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Sample records for mera trxa amoa

  1. Expression of merA, trxA, amoA, and hao in continuously cultured Nitrosomonas europaea cells exposed to cadmium sulfate additions.

    PubMed

    Radniecki, Tyler S; Semprini, Lewis; Dolan, Mark E

    2009-12-01

    The effects of CdSO(4) additions on the gene expressions of a mercury reductase, merA, an oxidative stress protein, trxA, the ammonia-monooxygenase enzyme (AMO), amoA, and the hydroxylamine oxidoreductase enzyme (HAO), hao, were examined in continuously cultured N. europaea cells. The reactor was fed 50 mM NH(4)+ and was operated for 78 days with a 6.9 days hydraulic retention time. Over this period, six successive batch additions of CdSO(4) were made with increasing maximum concentrations ranging from 1 to 60 microM Cd(2+). The expression of merA was highly correlated with the level of Cd(2+) within the reactor (Rs = 0.90) with significant up-regulation measured at non-inhibitory Cd(2+) concentrations. Cd(2+) appears to target AMO specifically at lower concentrations and caused oxidative stress at higher concentrations, as indicated by the SOURs (specific oxygen uptake rates) and the up-regulation of trxA. Since Cd(2+) inhibition is irreversible and amoA was up-regulated in response to Cd(2+) inhibition, it is hypothesized that de novo synthesis of the AMO enzyme occurred and was responsible for the observed recovery in activity. Continuously cultured N. europaea cells were more resistant to Cd(2+) inhibition than previously examined batch cultured cells due to the presence of Mg(2+) and Ca(2+) in the growth media, suggesting that Cd(2+) enters the cell through Mg(2+) and Ca(2+) import channels. The up-regulation of merA during exposure to non-inhibitory Cd(2+) levels indicates that merA is an excellent early warning signal for Cd(2+) inhibition.

  2. Expression of merA, amoA and hao in continuously cultured Nitrosomonas europaea cells exposed to zinc chloride additions.

    PubMed

    Radniecki, Tyler S; Semprini, Lewis; Dolan, Mark E

    2009-02-01

    The effects of ZnCl2 additions on a mercuric reductase, merA, ammonia monooxygenase, amoA, and hydroxylamine (NH2OH) oxidoreductase, hao, gene expression were examined in continuously cultured Nitrosomonas europaea cells. The reactor was operated for 85 days with a 6.9 d hydraulic retention time and with four successive additions of ZnCl2 achieving maximum concentrations from 3 to 90 microM Zn2+. Continuously cultured N. europaea cells were more resistant to Zn2+ inhibition than previously examined batch cultured cells due to the presence of Mg2+ in the growth media, suggesting that Zn2+ enters the cell through Mg2+ import channels. The maximum merA up-regulation was 45-fold and expression increased with increases in Zn2+ concentration and decreased as Zn2+ concentrations decreased. Although Zn2+ irreversibly inactivated ammonia oxidation in N. europaea, the addition of either 600 microM CuSO4 or 2250 microM MgSO4 protected N. europaea from ZnCl2 inhibition, indicating a competition between Zn2+ and Cu2+/Mg2+ for uptake and/or AMO active sites. Since ZnCl2 inhibition is irreversible and amoA was up-regulated at 30 and 90 microM additions, it is hypothesized that de novo synthesis of the AMO enzyme is needed to overcome inhibition. The up-regulation of merA during exposure to non-inhibitory Zn2+ levels indicates that merA is an excellent early warning signal for Zn2+ inhibition.

  3. Developing a Management System (AMOAS).

    ERIC Educational Resources Information Center

    Morrell, James E.; Price, Bonnie B.

    To evaluate their school management personnel, the Muhlenberg (Pennsylvania) School District adopted the Administrative Management by Objectives Appraisal System (AMOAS). Administrators are evaluated on the basis of objectives that they establish in conjunction with their immediate supervisor and on everyday job performance. Above satisfactory…

  4. Expression and purification of thioredoxin (TrxA) and thioredoxin reductase (TrxB) from Brevibacillus choshinensis.

    PubMed

    Tanaka, Ryoichi; Kosugi, Kotaro; Mizukami, Makoto; Ishibashi, Matsujiro; Tokunaga, Hiroko; Tokunaga, Masao

    2004-10-01

    Brevibacillus choshinensis (formerly Bacillus brevis) is a protein-hyperproducing bacterium and has been used for commercial protein production. Here, we cloned thioredoxin (trxA) and thioredoxin reductase (trxB) genes from B. choshinensis, and expressed the gene products in Escherichia coli with an amino-terminal hexa-His-tag for purification and characterization. His-TrxA and His-TrxB were purified to homogeneity with one-step Ni-NTA affinity column chromatography, and the two recombinant proteins showed identical specific activity with or without removal of the amino-terminal His-tag, indicating that the extrasequence containing the hexa-His-tag did not affect their enzymatic activities. The E. coli expression system used here resulted in a 40-fold increase in production of His-TrxB protein compared to the level of native TrxB produced in non-recombinant B. choshinensis cells. TrxA and TrxB proteins with carboxy-terminal His-tag (TrxA-His and TrxB-His) were successfully expressed in B. choshinensis and were purified by Ni-NTA column chromatography. Co-expression of TrxA-His with recombinant human epidermal growth factor (hEGF) in B. choshinensis promoted the extracellular production of hEGF by up to about 200%.

  5. Global occurrence of archaeal amoA genes in terrestrial hot springs.

    PubMed

    Zhang, Chuanlun L; Ye, Qi; Huang, Zhiyong; Li, Wenjun; Chen, Jinquan; Song, Zhaoqi; Zhao, Weidong; Bagwell, Christopher; Inskeep, William P; Ross, Christian; Gao, Lei; Wiegel, Juergen; Romanek, Christopher S; Shock, Everett L; Hedlund, Brian P

    2008-10-01

    Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86 degrees C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (amoA) gene and transcript sequences, representing a total of 41 amoA operational taxonomic units (OTUs) at 2% identity. The amoA gene sequences were highly diverse, yet they clustered within two major clades of archaeal amoA sequences known from water columns, sediments, and soils: clusters A and B. Eighty-four percent (711/846) of the sequences belonged to cluster A, which is typically found in water columns and sediments, whereas 16% (135/846) belonged to cluster B, which is typically found in soils and sediments. Although a few amoA OTUs were present in several geothermal regions, most were specific to a single region. In addition, cluster A amoA genes formed geographic groups, while cluster B sequences did not group geographically. With the exception of only one hot spring, principal-component analysis and UPGMA (unweighted-pair group method using average linkages) based on the UniFrac metric derived from cluster A grouped the springs by location, regardless of temperature or bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA). The amoA genes were distinct from those of low-temperature environments; in particular, pair-wise comparisons between hot spring amoA genes and those from sympatric soils showed less than 85% sequence identity, underscoring the distinctness of hot spring archaeal communities from those of the surrounding soil system. Reverse transcription-PCR showed that amoA genes were

  6. Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean

    PubMed Central

    Church, Matthew J; Wai, Brenner; Karl, David M; DeLong, Edward F

    2010-01-01

    Planktonic Crenarchaea are thought to play a key role in chemolithotrophic ammonia oxidation, a critical step of the marine nitrogen (N) cycle. In this study, we examined the spatial distributions of ammonia-oxidizing Crenarchaea across a large (∼5200 km) region of the central Pacific Ocean. Examination of crenarchaeal 16S rRNA, ammonia monooxygenase subunit A (amoA) genes, and amoA transcript abundances provided insight into their spatial distributions and activities. Crenarchaeal gene abundances increased three to four orders of magnitude with depth between the upper ocean waters and dimly lit waters of the mesopelagic zone. The resulting median value of the crenarchaeal amoA: 16S rRNA gene ratio was 1.3, suggesting the majority of Crenarchaea in the epi- and mesopelagic regions of the Pacific Ocean have the metabolic machinery for ammonia oxidation. Crenarchaeal amoA transcript abundances typically increased one to two orders of magnitude in the transitional zone separating the epipelagic waters from the mesopelagic (100–200 m), before decreasing into the interior of the mesopelagic zone. The resulting gene copy normalized transcript abundances revealed elevated amoA expression in the upper ocean waters (0–100 m) where crenarchaeal abundances were low, with transcripts decreasing into the mesopelagic zone as crenarchaeal gene abundances increased. These results suggest ammonia-oxidizing Crenarchaea are active contributors to the N cycle throughout the epi- and mesopelagic waters of the Pacific Ocean. PMID:20002133

  7. Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Pedneault, Estelle; Galand, Pierre E.; Potvin, Marianne; Tremblay, Jean-Éric; Lovejoy, Connie

    2014-04-01

    Thaumarchaeota and the gene encoding for a subunit of ammonia monooxygenase (amoA) are ubiquitous in Polar Seas, and some Thaumarchaeota also have a gene coding for ureC, diagnostic for urease. Using quantitative PCR we investigated the occurrence of genes and transcripts of ureC and amoA in Arctic samples from winter, spring and summer. AmoA genes, ureC genes and amoA transcripts were always present, but ureC transcripts were rarely detected. Over a 48 h light manipulation experiment amoA transcripts persisted under light and dark conditions, but not ureC transcripts. In addition, maxima for amoA transcript were nearer the surface compared to amoA genes. Clone libraries using DNA template recovered shallow and deep amoA clades but only the shallow clade was recovered from cDNA (from RNA). These results imply environmental control of amoA expression with direct or indirect light effects, and rare ureC expression despite its widespread occurrence in the Arctic Ocean.

