretically predicted barriers are 20.8 and 23.8 kcal mol(-1) for O and N attack, respectively, in very good agreement with the experimental values of 20.4 and 22.3 kcal mol(-1), respectively. Our results support the view that hydroxylamine is a very special nucleophile and the reactivity of this functional group should be further investigated. PMID:25960004

  16. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.

    PubMed

    Hallam, Steven J; Mincer, Tracy J; Schleper, Christa; Preston, Christina M; Roberts, Katie; Richardson, Paul M; DeLong, Edward F

    2006-04-01

    Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems. PMID:16533068

  17. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics.

    PubMed

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-01-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with "Ca. Nitrosotenuis chungbukensis"), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C-33 °C) and neutrophilic (pH 5.0-7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name "Candidatus Nitrosotenuis cloacae" for the strain SAT1. PMID:27030530

  18. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

    NASA Astrophysics Data System (ADS)

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-03-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1.

  19. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

    PubMed Central

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-01-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1. PMID:27030530

  20. INACTIVATION OF ENTERIC PATHOGENS DURING AEROBIC DIGESTION OF WASTEWATER SLUDGE

    EPA Science Inventory

    The effects of aerobic and anaerobic digestion on enteric viruses, enteric bacteria, total aerobic bacteria, and intestinal parasites were studied under laboratory and field conditions. Under laboratory conditions, the temperature of the sludge digestion was the major factor infl...

  1. Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo—Brazil)

    PubMed Central

    Cuadrat, Rafael R. C.; Ferrera, Isabel; Grossart, Hans-Peter; Dávila, Alberto M. R.

    2016-01-01

    Abstract Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean. PMID:26871866

  2. Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo--Brazil).

    PubMed

    Cuadrat, Rafael R C; Ferrera, Isabel; Grossart, Hans-Peter; Dávila, Alberto M R

    2016-02-01

    Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean. PMID:26871866

  3. Impact of herbicides on the abundance and structure of indigenous beta-subgroup ammonia-oxidizer communities in soil microcosms.

    PubMed

    Chang, Y J; Hussain, A K; Stephen, J R; Mullen, M D; White, D C; Peacock, A

    2001-11-01

    In this study, mixtures of five herbicide-formulated products (atrazine, dicamba, fluometuron, metolachlor, and sulfentrazone) were applied to soil microcosm columns in increasing concentrations. The toxic impact of herbicides on the indigenous beta-subclass Proteobacteria autotrophic ammonia-oxidizer (beta-AAO) community was assessed. The beta-AAO population abundances were estimated by competitive polymerase chain reaction (PCR) targeting the gene amoA, encoding the alpha-subunit of ammonia monooxygenase. Community structure was examined by PCR and denaturing gradient gel electrophoresis targeting 16S rDNA with band excision and sequence analysis, and by analysis of amoA gene fragment clone libraries. The 16S rDNA analyses showed that a single ribotype of Nitrosospira cluster 3 was the dominant beta-AAO in all treatments. At a finer scale, amoA clone library analysis suggested a shift in community structure corresponding to the 100-ppm application. Competitive PCR indicated significant differences between treatments. The control exhibited relatively stable population abundance over the time period examined. The 10-ppm treatment induced a population increase, but a significant decrease was induced by the 100-ppm application. At 1,000 ppm, the ammonia-oxidizer population dropped below the method detection limit by the first sampling point. An impact on ammonia oxidizers resulting from the application of herbicides was observed, both in abundance and community structure. PMID:11699770

  4. Isolation and characterization of aerobic culturable arsenic-resistant bacteria from surfacewater and groundwater of Rautahat District, Nepal.

    PubMed

    Shakya, S; Pradhan, B; Smith, L; Shrestha, J; Tuladhar, S

    2012-03-01

    Arsenic (As) contamination of groundwater is a serious Environmental Health Management issue of drinking water sources especially in Terai region of Nepal. Many studies have reported that due to natural abundance of arsenic in the environment, various bacteria have developed different resistance mechanisms for arsenic compound. In this study, the culturable arsenic-resistant bacteria indigenous to surfacewater as well as groundwater from Rautahat District of Nepal were randomly isolated by standard plate count method on the basis of viable growth on plate count agar amended with arsenate ranging from 0, 0.5, 10, 40, 80 to 160 milligram per liter (mg/l). With respect to the morphological and biochemical tests, nine morphologically distinct potent arsenate tolerant bacteria showed relatedness with Micrococcus varians, Micrococcus roseus, Micrococcus luteus, Pseudomonas maltophilia, Pseudomonas sp., Vibrio parahaemolyticus, Bacillus cereus, Bacillus smithii 1 and Bacillus smithii 2. The isolates were capable of tolerating more than 1000 mg/l of arsenate and 749 mg/l of arsenite. Likewise, bioaccumulation capability was highest with M. roseus (85.61%) and the least with B. smithii (47.88%) indicating the potential of the organisms in arsenic resistance and most probably in bioremediation. PMID:21868146

  5. Central Role of Dynamic Tidal Biofilms Dominated by Aerobic Hydrocarbonoclastic Bacteria and Diatoms in the Biodegradation of Hydrocarbons in Coastal Mudflats

    PubMed Central

    Coulon, Frédéric; Chronopoulou, Panagiota-Myrsini; Fahy, Anne; Païssé, Sandrine; Goñi-Urriza, Marisol; Peperzak, Louis; Acuña Alvarez, Laura; McKew, Boyd A.; Brussaard, Corina P. D.; Underwood, Graham J. C.; Timmis, Kenneth N.; Duran, Robert

    2012-01-01

    Mudflats and salt marshes are habitats at the interface of aquatic and terrestrial systems that provide valuable services to ecosystems. Therefore, it is important to determine how catastrophic incidents, such as oil spills, influence the microbial communities in sediment that are pivotal to the function of the ecosystem and to identify the oil-degrading microbes that mitigate damage to the ecosystem. In this study, an oil spill was simulated by use of a tidal chamber containing intact diatom-dominated sediment cores from a temperate mudflat. Changes in the composition of bacteria and diatoms from both the sediment and tidal biofilms that had detached from the sediment surface were monitored as a function of hydrocarbon removal. The hydrocarbon concentration in the upper 1.5 cm of sediments decreased by 78% over 21 days, with at least 60% being attributed to biodegradation. Most phylotypes were minimally perturbed by the addition of oil, but at day 21, there was a 10-fold increase in the amount of cyanobacteria in the oiled sediment. Throughout the experiment, phylotypes associated with the aerobic degradation of hydrocarbons, including polycyclic aromatic hydrocarbons (PAHs) (Cycloclasticus) and alkanes (Alcanivorax, Oleibacter, and Oceanospirillales strain ME113), substantively increased in oiled mesocosms, collectively representing 2% of the pyrosequences in the oiled sediments at day 21. Tidal biofilms from oiled cores at day 22, however, consisted mostly of phylotypes related to Alcanivorax borkumensis (49% of clones), Oceanospirillales strain ME113 (11% of clones), and diatoms (14% of clones). Thus, aerobic hydrocarbon biodegradation is most likely to be the main mechanism of attenuation of crude oil in the early weeks of an oil spill, with tidal biofilms representing zones of high hydrocarbon-degrading activity. PMID:22407688

  6. Evaluation of the Removal of Indicator Bacteria from Domestic Sludge Processed by Autothermal Thermophilic Aerobic Digestion (ATAD)

    PubMed Central

    Piterina, Anna V.; Bartlett, John; Pembroke, Tony J.

    2010-01-01

    The degradation of sludge solids in an insulated reactor during Autothermal Thermophilic Aerobic Digestion (ATAD) processing results in auto-heating, thermal treatment and total solids reduction, however, the ability to eliminate pathogenic organisms has not been analysed under large scale process conditions. We evaluated the ATAD process over a period of one year in a two stage, full scale Irish ATAD plant established in Killarney and treating mixed primary and secondary sludge, by examining the sludge microbiologically at various stages during and following ATAD processing to determine its ability to eliminate indicator organisms. Salmonella spp. (pathogen) and fecal-coliform (indicator) densities were well below the limits used to validate class A biosolids in the final product. Enteric pathogens present at inlet were deactivated during the ATAD process and were not detected in the final product using both traditional microbial culture and molecular phylogenetic techniques. A high DNase activity was detected in the bulk sludge during the thermophilic digestion stage which may be responsible for the rapid turn over of DNA from lysed cells and the removal of mobile DNA. These results offer assurance for the safe use of ATAD sludge as a soil supplement following processing. PMID:20948933

  7. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations.

    PubMed

    Rotthauwe, J H; Witzel, K P; Liesack, W

    1997-12-01

    The naturally occurring genetic heterogeneity of autotrophic ammonia-oxidizing populations belonging to the beta subclass of the Proteobacteria was studied by using a newly developed PCR-based assay targeting a partial stretch of the gene which encodes the active-site polypeptide of ammonia monooxygenase (amoA). The PCR yielded a specific 491-bp fragment with all of the nitrifiers tested, but not with the homologous stretch of the particulate methane monooxygenase, a key enzyme of methane-oxidizing bacteria. The assay also specifically detected amoA in DNA extracted from various aquatic and terrestrial environments. The resulting PCR products retrieved from rice roots, activated sludge, a freshwater sample, and an enrichment culture were used for the generation of amoA gene libraries. No false positives were detected in a set of 47 randomly selected clone sequences that were analyzed further. The majority of the environmental sequences retrieved from rice roots and activated sludge grouped within the phylogenetic radiation defined by cultured strains of the genera Nitrosomonas and Nitrosospira. The comparative analysis identified members of both of these genera in activated sludge; however, only Nitrosospira-like sequences with very similar amino acid patterns were found on rice roots. Further differentiation of these molecular isolates was clearly possible on the nucleic acid level due to the accumulation of synonymous mutations, suggesting that several closely related but distinct Nitrosospira-like populations are the main colonizers of the rhizosphere of rice. Each of the amoA gene libraries obtained from the freshwater sample and the enrichment culture was dominated by a novel lineage that shared a branch with the Nitrosospira cluster but could not be assigned to any of the known pure cultures. Our data suggest that amoA represents a very powerful molecular tool for analyzing indigenous ammonia-oxidizing communities due to (i) its specificity, (ii) its fine

  8. Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments▿

    PubMed Central

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

    2009-01-01

    Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like L. uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions. PMID:19304820

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

    PubMed

    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. PMID:24176706

  10. Matrix Extension Study: Validation of the Compact Dry TC Method for Enumeration of Total Aerobic Bacteria in Selected Foods.