  8. Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean.

    PubMed

    Pedneault, Estelle; Galand, Pierre E; Potvin, Marianne; Tremblay, Jean-Éric; Lovejoy, Connie

    2014-04-11

    Thaumarchaeota and the gene encoding for a subunit of ammonia monooxygenase (amoA) are ubiquitous in Polar Seas, and some Thaumarchaeota also have a gene coding for ureC, diagnostic for urease. Using quantitative PCR we investigated the occurrence of genes and transcripts of ureC and amoA in Arctic samples from winter, spring and summer. AmoA genes, ureC genes and amoA transcripts were always present, but ureC transcripts were rarely detected. Over a 48 h light manipulation experiment amoA transcripts persisted under light and dark conditions, but not ureC transcripts. In addition, maxima for amoA transcript were nearer the surface compared to amoA genes. Clone libraries using DNA template recovered shallow and deep amoA clades but only the shallow clade was recovered from cDNA (from RNA). These results imply environmental control of amoA expression with direct or indirect light effects, and rare ureC expression despite its widespread occurrence in the Arctic Ocean.

  9. Holographic geometry of cMERA for quantum quenches and finite temperature

    NASA Astrophysics Data System (ADS)

    Mollabashi, Ali; Naozaki, Masahiro; Ryu, Shinsei; Takayanagi, Tadashi

    2014-03-01

    We study the time evolution of cMERA (continuous MERA) under quantum quenches in free field theories. We calculate the corresponding holographic metric using the proposal in arXiv:1208.3469 and confirm that it qualitatively agrees with its gravity dual given by a half of the AdS black hole spacetime, argued by Hartman and Maldacena in arXiv:1303.1080. By doubling the cMERA for the quantum quench, we give an explicit construction of finite temperature cMERA. We also study cMERA in the presence of chemical potential and show that there is an enhancement of metric in the infrared region corresponding to the Fermi energy.

  10. Mercuric reductase genes (merA) and mercury resistance plasmids in High Arctic snow, freshwater and sea-ice brine.

    PubMed

    Møller, Annette K; Barkay, Tamar; Hansen, Martin A; Norman, Anders; Hansen, Lars H; Sørensen, Søren J; Boyd, Eric S; Kroer, Niels

    2014-01-01

    Bacterial reduction in Hg(2+) to Hg(0) , mediated by the mercuric reductase (MerA), is important in the biogeochemical cycling of Hg in temperate environments. Little is known about the occurrence and diversity of merA in the Arctic. Seven merA determinants were identified among bacterial isolates from High Arctic snow, freshwater and sea-ice brine. Three determinants in Bacteriodetes, Firmicutes and Actinobacteria showed < 92% (amino acid) sequence similarity to known merA, while one merA homologue in Alphaproteobacteria and 3 homologues from Betaproteobacteria and Gammaproteobacteria were > 99% similar to known merA's. Phylogenetic analysis showed the Bacteroidetes merA to be part of an early lineage in the mer phylogeny, whereas the Betaproteobacteria and Gammaproteobacteria merA appeared to have evolved recently. Several isolates, in which merA was not detected, were able to reduce Hg(2+) , suggesting presence of unidentified merA genes. About 25% of the isolates contained plasmids, two of which encoded mer operons. One plasmid was a broad host-range IncP-α plasmid. No known incompatibility group could be assigned to the others. The presence of conjugative plasmids, and an incongruent distribution of merA within the taxonomic groups, suggests horizontal transfer of merA as a likely mechanism for High Arctic microbial communities to adapt to changing mercury concentration.

  11. TESTING THE SPECIFICITY OF PRIMERS TO ENVIRONMENTAL AMMONIA MONOOXYGENASE (AMOA) GENES IN GROUNDWATER TREATED WITH UREA TO PROMOTE CALCITE PRECIPITATION

    SciTech Connect

    Stephanie Freeman; David Reed; Yoshiko Fujita

    2006-12-01

    The diversity of bacterial ammonia monooxygenase (amoA) genes in DNA isolated from microorganisms in groundwater was characterized by amplification of amoA DNA using polymerase chain reaction (PCR), Restriction Fragment Length Polymorphism (RFLP) analysis, and sequencing. The amoA gene is characteristic of ammonia oxidizing bacteria (AOB). The DNA extracts were acquired from an experiment where dilute molasses and urea were sequentially introduced into a well in the Eastern Snake River Plain Aquifer (ESRPA) in Idaho to examine whether such amendments could stimulate enhanced ureolytic activity. The hydrolysis of urea into ammonium and carbonate serves as the basis for a potential remediation technique for trace metals and radionuclide contaminants that co-precipitate in calcite. The ammonium ion resulting from ureolysis can promote the growth of AOB. The goal of this work was to investigate the effectiveness of primers designed for quantitative PCR of environmental amoA genes and to evaluate the effect of the molasses and urea amendments upon the population diversity of groundwater AOB. PCR primers designed to target a portion of the amoA gene were used to amplify amoA gene sequences in the groundwater DNA extracts. Following PCR, amplified gene products were cloned and the clones were characterized by RFLP, a DNA restriction technique that can distinguish different DNA sequences, to gauge the initial diversity. Clones exhibiting unique RFLP patterns were subjected to DNA sequencing. Initial sequencing results suggest that the primers were successful at specific detection of amoA sequences and the RFLP analyses indicated that the diversity of detected amoA sequences in the ESRPA decreased with the additions of molasses and urea.

  12. Geophysical Log Database for the Mississippi Embayment Regional Aquifer Study (MERAS)

    USGS Publications Warehouse

    Hart, Rheannon M.; Clark, Brian R.

    2008-01-01

    The Mississippi Embayment Regional Aquifer Study (MERAS) is an investigation of ground-water availability and sustainability within the Mississippi embayment as part of the U.S. Geological Survey Ground-Water Resources Program. The MERAS area consists of approximately 70,000 square miles and encompasses parts of eight states including Alabama, Arkansas, Illinois, Kentucky, Louisiana, Mississippi, Missouri, and Tennessee. More than 2,600 geophysical logs of test holes and wells within the MERAS area were compiled into a database and were used to develop a digital hydrogeologic framework from land surface to the top of the Midway Group of upper Paleocene age. The purpose of this report is to document, present, and summarize the geophysical log database, as well as to preserve the geophysical logs in a digital image format for online access.