    PubMed

    Mizuochi, Shingo; Nelson, Maria; Baylis, Chris; Jewell, Keith; Green, Becky; Limbum, Rob; Fernandez, Maria Cristina; Salfinger, Yvonne; Chen, Yi

    2016-01-01

    A validation study was conducted to extend the matrix claim for the Nissui Compact Dry Total Count (TC), Performance Tested Method(s)(SM) (PTM) Certification No. 010404, to cooked chicken, lettuce, frozen fish, milk powder, and pasteurized whole milk. The method was originally certified by the AOAC Research Institute Performance Tested Method(s)(SM) Program for raw meat products. The Compact Dry TC is a ready-to-use dry media sheet that is rehydrated by adding 1 mL of diluted sample. A total aerobic colony count can be determined in the sample following 48 h of incubation. Matrix extension studies were conducted by Campden BRI (formerly Campden and Chorleywood Food Research Association Technology Limited), Chipping Campden, UK. Single-laboratory data were collected for cooked chicken, lettuce, frozen fish, and milk powder, whereas a multilaboratory study was conducted on pasteurized milk. Fourteen laboratories participated in the collaborative study. The Compact Dry TC was tested at two time points, 48 ± 3 h and 72 ± 3 h and compared with the current International Organization for Standardization (ISO) method at the time of the study, ISO 4833:2003 (this standard is withdrawn and has been replaced by: ISO 4833-1:2013 and ISO 4833-2:2013), Microbiology of food and animal feeding stuffs-Horizontal method for the enumeration of microorganisms-Colony-count technique at 30°C. The data were logarithmically transformed and evaluated for repeatability (plus reproducibility for pasteurized milk), RSD of repeatability (plus RSD of reproducibility for milk), r(2), and mean difference between methods with 95% confidence interval (CI). A CI outside of (-0.5 to 0.5) on the log10 mean difference was used as the criterion to establish significant statistical difference between methods. No significant differences were found between the Compact Dry TC 48 and 72 h time points, with the exception of one contamination level of cooked chicken and one contamination level of dry milk

  11. Diversity, Abundance, and Spatial Distribution of Sediment Ammonia-Oxidizing Betaproteobacteria in Response to Environmental Gradients and Coastal Eutrophication in Jiaozhou Bay, China▿ †

    PubMed Central

    Dang, Hongyue; Li, Jing; Chen, Ruipeng; Wang, Lin; Guo, Lizhong; Zhang, Zhinan; Klotz, Martin G.

    2010-01-01

    Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments. PMID:20511433

  12. [Diversity of ammonia-oxidizing archaea in Tibetan Zoige plateau wetland ].

    PubMed

    Zheng, Youkun; Wang, Xianbin; Gu, Yunfu; Zhang, Xiaoping

    2014-09-01

    [ OBJECTIVE ] Investigation of ammonia-oxidizing archaea (AOA) in nature environments is important to understand the global nitrogen cycling. However, little is known about the AOA community in plateau wetland. Therefore, we studied the composition and diversity of AOA in Zoige plateau wetland swamp soil. [METHODS] Total DNA was extracted from the swamp soil of three typical wetlands including A'xi pastoral area, Maixi pastoral area and Fenqu pastoral area locate in Zoige plateau wetland, and amoA gene was amplified with universally AOA amoA gene primers and then cloned. Then 80 positive clones for each clone library were chosen for further restriction fragment length polymorphism (RFLP) analysis, and the typical RFLP types were selected for sequencing and clustered into operational taxonomic units (OTUs) at 98% cutoff using the Mothur software. The MEGA 5. 0 software was used for the amoA gene phylogeny analysis. [RESULTS] A total of 240 positive clones for all 3 libraries were used for RFLP analysis, and 15 specific amoA sequences were sequenced and clustered into 7 OTUs at 98% cutoff. Among them, OTU6 was detected in all of the 3 libraries and included 27% of the total specific clones. The phylogeny analysis showed that the 15 amoA sequences were grouped into 3 subgroups consisted of Zoige Wetland Clade 1 (4 OTUs), Zoige Wetland Clade 2 (2 OTUs) and Zoige Wetland Clade 3 (1 OTU). BLAST analysis showed that all OTUs were affiliated with the phylum Crenarchaeota. Correlation analysis showed that the Shannon diversity index (H') was significantly correlated with ammonia, nitrate/nitrite (P <0. 05). [ CONCLUSION] AOA in the Zoige plateau wetland swamp soil are all belonged to the Crenarchaeota, and their diversity is significantly correlated with soil ammonia, nitrate/nitrite content. PMID:25522598

  13. Evaluation of the use of PCR and reverse transcriptase PCR for detection of pathogenic bacteria in biosolids from anaerobic digestors and aerobic composters.

    PubMed

    Burtscher, Carola; Wuertz, Stefan

    2003-08-01

    A PCR-based method and a reverse transcriptase PCR (RT-PCR)-based method were developed for the detection of pathogenic bacteria in organic waste, using Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and Staphylococcus aureus as model organisms. In seeded organic waste samples, detection limits of less than 10 cells per g of organic waste were achieved after one-step enrichment of bacteria, isolation, and purification of DNA or RNA before PCR or RT-PCR amplification. To test the reproducibility and reliability of the newly developed methods, 46 unseeded samples were collected from diverse aerobic (composting) facilities and anaerobic digestors and analyzed by both culture-based classical and newly developed PCR-based procedures. No false-positive but some false-negative results were generated by the PCR- or RT-PCR-based methods after one-step enrichment when compared to the classical detection methods. The results indicated that the level of activity of the tested bacteria in unseeded samples was very low compared to that of freshly inoculated cells, preventing samples from reaching the cell density required for PCR-based detection after one-step enrichment. However, for Salmonella spp., a distinct PCR product could be obtained for all 22 nonamended samples that tested positive for Salmonella spp. by the classical detection procedure when a selective two-step enrichment (20 h in peptone water at 37 degrees C and 24 h in Rappaport Vassiliadis medium at 43 degrees C) was performed prior to nucleic acid extraction and PCR. Hence, the classical procedure was shortened, since cell plating and further differentiation of isolated colonies can be omitted, substituted for by highly sensitive and reliable detection based on nucleic acid extraction and PCR. Similarly, 2 of the 22 samples in which Salmonella spp. were detected also tested positive for Listeria monocytogenes according to a two-step enrichment procedure followed by PCR, compared to 3 samples

  14. Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification

    PubMed Central

    Hassan, Junaid; Bergaust, Linda L.; Wheat, I. David; Bakken, Lars R.