  13. Pesticide Side Effects in an Agricultural Soil Ecosystem as Measured by amoA Expression Quantification and Bacterial Diversity Changes

    PubMed Central

    Feld, Louise; Hjelmsø, Mathis Hjort; Nielsen, Morten Schostag; Jacobsen, Anne Dorthe; Rønn, Regin; Ekelund, Flemming; Krogh, Paul Henning; Strobel, Bjarne Westergaard; Jacobsen, Carsten Suhr

    2015-01-01

    Background and Methods Assessing the effects of pesticide hazards on microbiological processes in the soil is currently based on analyses that provide limited insight into the ongoing processes. This study proposes a more comprehensive approach. The side effects of pesticides may appear as changes in the expression of specific microbial genes or as changes in diversity. To assess the impact of pesticides on gene expression, we focused on the amoA gene, which is involved in ammonia oxidation. We prepared soil microcosms and exposed them to dazomet, mancozeb or no pesticide. We hypothesized that the amount of amoA transcript decreases upon pesticide application, and to test this hypothesis, we used reverse-transcription qPCR. We also hypothesized that bacterial diversity is affected by pesticides. This hypothesis was investigated via 454 sequencing and diversity analysis of the 16S ribosomal RNA and RNA genes, representing the active and total soil bacterial communities, respectively. Results and Conclusion Treatment with dazomet reduced both the bacterial and archaeal amoA transcript numbers by more than two log units and produced long-term effects for more than 28 days. Mancozeb also inhibited the numbers of amoA transcripts, but only transiently. The bacterial and archaeal amoA transcripts were both sensitive bioindicators of pesticide side effects. Additionally, the numbers of bacterial amoA transcripts correlated with nitrate production in N-amended microcosms. Dazomet reduced the total bacterial numbers by one log unit, but the population size was restored after twelve days. The diversity of the active soil bacteria also seemed to be re-established after twelve days. However, the total bacterial diversity as reflected in the 16S ribosomal RNA gene sequences was largely dominated by Firmicutes and Proteobacteria at day twelve, likely reflecting a halt in the growth of early opportunists and the re-establishment of a more diverse population. We observed no

  14. Sedimentary archaeal amoA gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake, Tibetan Plateau

    NASA Astrophysics Data System (ADS)

    Yang, Jian; Jiang, Hongchen; Dong, Hailiang; Hou, Weiguo; Li, Gaoyuan; Wu, Geng

    2015-12-01

    Integration of DNA derived from ancient phototrophs with their characteristic lipid biomarkers has been successfully employed to reconstruct paleoenvironmental conditions. However, it is poorly known that whether the DNA and lipids of microbial functional aerobes (such as ammonia-oxidizing archaea: AOA) can be used for reconstructing past environmental conditions. Here we identify and quantify the AOA amoA genes (encoding the alpha subunit of ammonia monooxygenases) preserved in a 5.8-m sediment core (spanning the last 18,500 years) from Qinghai Lake. Parallel analyses revealed that low amoA gene abundance corresponded to high total organic carbon (TOC) and salinity, while high amoA gene abundance corresponded to low TOC and salinity. In the Qinghai Lake region, TOC can serve as an indicator of paleo-productivity and paleo-precipitation, which is related to historic nutrient input and salinity. So our data suggest that temporal variation of AOA amoA gene abundance preserved in Qinghai Lake sediment may reflect the variations of nutrient level and salinity throughout the late Pleistocene and Holocene in the Qinghai Lake region.

  15. Sedimentary archaeal amoA gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake, Tibetan Plateau

    PubMed Central

    Yang, Jian; Jiang, Hongchen; Dong, Hailiang; Hou, Weiguo; Li, Gaoyuan; Wu, Geng

    2015-01-01

    Integration of DNA derived from ancient phototrophs with their characteristic lipid biomarkers has been successfully employed to reconstruct paleoenvironmental conditions. However, it is poorly known that whether the DNA and lipids of microbial functional aerobes (such as ammonia-oxidizing archaea: AOA) can be used for reconstructing past environmental conditions. Here we identify and quantify the AOA amoA genes (encoding the alpha subunit of ammonia monooxygenases) preserved in a 5.8-m sediment core (spanning the last 18,500 years) from Qinghai Lake. Parallel analyses revealed that low amoA gene abundance corresponded to high total organic carbon (TOC) and salinity, while high amoA gene abundance corresponded to low TOC and salinity. In the Qinghai Lake region, TOC can serve as an indicator of paleo-productivity and paleo-precipitation, which is related to historic nutrient input and salinity. So our data suggest that temporal variation of AOA amoA gene abundance preserved in Qinghai Lake sediment may reflect the variations of nutrient level and salinity throughout the late Pleistocene and Holocene in the Qinghai Lake region. PMID:26666501

  16. Short-term effect of elevated temperature on the abundance and diversity of bacterial and archaeal amoA genes in Antarctic Soils.

    PubMed

    Han, Jiwon; Jung, Jaejoon; Park, Minsuk; Hyun, Seunghun; Park, Woojun

    2013-09-28

    Global warming will have far-reaching effects on our ecosystem. However, its effects on Antarctic soils have been poorly explored. To assess the effects of warming on microbial abundance and community composition, we sampled Antarctic soils from the King George Island in the Antarctic Peninsula and incubated these soils at elevated temperatures of 5°C and 8°C for 14 days. The reduction in total organic carbon and increase in soil respiration were attributed to the increased proliferation of Bacteria, Fungi, and Archaea. Interestingly, bacterial ammonia monooxygenase (amoA) genes were predominant over archaeal amoA, unlike in many other environments reported previously. Phylogenetic analyses of bacterial and archaeal amoA communities via clone libraries revealed that the diversity of amoA genes in Antarctic ammonia-oxidizing prokaryotic communities were temperature-insensitive. Interestingly, our data also showed that the amoA of Antarctic ammonia-oxidizing bacteria (AOB) communities differed from previously described amoA sequences of cultured isolates and clone library sequences, suggesting the presence of novel Antarctic-specific AOB communities. Denitrification-related genes were significantly reduced under warming conditions, whereas the abundance of amoA and nifH increased. Barcoded pyrosequencing of the bacterial 16S rRNA gene revealed that Proteobacteria, Acidobacteria, and Actinobacteria were the major phyla in Antarctic soils and the effect of short-term warming on the bacterial community was not apparent.

  17. A conservative region of the mercuric reductase gene (mera) as a molecular marker of bacterial mercury resistance

    PubMed Central

    Sotero-Martins, Adriana; de Jesus, Michele Silva; Lacerda, Michele; Moreira, Josino Costa; Filgueiras, Ana Luzia Lauria; Barrocas, Paulo Rubens Guimarães

    2008-01-01

    The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains. PMID:24031221

  18. Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean.

    PubMed

    Sintes, Eva; Bergauer, Kristin; De Corte, Daniele; Yokokawa, Taichi; Herndl, Gerhard J

    2013-05-01

    Mesophilic ammonia-oxidizing Archaea (AOA) are abundant in a diverse range of marine environments, including the deep ocean, as revealed by the quantification of the archaeal amoA gene encoding the alpha-subunit of the ammonia monooxygenase. Using two different amoA primer sets, two distinct ecotypes of marine Crenarchaeota Group I (MCGI) were detected in the waters of the tropical Atlantic and the coastal Arctic. The HAC-AOA ecotype (high ammonia concentration AOA) was ≈ 8000 times and 15 times more abundant in the coastal Arctic and the top 300 m layer of the open equatorial Atlantic, respectively, than the LAC-AOA (low ammonia concentration AOA) ecotype. In contrast, the LAC-AOA ecotype dominated the lower meso- and bathypelagic waters of the tropical Atlantic (≈ 50 times more abundant than the HAC-AOA) where ammonia concentrations are well below the detection limit using conventional spectrophotometric or fluorometric methods. Cluster analysis of the sequences from the clone libraries obtained by the two amoA primer sets revealed two phylogenetically distinct clusters. Taken together, our results suggest the presence of two ecotypes of archaeal ammonia oxidizers corresponding to the medium (1.24 µM on average in the coastal Arctic) and low ammonia concentration (< 0.01 µM) in the shallow and the deep waters respectively.

  19. Nanosilver inhibits nitrification and reduces ammonia-oxidising bacterial but not archaeal amoA gene abundance in estuarine sediments.

    PubMed

    Beddow, Jessica; Stolpe, Björn; Cole, Paula A; Lead, Jamie R; Sapp, Melanie; Lyons, Brett P; Colbeck, Ian; Whitby, Corinne

    2017-02-01

    Silver nanoparticles (AgNPs) enter estuaries via wastewater treatment effluents, where they can inhibit microorganisms, because of their antimicrobial properties. Ammonia-oxidising bacteria (AOB) and archaea (AOA) are involved in the first step of nitrification and are important to ecosystem function, especially where effluent discharge results in high nitrogen inputs. Here, we investigated the effect of a pulse addition of AgNPs on AOB and AOA ammonia monooxygenase (amoA) gene abundances and benthic nitrification potential rates (NPR) in low-salinity and mesohaline estuarine sediments. Whilst exposure to 0.5 mg L(-1) AgNPs had no significant effect on amoA gene abundances or NPR, 50 mg L(-1) AgNPs significantly decreased AOB amoA gene abundance (up to 76% over 14 days), and significantly decreased NPR by 20-fold in low-salinity sediments and by twofold in mesohaline sediments, after one day. AgNP behaviour differed between sites, whereby greater aggregation occurred in mesohaline waters (possibly due to higher salinity), which may have reduced toxicity. In conclusion, AgNPs have the potential to reduce ammonia oxidation in estuarine sediments, particularly where AgNPs accumulate over time and reach high concentrations. This could lead to long-term risks to nitrification, especially in polyhaline estuaries where ammonia-oxidation is largely driven by AOB.

  20. Testing the Specificity of Primers to Environmental Ammonia Monooxygenase (amoA) Genes in Groundwater Treated with Urea to Promote Calcite Precipitation

    SciTech Connect

    Freeman, S.; Reed, D.W.; Fujita, Y.

    2006-01-01

    Bacterial ammonia monooxygenase (amoA) genes in DNA isolated from microorganisms in groundwater were characterized by amplification of amoA DNA using polymerase chain reaction (PCR), Restriction Fragment Length Polymorphism (RFLP) analysis, and sequencing. The amoA gene is characteristic of ammonia oxidizing bacteria (AOB). The DNA extracts were acquired from an experiment where dilute molasses and urea were sequentially introduced into a well in the Eastern Snake River Plain Aquifer (ESRPA) in Idaho to examine whether such amendments could stimulate enhanced ureolytic activity. The hydrolysis of urea into ammonium and carbonate serves as the basis for a potential remediation technique for trace metals and radionuclide contaminants that can co-precipitate in calcite. The ammonium ion resulting from ureolysis can promote the growth of AOB. The goal of this work was to investigate the effectiveness of primers designed for quantitative PCR of environmental amoA genes and to evaluate the effect of the molasses and urea amendments upon the population diversity of groundwater AOB. PCR primers designed to target a portion of the amoA gene were used to amplify amoA gene sequences in the groundwater DNA extracts. Following PCR, amplified gene products were cloned and the clones were characterized by RFLP, a DNA restriction technique that can distinguish different DNA sequences, to gauge the initial diversity. Clones exhibiting unique RFLP patterns were subjected to DNA sequencing. Initial sequencing results suggest that the primers were successful at specific detection of amoA sequences and the RFLP analyses indicated that the diversity of detected amoA sequences in the ESRPA decreased with the additions of molasses and urea.

  1. Apis mellifera octopamine receptor 1 (AmOA1) expression in antennal lobe networks of the honey bee (Apis mellifera) and fruit fly (Drosophila melanogaster)

    PubMed Central

    Sinakevitch, Irina T.; Smith, Adrian N.; Locatelli, Fernando; Huerta, Ramon; Bazhenov, Maxim; Smith, Brian H.

    2013-01-01

    Octopamine (OA) underlies reinforcement during appetitive conditioning in the honey bee and fruit fly, acting via different subtypes of receptors. Recently, antibodies raised against a peptide sequence of one honey bee OA receptor, AmOA1, were used to study the distribution of these receptors in the honey bee brain (Sinakevitch et al., 2011). These antibodies also recognize an isoform of the AmOA1 ortholog in the fruit fly (OAMB, mushroom body OA receptor). Here we describe in detail the distribution of AmOA1 receptors in different types of neurons in the honey bee and fruit fly antennal lobes. We integrate this information into a detailed anatomical analysis of olfactory receptor neurons (ORNs), uni- and multi-glomerular projection neurons (uPNs, and mPNs) and local interneurons (LNs) in glomeruli of the antennal lobe. These neurons were revealed by dye injection into the antennal nerve, antennal lobe, medial and lateral antenno-protocerbral tracts (m-APT and l-APT), and lateral protocerebral lobe (LPL) by use of labeled cell lines in the fruit fly or by staining with anti-GABA. We found that ORN receptor terminals and uPNs largely do not show immunostaining for AmOA1. About seventeen GABAergic mPNs leave the antennal lobe through the ml-APT and branch into the LPL. Many, but not all, mPNs show staining for AmOA1. AmOA1 receptors are also in glomeruli on GABAergic processes associated with LNs. The data suggest that in both species one important action of OA in the antennal lobe involves modulation of different types of inhibitory neurons via AmOA1 receptors. We integrated this new information into a model of circuitry within glomeruli of the antennal lobes of these species. PMID:24187534

  2. Apis mellifera octopamine receptor 1 (AmOA1) expression in antennal lobe networks of the honey bee (Apis mellifera) and fruit fly (Drosophila melanogaster).

    PubMed

    Sinakevitch, Irina T; Smith, Adrian N; Locatelli, Fernando; Huerta, Ramon; Bazhenov, Maxim; Smith, Brian H

    2013-01-01

    Octopamine (OA) underlies reinforcement during appetitive conditioning in the honey bee and fruit fly, acting via different subtypes of receptors. Recently, antibodies raised against a peptide sequence of one honey bee OA receptor, AmOA1, were used to study the distribution of these receptors in the honey bee brain (Sinakevitch et al., 2011). These antibodies also recognize an isoform of the AmOA1 ortholog in the fruit fly (OAMB, mushroom body OA receptor). Here we describe in detail the distribution of AmOA1 receptors in different types of neurons in the honey bee and fruit fly antennal lobes. We integrate this information into a detailed anatomical analysis of olfactory receptor neurons (ORNs), uni- and multi-glomerular projection neurons (uPNs, and mPNs) and local interneurons (LNs) in glomeruli of the antennal lobe. These neurons were revealed by dye injection into the antennal nerve, antennal lobe, medial and lateral antenno-protocerbral tracts (m-APT and l-APT), and lateral protocerebral lobe (LPL) by use of labeled cell lines in the fruit fly or by staining with anti-GABA. We found that ORN receptor terminals and uPNs largely do not show immunostaining for AmOA1. About seventeen GABAergic mPNs leave the antennal lobe through the ml-APT and branch into the LPL. Many, but not all, mPNs show staining for AmOA1. AmOA1 receptors are also in glomeruli on GABAergic processes associated with LNs. The data suggest that in both species one important action of OA in the antennal lobe involves modulation of different types of inhibitory neurons via AmOA1 receptors. We integrated this new information into a model of circuitry within glomeruli of the antennal lobes of these species.

  3. Enhancement of hemocompatibility of the MERA monopivot centrifugal pump: toward medium-term use.

    PubMed

    Yamane, Takashi; Kosaka, Ryo; Nishida, Masahiro; Maruyama, Osamu; Yamamoto, Yoshihiro; Kuwana, Katsuyuki; Kawamura, Hiroshi; Shiraishi, Yasuyuki; Yambe, Tomoyuki; Sankai, Yoshiyuki; Tsutsui, Tatsuo

    2013-02-01

    The MERA monopivot centrifugal pump has been developed for use in open-heart surgery, circulatory support, and bridge-to-decision for up to 4 weeks. The pump has a closed-type, 50-mm diameter impeller with four straight paths. The impeller is supported by a monopivot bearing and is driven by a radial-flux magnet-coupling motor. Because flow visualization experiments have clarified sufficient pivot wash and stagnation at the sharp corner of the pivot support was suggested, sharp corners were removed in the design stage. The index of hemolysis of the pump operating at more than 200 mm Hg was found to be lower than that of a commercial pump. Four-week animal tests were then conducted two times; improvement of thrombus formation was seen in the female pivot through modification of female pivot geometry. Overall antithrombogenicity was also recorded. Finally, to assure mid-term use, an additional 4-week durability test revealed that the rate of the axial pivot wear was as small as 1.1 µm/day. The present in vitro and in vivo studies revealed that the MERA monopivot centrifugal pump has sufficient hemocompatibility and durability for up to 4 weeks.

  4. Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture.

    PubMed

    Xu, Mouzhong; Schnorr, Jon; Keibler, Brandon; Simon, Holly M

    2012-04-01

    We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.

  5. Environmental conditions constrain the distribution and diversity of archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

    PubMed

    Wang, Yanping; Boyd, Eric; Crane, Sharron; Lu-Irving, Patricia; Krabbenhoft, David; King, Susan; Dighton, John; Geesey, Gill; Barkay, Tamar

    2011-11-01

    The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient.