    2014-01-01

    In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NOx) to N2 (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O2 is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e−-flow rates to O2 and NOx. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (, h−1) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O2] falls below a critical threshold and terminates (assuming energy-limitation) as [O2] exhausts. With  = 0.005 h−1, the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting (fraction of the cells recruited to denitrification) falls within 0.038–0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a ‘bet-hedging strategy’: switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia

  15. Microbiological Quality of Ready-to-Eat Vegetables Collected in Mexico City: Occurrence of Aerobic-Mesophilic Bacteria, Fecal Coliforms, and Potentially Pathogenic Nontuberculous Mycobacteria

    PubMed Central

    Cerna-Cortes, Jorge Francisco; Leon-Montes, Nancy; Cortes-Cueto, Ana Laura; Salas-Rangel, Laura P.; Helguera-Repetto, Addy Cecilia; Lopez-Hernandez, Daniel; Rivera-Gutierrez, Sandra; Fernandez-Rendon, Elizabeth; Gonzalez-y-Merchand, Jorge Alberto

    2015-01-01

    The aims of this study were to evaluate the microbiological quality and the occurrence of nontuberculous mycobacteria (NTM) in a variety of salads and sprouts from supermarkets and street vendors in Mexico City. Aerobic-mesophilic bacteria (AMB) were present in 100% of RTE-salads samples; 59% of samples were outside guidelines range (>5.17 log10 CFU per g). Although fecal coliforms (FC) were present in 32% of samples, only 8% of them exceeded the permissible limit (100 MPN/g). Regarding the 100 RTE-sprouts, all samples were also positive for AMB and total coliforms (TC) and 69% for FC. Seven NTM species were recovered from 7 salad samples; they included three M. fortuitum, two M. chelonae, one M. mucogenicum, and one M. sp. Twelve RTE-sprouts samples harbored NTM, which were identified as M. porcinum (five), M. abscessus (two), M. gordonae (two), M. mucogenicum (two), and M. avium complex (one). Most RTE-salads and RTE-sprouts had unsatisfactory microbiological quality and some harbored NTM associated with illness. No correlation between the presence of coliforms and NTM was found. Overall, these results suggest that RTE-salads and RTE-sprouts might function as vehicles for NTM transmission in humans; hence, proper handling and treatment before consumption of such products might be recommendable. PMID:25918721

  16. Adequacy of Petrifilm™ Aerobic Count plates supplemented with de Man, Rogosa & Sharpe broth and chlorophenol red for enumeration of lactic acid bacteria in salami.

    PubMed

    de Castilho, Natália Parma Augusto; Okamura, Vivian Tiemi; Camargo, Anderson Carlos; Pieri, Fábio Alessandro; Nero, Luís Augusto

    2015-12-01

    The present study aimed to assess the performance of alternative protocols to enumerate lactic acid bacteria (LAB) in salami. Fourteen cultures and two mixed starter cultures were plated using six protocols: 1) Petrifilm™ Aerobic Count (AC) with MRS broth and chlorophenol red (CR), incubated under aerobiosis or 2) under anaerobiosis, 3) MRS agar with CR, 4) MRS agar with bromocresol purple, 5) MRS agar at pH5.7, and 6) All Purpose Tween agar. Samples of salami were obtained and the LAB microbiota was enumerated by plating according protocols 1, 2, 3 and 5. Regression analysis showed a significant correlation between the tested protocols, based on culture counts (p<0.05). Similar results were observed for salami, and no significant differences of mean LAB counts between selected protocols (ANOVA, p>0.05). Colonies were confirmed as LAB, indicating proper selectivity of the protocols. The results showed the adequacy of Petrifilm™ AC supplemented with CR for the enumeration of LAB in salami. PMID:26291606

  17. Menadione-catalyzed luminol chemiluminescence assay for the rapid detection of viable bacteria in foods under aerobic conditions.

    PubMed

    Kawasaki, S; Yamashoji, S; Asakawa, A; Isshiki, K; Kawamoto, S

    2004-12-01

    A menadione-catalyzed luminol chemiluminescence assay was developed for the rapid detection and estimation of viable bacteria in foods. The principle of this assay is based on the extracellular menadione-catalyzed active oxygen spieces (O2- and H2O2) generated by the activity of NAD(P)H:menadione oxidoreductase in viable cells. This luminol chemiluminescence assay requires 10 min for the incubation of cells with menadione and then 2 s for the measurement of chemiluminescence intensity after an injection of luminol solution without the treatment of cell lysis. This method was evaluated using liquid food samples of milk, vegetable juice, green tea, and coffee spiked with Escherichia coli ATCC 25922. The study result revealed that E. coli contamination at 1 to 10 CFU/ml in these foods could be detected after incubation at 37 degrees C for 7 h in an enrichment medium; however, the green tea and coffee samples requires filtration. This method could be a useful tool for the rapid evaluation of microbial food contamination. PMID:15633684

  18. The potential for hydrocarbon biodegradation and production of extracellular polymeric substances by aerobic bacteria isolated from a Brazilian petroleum reservoir.