  6. Environmental Conditions Constrain the Distribution and Diversity of Archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

    USGS Publications Warehouse

    Wang, Y.; Boyd, E.; Crane, S.; Lu-Irving, P.; Krabbenhoft, D.; King, S.; Dighton, J.; Geesey, G.; Barkay, T.

    2011-01-01

    The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient. ?? 2011 Springer Science+Business Media, LLC.

  7. Engineering MerR for Sequestration and MerA for Reduction of Toxic Metals and Radionuclides

    SciTech Connect

    Anne O. Summers

    2008-12-15

    The objectives of this project were (1) to alter a metalloregulatory protein (MerR) so that it would bind other toxic metals or radionuclides with similar affinity so that the engineered protein itself and/or bacteria expressing it could be deployed in the environment to specifically sequester such metals and (2) to alter the mercuric reductase, MerA, to reduce radionuclides and render them less mobile. Both projects had a basic science component. In the first case, such information about MerR illuminates how proteins discriminate very similar metals/elements. In the second case, information about MerA reveals the criteria for transmission of reducing equivalents from NADPH to redox-active metals. The work involved genetic engineering of all or parts of both proteins and examination of their resultant properties both in vivo and in vitro, the latter with biochemical and biophysical tools including equilibrium and non-equilibrium dialysis, XAFS, NMR, x-ray crystallography, and titration calorimetry. We defined the basis for metal specificity in MerR, devised a bacterial strain that sequesters Hg while growing, characterized gold reduction by MerA and the role of the metallochaperone domain of MerA, and determined the 3-D structure of MerB, the organomercurial lyase.

  8. Variability in abundance of the Bacterial and Archaeal 16S rRNA and amoA genes in water columns of northern South China Sea

    NASA Astrophysics Data System (ADS)

    Liu, H.; Yang, C.; Chen, S.; Xie, W.; Wang, P.; Zhang, C. L.

    2014-12-01

    Recent advances in marine microbial ecology have shown that ammonia-oxidizing Archaea (AOA) are more abundant than ammonia-oxidizing bacteria (AOB), although total Bacteria are more abundant than total Archaea in marine environments. This study aimed to examine the spatial distribution and abundance of planktonic archaeal and bacterial 16S rRNA- and amoA genes in the northern South China Sea. Water samples were collected at different depths at six stations (maximum depth ranging from 1800 m to 3200 m)with four stations (B2, B3, B6, B7) located along a transect from the northeastern continental slope to the Bashi Strait and the other two (D3, D5) located southwest of this transect. Quantitative PCR of the 16S rRNA- and amoA genes was used to estimate the abundances of total Archaea, total Bacteria, and AOA and AOB, respectively. At the B series stations, the abundance of bacterial 16S rRNA gene was twofold to 36fold higher than that of the archaeal 16S rRNA gene while fivefold lower to sixfold higher at the two D stations, with both genes showing peak values slightly below sea surface (5-75 m depths) at all stations. The archaeal amoA gene had similar variations with the archaeal 16S rRNA gene, but was 1-4 orders of magnitude lower than the archaeal 16S rRNA gene at all stations. Bacterial amoA gene was below the detection at all stations. Our results also show the difference in depth profiles among these stations, which may be caused by the difference in water movement between these regions. The non-detection of bacterial amoA gene indicates that ammonia-oxidizing Archaea are the dominant group of microorganisms in nitrification of the South China Sea, which is consistent with observations in other oceans.

  9. Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences.

    PubMed

    Rasmussen, L D; Zawadsky, C; Binnerup, S J; Oregaard, G; Sørensen, S J; Kroer, N

    2008-06-01

    Mercury-resistant bacteria may be important players in mercury biogeochemistry. To assess the potential for mercury reduction by two subsurface microbial communities, resistant subpopulations and their merA genes were characterized by a combined molecular and cultivation-dependent approach. The cultivation method simulated natural conditions by using polycarbonate membranes as a growth support and a nonsterile soil slurry as a culture medium. Resistant bacteria were pregrown to microcolony-forming units (mCFU) before being plated on standard medium. Compared to direct plating, culturability was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25 different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of the sequences did not result in a match in the BLAST search. The results illustrate the power of integrating advanced cultivation methodology with molecular techniques for the characterization of the diversity of mercury-resistant populations and assessing the potential for mercury reduction in contaminated environments.

  10. Digital Surfaces and Thicknesses of Selected Hydrogeologic Units within the Mississippi Embayment Regional Aquifer Study (MERAS)

    USGS Publications Warehouse

    Hart, Rheannon M.; Clark, Brian R.; Bolyard, Susan E.

    2008-01-01

    Digital surfaces of selected Tertiary and younger age hydrogeologic units within the Mississippi embayment aquifer system were created using more than 2,600 geophysical logs for an area that covers approximately 70,000 square miles and encompasses parts of eight states. The digital surfaces were developed to define and display the hydrogeologic framework for the Mississippi Embayment Regional Aquifer Study (MERAS). The digital surfaces also provide a foundation of the selected hydrogeologic units for development of a steady-state and transient regional ground-water flow model of the Mississippi embayment aquifer system from the top of the Midway confining unit upwards to land surface. The ground-water flow model is under development as part of the U.S. Geological Survey Ground-Water Resources Program. Using a Geographic Information System, nine digital surfaces of the tops of selected hydrogeologic units were created using the Australian National University Digital Elevation Model method as an interpolation scheme. Thickness maps also were constructed using the Geographic Information System by calculating the difference between the altitude of the interpreted base of an overlying unit and the altitude of the interpreted top of an underlying unit. In general, the highest hydrogeologic unit altitudes are located along the eastern edge of the study area in the outcrop, and the lowest altitudes, in general, are located along the southern edge of the study area along the axis of the embayment. The Mississippi River Valley alluvial aquifer and the lower Claiborne aquifer are the thinnest aquifers of importance in the study area; the thickest aquifer of importance is the middle Claiborne aquifer.

  11. Analysis and quantification of ammonia-oxidizing bacteria community with amoA gene in sewage treatment plants.

    PubMed

    Hong, Sun Hwa; Jeong, Hyun Duck; Jung, Bongjin; Lee, Eun Young

    2012-09-01

    The analysis and quantification of ammonia-oxidizing bacteria (AOB) is crucial, as they initiate the biological removal of ammonia-nitrogen from sewage. Previous methods for analyzing the microbial community structure, which involve the plating of samples or culture media over agar plates, have been inadequate because many microorganisms found in a sewage plant are unculturable. In this study, to exclusively detect AOB, the analysis was carried out via denaturing gradient gel electrophoresis using a primer specific to the amoA gene, which is one of the functional genes known as ammonia monooxygenase. An AOB consortium (S1 sample) that could oxidize an unprecedented 100% of ammonia in 24 h was obtained from sewage sludge. In addition, real-time PCR was used to quantify the AOB. Results of the microbial community analysis in terms of carbon utilization ability of samples showed that the aeration tank water sample (S2), influent water sample (S3), and effluent water sample (S4) used all the 31 substrates considered, whereas the AOB consortium (S1) used only Tween 80, D-galacturonic acid, itaconic acid, D-malic acid, and L-serine after 192 h. The largest concentration of AOB was detected in S1 (7.6 × 10(6) copies/microliter), followed by S2 (3.2 × 10(6) copies/microliter), S4 (2.8 × 10(6) copies/microliter), and S3 (2.4 × 10(6) copies/microliter).

  12. 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 (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.

  13. Ecological Resilience and Resistance in the Hyper Diverse Forests on the Eastern Andean Flank (Mera, Ecuador)

    NASA Astrophysics Data System (ADS)

    Keen, H. F.; Gosling, W. D.; Montoya, E.; Sherlock, S.; Mothes, P. A.