    PubMed

    Vasconcellos, S P; Dellagnezze, B M; Wieland, A; Klock, J-H; Santos Neto, E V; Marsaioli, A J; Oliveira, V M; Michaelis, W

    2011-06-01

    Extracellular polymeric substances (EPS) can contribute to the cellular degradation of hydrocarbons and have a huge potential for application in biotechnological processes, such as bioremediation and microbial enhanced oil recovery (MEOR). Four bacterial strains from a Brazilian petroleum reservoir were investigated for EPS production, emulsification ability and biodegradation activity when hydrocarbons were supplied as substrates for microbial growth. Two strains of Bacillus species had the highest EPS production when phenanthrene and n-octadecane were offered as carbon sources, either individually or in a mixture. While Pseudomonas sp. and Dietzia sp., the other two evaluated strains, had the highest hydrocarbon biodegradation indices, EPS production was not detected. Low EPS production may not necessarily be indicative of an absence of emulsifier activity, as indicated by the results of a surface tension reduction assay and emulsification indices for the strain of Dietzia sp. The combined results gathered in this work suggest that a microbial consortium consisting of bacteria with interdependent metabolisms could thrive in petroleum reservoirs, thus overcoming the limitations imposed on each individual species by the harsh conditions found in such environments. PMID:25187151

  19. Worldwide distribution of Nitrosococcus oceani, a marine ammonia-oxidizing gamma-proteobacterium, detected by PCR and sequencing of 16S rRNA and amoA genes.

    PubMed

    Ward, Bess B; O'Mullan, Gregory D

    2002-08-01

    Diversity of cultured ammonia-oxidizing bacteria in the gamma-subdivision of the Proteobacteria was investigated by using strains isolated from various parts of the world ocean. All the strains were very similar to each other on the basis of the sequences of both the 16S rRNA and ammonia monooxygenase genes and could be characterized as a single species. Sequences were also cloned directly from environmental DNA from coastal Pacific and Atlantic sites, and these sequences represented the first Nitrosococcus oceani-like sequences obtained directly from the ocean. Most of the environmental sequences clustered tightly with those of the cultivated strains, but some sequences could represent new species of NITROSOCOCCUS: These findings imply that organisms similar to the cultivated N. oceani strains have a worldwide distribution. PMID:12147525

  20. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments

    PubMed Central

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L−1 (200 NH4+-N) and 400 mg NH4+-N L−1 (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater. PMID:26444015

  1. Polyclonal Antibodies Recognizing the AmoB Protein of Ammonia Oxidizers of the β-Subclass of the Class Proteobacteria

    PubMed Central

    Pinck, Claudia; Coeur, Caroline; Potier, Patrick; Bock, Eberhard

    2001-01-01

    A 41-kDa protein of Nitrosomonas eutropha was purified, and the N-terminal amino acid sequence was found to be nearly identical with the sequence of AmoB, a subunit of ammonia monooxygenase. This protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the β-subclass of Proteobacteria (Nitrosomonas, including Nitrosococcus mobilis, which belongs phylogenetically to Nitrosomonas; Nitrosospira; Nitrosolobus; and Nitrosovibrio). In contrast, the antibodies did not react with ammonia oxidizers affiliated with the γ-subclass of Proteobacteria (Nitrosococcus oceani and Nitrosococcus halophilus). Moreover, methane oxidizers (Methylococcus capsulatus, Methylocystis parvus, and Methylomonas methanica) containing the related particulate methane monooxygenase were not detected. Quantitative immunoblot analysis revealed that total cell protein of N. eutropha consisted of approximately 6% AmoB, when cells were grown using standard conditions (mineral medium containing 10 mM ammonium). This AmoB amount was shown to depend on the ammonium concentration in the medium. About 14% AmoB of total protein was found when N. eutropha was grown with 1 mM ammonium, whereas 4% AmoB was detected when 100 mM ammonium were used. In addition, the cellular amount of AmoB was influenced by the absence of the substrate. Cells starved for more than 2 months contained nearly twice as much AmoB as actively growing cells, although these cells possessed low ammonia-oxidizing activity. AmoB was always present and could even be detected in cells of Nitrosomonas after 1 year of ammonia starvation. PMID:11133435

  2. Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant.

    PubMed

    Tokuyama, Tatsuaki; Mine, Atsusi; Kamiyama, Kaoru; Yabe, Ryuichi; Satoh, Kazuo; Matsumoto, Hirotoshi; Takahashi, Reiji; Itonaga, Koji

    2004-01-01

    An ammonia-oxidizing bacterium (strain YNSRA) was isolated from the rhizoplane of the reed (Phragmites communis) used in an aquaponics plant which is a wastewater treatment plant. Strain YNSRA was identified as Nitrosomonas communis by taxonomic studies. The hydroxylamine-cytochrome c reductase (HCR) of strain YNSRA was found to have a higher activity (25.60 u/mg) than that of Nitrosomonas europaea ATCC25978T (8.94 u/mg). Ribulose-1,5-bisphosphate carboxylase (RubisCO) activity was detected at very low levels in strain YNSRA, whereas strain ATCC25978T had definite activity. PMID:16233712

  3. Aerobic bacteria from mucous membranes, ear canals, and skin wounds of feral cats in Grenada, and the antimicrobial drug susceptibility of major isolates.