    2014-12-01

    Today the Neotropics contain some of the world's most biodiverse and threatened ecosystems. Sediments obtained from two radiocarbon infinite (>48,000 years) stratigraphic sections on the eastern Andean flank, provide new insight into the relationship between biodiversity and disturbance during the Pleistocene (~200,000 years). Pollen analysis of modern and fossil material indicates that hyper diverse forest vegetation has been a feature of the Andean flank landscape for 100,000 years (pollen richness: modern = 44, fossil = 48). Correlation of past vegetation with disturbance events (volcanic and fluvial) indicates the response of hyper-diverse forest to past landscape scale change. Pollen records from near Mera (01°27 S, 78°06 W; 1117 m asl) indicate two major changes in the pollen assemblage, with forest communities dominated by: i) Hedyosmum-Alnus-Ilex, and ii) Combretaceae-Melastomataceae-Myrtaceae. These two pollen assemblages most closely resemble modern vegetation cloud forest (2500-3400m asl) and lower montane rain forest (700-2499 m asl) respectively. Sedimentary evidence suggests that at least 21 volcanic events and three changes in the local fluvial regime perturbed the regional landscape during the period of deposition. However, there is no evidence for volcanic or fluvial disturbance events causing a persistent change in vegetation community. Volcanic events (tephra deposits) are associated with increased fire (charcoal particles), and changes in vegetation (pollen grains); however, within ~50cm of sediment accumulation above each tephra, pollen assemblages revert to pre-deposition compositions. Increased fluvial influence (gravel deposits) is associated with elevated input of pollen from taxa today found at higher elevations (Podocarpus-Celtis). The input of high elevation taxa concomitant with fluvial deposits is most likely indicative of an increase in long-distance transport of pollen along water courses originating in the Andes. Our data indicate

  14. 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

  15. Effects of high organic load on amoA and nirS gene diversity of an intermittently aerated and fed membrane bioreactor treating landfill leachate.

    PubMed

    Remmas, Nikolaos; Melidis, Paraschos; Katsioupi, Efthymia; Ntougias, Spyridon

    2016-11-01

    The effects of external carbon source addition on the nitrification and denitrification process were investigated in an intermittently aerated and fed membrane bioreactor treating landfill leachate by recording system performance, and amoA and nirS diversity dynamics using pyrosequencing. By adding 950mg/L glycerol, denitrification was optimized, resulting in total nitrogen removal efficiency of 81.0±2.4%. Under these conditions, amoA diversity was dominated by genotypes related to Nitrosomonas europaea, while increase in leachate's content and in glycerol addition by 50% led to irreversible inhibition of nitrification and enhanced ammonia accumulation, causing a severe suppression of Nitrosomonas and an increase in the relative abundance of Nitrosospira. However, this increase not only affected ammonia oxidizers, but also caused a massive shift in denitrifying community structure, resulting in the suppression of Arenimonas metalli-, Candidatus Accumulibacter- and Sulfuritalea hydrogenivorans-nirS related genotypes and the predominance of nirS-associated with Acidovorax and Thaurea sp.

  16. Abundance and activity of 16S rRNA, amoA and nifH bacterial genes during assisted phytostabilization of mine tailings

    PubMed Central

    Nelson, Karis N.; Neilson, Julia W.; Root, Robert A.; Chorover, Jon; Maier, Raina M.

    2014-01-01

    Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nifH, and amoA were monitored during a nine month phytostabilization study using buffalo grass and quailbush grown in compost-amended, metalliferous tailings. The compost amendment provided a greater than 5-log increase in bacterial abundance, and survival of this compost-inoculum was more stable in planted treatments. Despite increased abundance, the activity of the introduced community was low, and significant increases were not detected until six and nine months in quailbush, and unplanted compost and buffalo grass treatments, respectively. In addition, increased abundances of nitrogen-fixation (nifH) and ammonia-oxidizing (amoA) genes were observed in rhizospheres of buffalo grass and quailbush, respectively. Thus, plant establishment facilitated the short term stabilization of introduced bacterial biomass and supported the growth of two key nitrogen-cycling populations in compost-amended tailings. PMID:25495940

  17. Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment-water interface of two lakes and the Baltic Sea.

    PubMed

    Kim, Ok-Sun; Junier, Pilar; Imhoff, Johannes F; Witzel, Karl-Paul

    2008-11-01

    The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment-water interface of the two freshwater lakes Plusssee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plusssee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plusssee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments.

  18. A stable mercury-containing complex of the organomercurial lyase MerB: catalysis, product release, and direct transfer to MerA.

    PubMed

    Benison, Gregory C; Di Lello, Paola; Shokes, Jacob E; Cosper, Nathaniel J; Scott, Robert A; Legault, Pascale; Omichinski, James G

    2004-07-06

    Bacteria isolated from organic mercury-contaminated sites have developed a system of two enzymes that allows them to efficiently convert both ionic and organic mercury compounds to the less toxic elemental mercury. Both enzymes are encoded on the mer operon and require sulfhydryl-bound substrates. The first enzyme is an organomercurial lyase (MerB), and the second enzyme is a mercuric ion reductase (MerA). MerB catalyzes the protonolysis of the carbon-mercury bond, resulting in the formation of a reduced carbon compound and inorganic ionic mercury. Of several mercury-containing MerB complexes that we attempted to prepare, the most stable was a complex consisting of the organomercurial lyase (MerB), a mercuric ion, and a molecule of the MerB inhibitor dithiothreitol (DTT). Nuclear magnetic resonance (NMR) spectroscopy and extended X-ray absorption fine structure spectroscopy of the MerB/Hg/DTT complex have shown that the ligands to the mercuric ion in the complex consist of both sulfurs from the DTT molecule and one cysteine ligand, C96, from the protein. The stability of the MerB/Hg/DTT complex, even in the presence of a large excess of competing cysteine, has been demonstrated by NMR and dialysis. We used an enzyme buffering test to determine that the MerB/Hg/DTT complex acts as a substrate for the mercuric reductase MerA. The observed MerA activity is higher than the expected activity assuming free diffusion of the mercuric ion from MerB to MerA. This suggests that the mercuric ion can be transferred between the two enzymes by a direct transfer mechanism.

  19. 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

  20. Assessing bacterial diversity in a seawater-processing wastewater treatment plant by 454-pyrosequencing of the 16S rRNA and amoA genes.

    PubMed

    Sánchez, Olga; Ferrera, Isabel; González, Jose M; Mas, Jordi

    2013-07-01

    The bacterial community composition of activated sludge from a wastewater treatment plant (Almería, Spain) with the particularity of using seawater was investigated by applying 454-pyrosequencing. The results showed that Deinococcus-Thermus, Proteobacteria, Chloroflexi and Bacteroidetes were the most abundant retrieved sequences, while other groups, such as Actinobacteria, Chlorobi, Deferribacteres, Firmicutes, Planctomycetes, Spirochaetes and Verrumicrobia were reported at lower proportions. Rarefaction analysis showed that very likely the diversity is higher than what could be described despite most of the unknown microorganisms probably correspond to rare diversity. Furthermore, the majority of taxa could not be classified at the genus level and likely represent novel members of these groups. Additionally, the nitrifiers in the sludge were characterized by pyrosequencing the amoA gene. In contrast, the nitrifying bacterial community, dominated by the genera Nitrosomonas, showed a low diversity and rarefaction curves exhibited saturation. These results suggest that only a few populations of low abundant but specialized bacteria are responsible for removal of ammonia in these saline wastewater systems.

  1. The Mississippi Embayment Regional Aquifer Study (MERAS): Documentation of a Groundwater-Flow Model Constructed to Assess Water Availability in the Mississippi Embayment

    USGS Publications Warehouse

    Clark, Brian R.; Hart, Rheannon M.

    2009-01-01

    The Mississippi Embayment Regional Aquifer Study (MERAS) was conducted with support from the Groundwater Resources Program of the U.S. Geological Survey Office of Groundwater. This report documents the construction and calibration of a finite-difference groundwater model for use as a tool to quantify groundwater availability within the Mississippi embayment. To approximate the differential equation, the MERAS model was constructed with the U.S. Geological Survey's modular three-dimensional finite-difference code, MODFLOW-2005; the preconditioned conjugate gradient solver within MODFLOW-2005 was used for the numerical solution technique. The model area boundary is approximately 78,000 square miles and includes eight States with approximately 6,900 miles of simulated streams, 70,000 well locations, and 10 primary hydrogeologic units. The finite-difference grid consists of 414 rows, 397 columns, and 13 layers. Each model cell is 1 square mile with varying thickness by cell and by layer. The simulation period extends from January 1, 1870, to April 1, 2007, for a total of 137 years and 69 stress periods. The first stress period is simulated as steady state to represent predevelopment conditions. Areal recharge is applied throughout the MERAS model area using the MODFLOW-2005 Recharge Package. Irrigation, municipal, and industrial wells are simulated using the Multi-Node Well Package. There are 43 streams simulated by the MERAS model. Each stream or river in the model area was simulated using the Streamflow-Routing Package. The perimeter of the model area and the base of the flow system are represented as no-flow boundaries. The downgradient limit of each model layer is a no-flow boundary, which approximates the extent of water with less than 10,000 milligrams per liter of dissolved solids. The MERAS model was calibrated by making manual changes to parameter values and examining residuals for hydraulic heads and streamflow. Additional calibration was achieved through

  2. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    PubMed

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further.