    PubMed

    Hariharan, Harry; Matthew, Vanessa; Fountain, Jacqueline; Snell, Alicia; Doherty, Devin; King, Brittany; Shemer, Eran; Oliveira, Simone; Sharma, Ravindra N

    2011-03-01

    In a 2-year period 54 feral cats were captured in Grenada, West Indies, and a total of 383 samples consisting of swabs from rectum, vagina, ears, eyes, mouth, nose and wounds/abscesses, were cultured for aerobic bacteria and campylobacters. A total of 251 bacterial isolates were obtained, of which 205 were identified to species level and 46 to genus level. A commercial bacterial identification system (API/Biomerieux), was used for this purpose. The most common species was Escherichia coli (N=60), followed by Staphylococcus felis/simulans (40), S. hominis (16), S. haemolyticus (12), Streptococcus canis (9), Proteus mirabilis (8), Pasteurella multocida (7), Streptococcus mitis (7), Staphylococcus xylosus (7), S. capitis (6), S. chromogenes (4), S. sciuri (3), S. auricularis (2), S. lentus (2), S. hyicus (2), Streptococcus suis (2) and Pseudomonas argentinensis (2). Sixteen other isolates were identified to species level. A molecular method using 16S rRNA sequencing was used to confirm/identify 22 isolates. Salmonella or campylobacters were not isolated from rectal swabs. E. coli and S. felis/simulans together constituted 50% of isolates from vagina. S. felis/simulans was the most common species from culture positive ear and eye samples. P. multocida was isolated from 15% of mouth samples. Coagulase-negative staphylococci were the most common isolates from nose and wound swabs. Staphylococcus aureus, or S. intemedius/S. pseudintermedius were not isolated from any sample. Antimicrobial drug resistance was minimal, most isolates being susceptible to all drugs tested against, including tetracycline. PMID:20627391

  4. Comparison of ammonia-oxidizing bacterial community structure in membrane-assisted bioreactors using PCR-DGGE and FISH.

    PubMed

    Ziembińska, A; Ciesielski, S; Gnida, A; Zabczyńki, S; Surmacz-Górska, J; Miksch, K

    2012-08-01

    The ammonia-oxidizing bacterial (AOB) communities in three membrane bioreactors (MBRs) were monitored for 2 months after an acclimation period in order to investigate the influence of sludge age and medium type on AOB changeability and its connection with nitrification effectiveness. One MBR with a sludge age of 4 days was fed with a synthetic medium, whereas the other two with sludge ages of 8 and 32 days were fed with landfill leachate. The research revealed that landfill leachate can be effectively treated in an MBR with a higher sludge age for longer periods of time and that this improvement in performance was correlated with an increase in AOB biodiversity. Interestingly, the medium type has a stronger influence on AOB biocenosis formation than the sludge age. PMID:22713978

  5. A combined upflow anaerobic sludge bed, aerobic, and anoxic fixed-bed reactor system for removing tetramethylammonium hydroxide and nitrogen from light-emitting diode wastewater.

    PubMed

    Lin, Han-Lin; Chen, Sheng-Kun; Huang, Yu-Wen; Chen, Wei-Cheng; Chien, Wei-Cheng; Cheng, Sheng-Shung

    2016-06-01

    A laboratory study using a combined upflow anaerobic sludge bed (UASB) and aerobic and anoxic fixed-bed reactor system was undertaken to explore its capability for removing tetramethylammonium hydroxide (TMAH) and nitrogen from light-emitting diode wastewater. When the organic loading rate was maintained at 0.26-0.65 kg TMAH m(-3 )d(-1), the UASB reactor removed 70-100% of TMAH through methanogenesis. When the [Formula: see text] -N loading rate was maintained at 0.73-1.4 kg [Formula: see text]-N m(-3 )d(-1), the aerobic reactor oxidized 31-59% of [Formula: see text]-N to [Formula: see text]-N through nitritation. When the nitrogen loading rate was maintained at 0.42-0.75 kg N m(-3 )d(-1), the anoxic reactor removed 27-63% of nitrogen through anammox. The performance data of the combined reactor system agreed well with the stoichiometric relationships of methanogenesis, nitritation, and anammox. The batch studies showed that a higher initial TMAH concentration of up to 2520 mg L(-1) gave a higher methanogenic activity of up to 16 mL CH4 g(-1) VSS d(-1). An increase in the initial TMAH concentration of up to 500 mg L(-1) gradually decreased the activity of ammonia-oxidizing bacteria; whereas an increase in the initial TMAH concentration of up to 47 mg L(-1) imposed a marked inhibiting effect on the activity of anammox bacteria. PMID:26583577

  6. Growth parameters of escherichia coli O157:H7, salmonella and listeria monocytogenes and aerobic mesophilic bacteria of apple cider amended with nisin-EDTA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effect of nisin (0 or 300 IU), Ethylenediamine Tetraacetic Acid (EDTA, 20 mM) and (nisin 300 IU+ EDTA 20 mM) on growth parameters; including lag period (LP) and growth rate (GR) of Escherichia coli O157:H7, L. monocytogenes and Salmonella spp. in the presence or absence of aerobic mesophilic bac...

  7. (Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor

    PubMed Central

    Carlström, Charlotte I.; Loutey, Dana; Bauer, Stefan; Clark, Iain C.; Rohde, Robert A.; Iavarone, Anthony T.; Lucas, Lauren

    2015-01-01

    ABSTRACT The pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2−), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms. PMID:25805732

  8. Phylogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys

    PubMed Central

    Purkhold, Ulrike; Pommerening-Röser, Andreas; Juretschko, Stefan; Schmid, Markus C.; Koops, Hans-Peter; Wagner, Michael

    2000-01-01

    The current perception of evolutionary relationships and the natural diversity of ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA). However, only partial 16S rRNA sequences are available for many AOB species and most AOB have not yet been analyzed on the amoA level. In this study, the 16S rDNA sequence data of 10 Nitrosomonas species and Nitrosococcus mobilis were completed. Furthermore, previously unavailable 16S rRNA sequences were determined for three Nitrosomonas sp. isolates and for the gamma-subclass proteobacterium Nitrosococcus halophilus. These data were used to revaluate the specificities of published oligonucleotide primers and probes for AOB. In addition, partial amoA sequences of 17 AOB, including the above-mentioned 15 AOB, were obtained. Comparative phylogenetic analyses suggested similar but not identical evolutionary relationships of AOB by using 16S rRNA and AmoA as marker molecules, respectively. The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB. For 16S rRNA-independent evaluation of AOB species-level diversity in environmental samples, amoA and AmoA sequence similarity threshold values were determined which can be used to tentatively identify novel species based on cloned amoA sequences. Subsequently, 122 amoA sequences were obtained from 11 nitrifying wastewater treatment plants. Phylogenetic analyses of the molecular isolates showed that in all but two plants only nitrosomonads could be detected. Although several of the obtained amoA sequences were only relatively distantly related to known AOB, none of these sequences unequivocally suggested the existence of previously unrecognized species in the

  9. Comparative in vitro activity of ceftaroline, ceftaroline-avibactam, and other antimicrobial agents against aerobic and anaerobic bacteria cultured from infected diabetic foot wounds.

    PubMed

    Goldstein, Ellie J C; Citron, Diane M; Merriam, C Vreni; Tyrrell, Kerin L

    2013-07-01

    Foot infections are the most common infectious complication of diabetes. Moderate to severe diabetic foot infections (DFI) are typically polymicrobial with both aerobic and anaerobic organisms. The role of MRSA in these wounds has become an increasing concern. To determine if the addition of avibactam, a novel non-beta-lactam beta-lactamase inhibitor, to ceftaroline would be more active than ceftaroline alone, we tested 316 aerobic pathogens and 154 anaerobic recovered from patients with moderate to severe DFI, and compared ceftaroline with and without avibactam to other agents. Testing on aerobes was done by broth microdilution and by agar dilution for anaerobes, according to CLSI M11-A8, and M7-A8 standards. Ceftaroline-avibactam MIC90 for all Staphylococcus spp. including MRSA was 0.5 μg/mL, and for enterococci was 1 μg/mL. The MIC90s for enteric Gram-negative rods was 0.125 μg/mL. The addition of avibactam to ceftaroline reduced the ceftaroline MICs for 2 strains of resistant Enterobacter spp. and for 1 strain of Morganella. Against anaerobic Gram-positive cocci ceftaroline-avibactam had an MIC90 0.125 μg/mL and for clostridia 1 μg/mL. Avibactam improved ceftaroline's MIC90s for Bacteroides fragilis from >32 to 2 μg/mL and for Prevotella spp. from >32 to 1 μg/mL. Ceftaroline alone demonstrates excellent in vitro activity against most of the aerobes found in moderate to severe DFI. The addition of avibactam provides an increased spectrum of activity including the beta-lactamase producing Prevotella, Bacteroides fragilis and ceftaroline resistant gram-negative enteric organisms. PMID:23623385

  10. Aerobic microbial enhanced oil recovery

    SciTech Connect

    Torsvik, T.; Gilje, E.; Sunde, E.

    1995-12-31

    In aerobic MEOR, the ability of oil-degrading bacteria to mobilize oil is used to increase oil recovery. In this process, oxygen and mineral nutrients are injected into the oil reservoir in order to stimulate growth of aerobic oil-degrading bacteria in the reservoir. Experiments carried out in a model sandstone with stock tank oil and bacteria isolated from offshore wells showed that residual oil saturation was lowered from 27% to 3%. The process was time dependent, not pore volume dependent. During MEOR flooding, the relative permeability of water was lowered. Oxygen and active bacteria were needed for the process to take place. Maximum efficiency was reached at low oxygen concentrations, approximately 1 mg O{sub 2}/liter.

  11. Spatial distribution patterns of ammonia-oxidizing archaea abundance in subtropical forests at early and late successional stages

    PubMed Central

    Chen, Jie; Zhang, Hui; Liu, Wei; Lian, Juyu; Ye, Wanhui; Shen, Weijun

    2015-01-01

    Characterizing the spatial distribution patterns of soil microorganisms is helpful in understanding the biogeochemical processes they perform, but has been less studied relative to those of macroorganisms. In this study, we investigated and compared the spatially explicit distribution patterns of ammonia-oxidizing archaea (AOA) abundance and the influential factors between an early (ES) and a late successional (LS) subtropical forest stand. The average AOA abundance, vegetational attributes, and soil nutrient contents were mostly greater in the LS than the ES stand (P = 0.085 or smaller), but their spatial variations were more pronounced in the ES than the LS stand. The spatial distribution patches of AOA abundance were smaller and more irregular in the ES stand (patch size <50 m) than in the LS stand (patch size about 120 m). Edaphic and vegetational variables contributed more to the spatial variations of AOA abundance for the ES (9.3%) stand than for LS stand, whereas spatial variables (MEMs) were the main contributors (62%) for the LS stand. These results suggest that environmental filtering likely influence the spatial distribution of AOA abundance at early successional stage more than that at late successional stage, while spatial dispersal is dominant at late successional stage. PMID:26565069

  12. Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

    PubMed Central

    Santoro, Alyson E.; Dupont, Christopher L.; Richter, R. Alex; Craig, Matthew T.; Carini, Paul; McIlvin, Matthew R.; Yang, Youngik; Orsi, William D.; Moran, Dawn M.; Saito, Mak A.