  3. A first insight into the occurrence and expression of functional amoA and accA genes of autotrophic and ammonia-oxidizing bathypelagic Crenarchaeota of Tyrrhenian Sea

    NASA Astrophysics Data System (ADS)

    Yakimov, Michail M.; Cono, Violetta La; Denaro, Renata

    2009-05-01

    The autotrophic and ammonia-oxidizing crenarchaeal assemblage at offshore site located in the deep Mediterranean (Tyrrhenian Sea, depth 3000 m) water was studied by PCR amplification of the key functional genes involved in energy (ammonia mono-oxygenase alpha subunit, amoA) and central metabolism (acetyl-CoA carboxylase alpha subunit, accA). Using two recently annotated genomes of marine crenarchaeons, an initial set of primers targeting archaeal accA-like genes was designed. Approximately 300 clones were analyzed, of which 100% of amoA library and almost 70% of accA library were unambiguously related to the corresponding genes from marine Crenarchaeota. Even though the acetyl-CoA carboxylase is phylogenetically not well conserved and the remaining clones were affiliated to various bacterial acetyl-CoA/propionyl-CoA carboxylase genes, the pool of archaeal sequences was applied for development of quantitative PCR analysis of accA-like distribution using TaqMan ® methodolgy. The archaeal accA gene fragments, together with alignable gene fragments from the Sargasso Sea and North Pacific Subtropical Gyre (ALOHA Station) metagenome databases, were analyzed by multiple sequence alignment. Two accA-like sequences, found in ALOHA Station at the depth of 4000 m, formed a deeply branched clade with 64% of all archaeal Tyrrhenian clones. No close relatives for residual 36% of clones, except of those recovered from Eastern Mediterranean, was found, suggesting the existence of a specific lineage of the crenarchaeal accA genes in deep Mediterranean water. Alignment of Mediterranean amoA sequences defined four cosmopolitan phylotypes of Crenarchaeota putative ammonia mono-oxygenase subunit A gene occurring in the water sample from the 3000 m depth. Without exception all phylotypes fell into Deep Marine Group I cluster that contain the vast majority of known sequences recovered from global deep-sea environment. Remarkably, three phylotypes accounted for 91% of all Mediterranean

  4. Evaluation of metabolic enzymes in response to Excel Mera 71, a glyphosate-based herbicide, and recovery pattern in freshwater teleostean fishes.

    PubMed

    Samanta, Palas; Pal, Sandipan; Mukherjee, Aloke Kumar; Ghosh, Apurba Ratan

    2014-01-01

    Metabolic enzymes such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALP) were evaluated in Indian teleostean fishes, namely, Anabas testudineus (Bloch) and Heteropneustes fossilis (Bloch), for an exposure to 30 days of Excel Mera 71 (17.2 mg/L), a glyphosate formulation, and subsequent depuration under Liv.52, a plant extract at a dose of 187.5 mg/d/250 L for the same period in the same tissues under laboratory condition. ALT activity was significantly increased (P<0.05) in all the tissues and raised up to 229.19% in liver of A. testudineus (229.19%) and 128.61% in liver of H. fossilis. AST also increased significantly (P<0.05) and was maximum in liver of H. fossilis (526.19%) and minimum in gill of A. testudineus (124.38%). ALP activity was also raised highly in intestine of H. fossilis (490.61%) but was less in kidney of H. fossilis (149.48%). The results indicated that Excel Mera 71 caused alterations in the metabolic enzymatic activities in fish tissues and AST showed the highest alteration in both the fishes, while lowest in ALP and ALT in A. testudineus and H. fossilis, respectively. During depuration under Liv.52, all the enzyme activities came down towards the control condition which indicated the compensatory response by the fish against this herbicidal stress and it was in the following order: AST>ALT>ALP, in A. testudineus, while H. fossilis showed the following trend: ALT>AST>ALP. Therefore, these parameters could be used as indicators of herbicidal pollution in aquatic organisms and were recommended for environmental monitoring for investigating the mechanism involved in the recovery pattern.

  5. Evaluation of Metabolic Enzymes in Response to Excel Mera 71, a Glyphosate-Based Herbicide, and Recovery Pattern in Freshwater Teleostean Fishes

    PubMed Central

    Samanta, Palas; Pal, Sandipan; Mukherjee, Aloke Kumar; Ghosh, Apurba Ratan

    2014-01-01

    Metabolic enzymes such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALP) were evaluated in Indian teleostean fishes, namely, Anabas testudineus (Bloch) and Heteropneustes fossilis (Bloch), for an exposure to 30 days of Excel Mera 71 (17.2 mg/L), a glyphosate formulation, and subsequent depuration under Liv.52, a plant extract at a dose of 187.5 mg/d/250 L for the same period in the same tissues under laboratory condition. ALT activity was significantly increased (P < 0.05) in all the tissues and raised up to 229.19% in liver of A. testudineus (229.19%) and 128.61% in liver of H. fossilis. AST also increased significantly (P < 0.05) and was maximum in liver of H. fossilis (526.19%) and minimum in gill of A. testudineus (124.38%). ALP activity was also raised highly in intestine of H. fossilis (490.61%) but was less in kidney of H. fossilis (149.48%). The results indicated that Excel Mera 71 caused alterations in the metabolic enzymatic activities in fish tissues and AST showed the highest alteration in both the fishes, while lowest in ALP and ALT in A. testudineus and H. fossilis, respectively. During depuration under Liv.52, all the enzyme activities came down towards the control condition which indicated the compensatory response by the fish against this herbicidal stress and it was in the following order: AST > ALT > ALP, in A. testudineus, while H. fossilis showed the following trend: ALT > AST > ALP. Therefore, these parameters could be used as indicators of herbicidal pollution in aquatic organisms and were recommended for environmental monitoring for investigating the mechanism involved in the recovery pattern. PMID:25013782

  6. Enhancements to the Mississippi Embayment Regional Aquifer Study (MERAS) groundwater-flow model and simulations of sustainable water-level scenarios

    USGS Publications Warehouse

    Clark, Brian R.; Westerman, Drew A.; Fugitt, D. Todd

    2013-01-01

    Arkansas continues to be one of the largest users of groundwater in the Nation. As such, long-term planning and management are essential to ensure continued availability of groundwater and surface water for years to come. The Mississippi Embayment Regional Aquifer Study (MERAS) model was developed previously as a tool to evaluate groundwater availability within the Mississippi embayment, which encompasses much of eastern Arkansas where the majority of groundwater is used. The Arkansas Water Plan is being updated for the first time since 1990 and serves as the State’s primary, comprehensive water-resources planning and guidance document. The MERAS model was selected as the best available tool for evaluation of specific water-use pumping scenarios that are currently being considered by the State of Arkansas. The model, developed as part of the U.S. Geological Survey Groundwater Resources Program’s assessment of the Nation’s groundwater availability, is proving to be invaluable to the State as it works toward development of a sustained yield pumping strategy. One aspect of this investigation was to evaluate multiple methods to improve the match of observed to simulated groundwater levels within the Mississippi River Valley alluvial and middle Claiborne (Sparta) aquifers in the MERAS model. Five primary methods were evaluated: (1) explicit simulation of evapotranspiration (ET), (2) upgrade of the Multi-Node Well (MNW2) Package, (3) geometry improvement within the Streamflow Routing (SFR) Package, (4) parameter estimation of select aquifer properties with pilot points, and (5) modification of water-use estimates. For the planning purposes of the Arkansas Water Plan, three scenarios were developed to evaluate potential future conditions: (1) simulation of previously optimized pumping values within the Mississippi River Valley alluvial and the middle Claiborne aquifers, (2) simulated prolonged effects of pumping at average recent (2000–5) rates, and (3) simulation

  7. Source of Nitrous Oxide Emissions during the Cow Manure Composting Process as Revealed by Isotopomer Analysis of and amoA Abundance in Betaproteobacterial Ammonia-Oxidizing Bacteria▿ †