    2015-01-01

    Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name “Candidatus Nitrosopelagicus brevis” str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean. PMID:25587132

  13. High abundance of ammonia-oxidizing Archaea in coastal waters, determined using a modified DNA extraction method.

    PubMed

    Urakawa, Hidetoshi; Martens-Habbena, Willm; Stahl, David A

    2010-04-01

    Molecular characterizations of environmental microbial populations based on recovery and analysis of DNA generally assume efficient or unbiased extraction of DNA from different sample matrices and microbial groups. Appropriate controls to verify this basic assumption are rarely included. Here three different DNA extractions, performed with two commercial kits (FastDNA and UltraClean) and a standard phenol-chloroform method, and two alternative filtration methods (Sterivex and 25-mm-diameter polycarbonate filters) were evaluated, using the addition of Nitrosopumilus maritimus cells to track the recovery of DNA from marine Archaea. After the comparison, a simplified phenol-chloroform extraction method was developed and shown to be significantly superior, in terms of both the recovery and the purity of DNA, to other protocols now generally applied to environmental studies. The simplified and optimized method was used to quantify ammonia-oxidizing Archaea at different depth intervals in a fjord (Hood Canal) by quantitative PCR. The numbers of Archaea increased with depth, often constituting as much as 20% of the total bacterial community. PMID:20118363

  14. Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality.

    PubMed

    Zhang, Fan; Pita, Lucía; Erwin, Patrick M; Abaid, Summara; López-Legentil, Susanna; Hill, Russell T

    2014-12-01

    Archaea associated with marine sponges are active and influence the nitrogen metabolism of sponges. However, we know little about their occurrence, specificity, and persistence. We aimed to elucidate the relative importance of host specificity and biogeographic background in shaping the symbiotic archaeal communities. We investigated these communities in sympatric sponges from the Mediterranean (Ircinia fasciculata and Ircinia oros, sampled in summer and winter) and from the Caribbean (Ircinia strobilina and Mycale laxissima). PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. We found that the communities were dominated by ammonia-oxidizing archaea closely related to Nitrosopumilus. The community in M. laxissima differed from that in Ircinia spp., including the sympatric sponge I. strobilina; yet, geographical clusters within Ircinia spp. were observed. Whereas archaeal phylotypes in Ircinia spp. were persistent and belong to 'sponge-enriched' clusters, archaea in M. laxissima were closely related with those from diverse habitats (i.e. seawater and sediments). For all four sponge species, the expression of the archaeal amoA gene was confirmed. Our results indicate that host-specific processes, such as host ecological strategy and evolutionary history, control the sponge-archaeal communities. PMID:25227989

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Spatial distribution patterns of ammonia-oxidizing archaea abundance in subtropical forests at early and late successional stages

    NASA Astrophysics Data System (ADS)

    Chen, Jie; Zhang, Hui; Liu, Wei; Lian, Juyu; Ye, Wanhui; Shen, Weijun

    2015-11-01

    Characterizing the spatial distribution patterns of soil microorganisms is helpful in understanding the biogeochemical processes they perform, but has been less studied relative to those of macroorganisms. In this study, we investigated and compared the spatially explicit distribution patterns of ammonia-oxidizing archaea (AOA) abundance and the influential factors between an early (ES) and a late successional (LS) subtropical forest stand. The average AOA abundance, vegetational attributes, and soil nutrient contents were mostly greater in the LS than the ES stand (P = 0.085 or smaller), but their spatial variations were more pronounced in the ES than the LS stand. The spatial distribution patches of AOA abundance were smaller and more irregular in the ES stand (patch size <50 m) than in the LS stand (patch size about 120 m). Edaphic and vegetational variables contributed more to the spatial variations of AOA abundance for the ES (9.3%) stand than for LS stand, whereas spatial variables (MEMs) were the main contributors (62%) for the LS stand. These results suggest that environmental filtering likely influence the spatial distribution of AOA abundance at early successional stage more than that at late successional stage, while spatial dispersal is dominant at late successional stage.

  17. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill

    PubMed Central

    Bernhard, Anne E.; Sheffer, Roberta; Giblin, Anne E.; Marton, John M.; Roberts, Brian J.

    2016-01-01

    The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain. PMID:27375576

  18. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill.

    PubMed

    Bernhard, Anne E; Sheffer, Roberta; Giblin, Anne E; Marton, John M; Roberts, Brian J

    2016-01-01

    The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain. PMID:27375576

  19. [Impact of land-use type changes on soil nitrification and ammonia-oxidizing bacterial community composition].

    PubMed

    Yang, Li-Lin; Mao, Ren-Zhao; Liu, Jun-Jie; Liu, Xiao-Jing

    2011-11-01

    A comparative study was conducted to determine nitrification potentials and ammonia-oxidizing bacterial (AOB) community composition in 0-20 cm soil depth in adjacent native forest,natural grassland, and cropland soils on the Tibetan Plateau, by incubation experiment and by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA, respectively. Cropland has the highest nitrification potential and nitrate concentration among the three land-use types (LUT), approximately 9 folds and more than 11 folds than that of the forests and grasslands, respectively. NO3(-) -N accounted for 70%-90% of inorganic N in cropland soil, while NH4(+) -N was the main form of inorganic N in forest and grassland soils. Nitrification potentials and nitrate concentrations showed no significant difference between native forest and grassland soils. The native forest showed the lowest nitrification potentials and the lowest AOB diversity and community composition among