    PubMed Central

    Maeda, Koki; Toyoda, Sakae; Shimojima, Ryosuke; Osada, Takashi; Hanajima, Dai; Morioka, Riki; Yoshida, Naohiro

    2010-01-01

    A molecular analysis of betaproteobacterial ammonia oxidizers and a N2O isotopomer analysis were conducted to study the sources of N2O emissions during the cow manure composting process. Much NO2−-N and NO3−-N and the Nitrosomonas europaea-like amoA gene were detected at the surface, especially at the top of the composting pile, suggesting that these ammonia-oxidizing bacteria (AOB) significantly contribute to the nitrification which occurs at the surface layer of compost piles. However, the 15N site preference within the asymmetric N2O molecule (SP = δ15Nα − δ15Nβ, where 15Nα and 15Nβ represent the 15N/14N ratios at the center and end sites of the nitrogen atoms, respectively) indicated that the source of N2O emissions just after the compost was turned originated mainly from the denitrification process. Based on these results, the reduction of accumulated NO2−-N or NO3−-N after turning was identified as the main source of N2O emissions. The site preference and bulk δ15N results also indicate that the rate of N2O reduction was relatively low, and an increased value for the site preference indicates that the nitrification which occurred mainly in the surface layer of the pile partially contributed to N2O emissions between the turnings. PMID:20048060

  8. Biochemical effects of glyphosate based herbicide, Excel Mera 71 on enzyme activities of acetylcholinesterase (AChE), lipid peroxidation (LPO), catalase (CAT), glutathione-S-transferase (GST) and protein content on teleostean fishes.

    PubMed

    Samanta, Palas; Pal, Sandipan; Mukherjee, Aloke Kumar; Ghosh, Apurba Ratan

    2014-09-01

    Effects of glyphosate based herbicide, Excel Mera 71 at a dose of 17.20mg/l on enzyme activities of acetylcholinesterase (AChE), lipid peroxidation (LPO), catalase (CAT), glutathione-S-transferase (GST) and protein content were measured in different tissues of two Indian air-breathing teleosts, Anabas testudineus (Bloch) and Heteropneustes fossilis (Bloch) during an exposure period of 30 days under laboratory condition. AChE activity was significantly increased in all the investigated tissues of both fish species and maximum elevation was observed in brain of H. fossilis, while spinal cord of A. testudineus showed minimum increment. Fishes showed significant increase LPO levels in all the tissues; highest was observed in gill of A. testudineus but lowest LPO level was observed in muscle of H. fossilis. CAT was also enhanced in both the fishes, while GST activity in liver diminished substantially and minimum was observed in liver of A. testudineus. Total protein content showed decreased value in all the tissues, maximum reduction was observed in liver and minimum in brain of A. testudineus and H. fossilis respectively. The results indicated that Excel Mera 71 caused serious alterations in the enzyme activities resulting into severe deterioration of fish health; so, AChE, LPO, CAT and GST can be used as suitable indicators of herbicidal toxicity.

  9. Adapting a Common Photographic Camera to Take Pictures of the Sky. (Spanish Title: Adaptando Una Camara Fotografica Comun Para Obtener Fotografias del Cielo.) Adaptando Uma Câmera Fotográfica Manual Simples Para Fotografar o Céu

    NASA Astrophysics Data System (ADS)

    Danhoni Neves, Marcos Cesar; Pereira, Ricardo Francisco

    2007-12-01

    In this paper will be introduced a method of astrophotography using a non-reflex photographic camera (a low-cost method). It will be revised some photographic processes commonly used nowadays for comparison with the aims of this paper. En este trabajo será introducido un método de astrofotografia que utiliza una cámara fotográfica non-reflex (un método de bajo costo). Serán revisados algunos procesos fotográficos comúnmente utilizados actualmente para comparación con los objetivos de este trabajo. O presente artigo procura introduzir um método de astrofotografia utilizando uma câmera fotográfica não reflex, de baixo custo. É feita uma revisão do processo fotográfico comumente empregado para fins de comparação com os objetivos pretendidos no presente trabalho.

  10. X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs

    PubMed Central

    2015-01-01

    Mercuric reductase, MerA, is a key enzyme in bacterial mercury resistance. This homodimeric enzyme captures and reduces toxic Hg2+ to Hg0, which is relatively unreactive and can exit the cell passively. Prior to reduction, the Hg2+ is transferred from a pair of cysteines (C558′ and C559′ using Tn501 numbering) at the C-terminus of one monomer to another pair of cysteines (C136 and C141) in the catalytic site of the other monomer. Here, we present the X-ray structure of the C-terminal Hg2+ complex of the C136A/C141A double mutant of the Tn501 MerA catalytic core and explore the molecular mechanism of this Hg transfer with quantum mechanical/molecular mechanical (QM/MM) calculations. The transfer is found to be nearly thermoneutral and to pass through a stable tricoordinated intermediate that is marginally less stable than the two end states. For the overall process, Hg2+ is always paired with at least two thiolates and thus is present at both the C-terminal and catalytic binding sites as a neutral complex. Prior to Hg2+ transfer, C141 is negatively charged. As Hg2+ is transferred into the catalytic site, a proton is transferred from C136 to C559′ while C558′ becomes negatively charged, resulting in the net transfer of a negative charge over a distance of ∼7.5 Å. Thus, the transport of this soft divalent cation is made energetically feasible by pairing a competition between multiple Cys thiols and/or thiolates for Hg2+ with a competition between the Hg2+ and protons for the thiolates. PMID:25343681

  11. Genome Sequence of Photobacterium halotolerans MELD1, with Mercury Reductase (merA), Isolated from Phragmites australis.

    PubMed

    Mathew, Dony Chacko; Mathew, Gincy Marina; Gicana, Ronnie Gicaraya; Huang, Chieh-Chen

    2015-06-04

    Here, we present the whole-genome sequence of Photobacterium halotolerans strain, MELD1, isolated from the roots of a terrestrial plant Phragmites australis grown in soil heavily contaminated with mercury and dioxin. The genome provides further insight into the adaptation of bacteria to the toxic environment from where it was isolated.

  12. Candidate stress genes of Nitrosomonas europaea for monitoring inhibition of nitrification by heavy metals.

    PubMed

    Park, Sunhwa; Ely, Roger L

    2008-09-01

    Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury on Nitrosomonas europaea were studied in quasi-steady-state batch reactors. When cells were exposed to 1 microM CdCl2, 6 microM HgCl2, or 8 microM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses of N. europaea to cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 microM CdCl2 for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 microM CdCl2, with merA (mercuric reductase) showing 297-fold upregulation. In N. europaea cells exposed to 6 microM HgCl2 or to 8 microM CuCl2, merA showed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes and amoA, but no such recovery was evident in Cd2+-exposed cells even though merTPCADE were highly upregulated. We suggest that the upregulation of merA in response to CdCl2 and HgCl2 exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals.

  13. Candidate Stress Genes of Nitrosomonas europaea for Monitoring Inhibition of Nitrification by Heavy Metals ▿

    PubMed Central

    Park, Sunhwa; Ely, Roger L.

    2008-01-01

    Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury on Nitrosomonas europaea were studied in quasi-steady-state batch reactors. When cells were exposed to 1 μM CdCl2, 6 μM HgCl2, or 8 μM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses of N. europaea to cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 μM CdCl2 for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 μM CdCl2, with merA (mercuric reductase) showing 297-fold upregulation. In N. europaea cells exposed to 6 μM HgCl2 or to 8 μM CuCl2, merA showed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes and amoA, but no such recovery was evident in Cd2+-exposed cells even though merTPCADE were highly upregulated. We suggest that the upregulation of merA in response to CdCl2 and HgCl2 exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals. PMID:18606795

  14. Worldwide Distribution of Nitrosococcus oceani, a Marine Ammonia-Oxidizing γ-Proteobacterium, Detected by PCR and Sequencing of 16S rRNA and amoA Genes

    PubMed Central

    Ward, Bess B.; O'Mullan, Gregory D.

    2002-01-01

    Diversity of cultured ammonia-oxidizing bacteria in the γ-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

  15. Variability in gene content and expression of the thioredoxin system in Oenococcus oeni.

    PubMed

    Margalef-Català, Mar; Stefanelli, Elena; Araque, Isabel; Wagner, Karoline; Felis, Giovanna E; Bordons, Albert; Torriani, Sandra; Reguant, Cristina

    2017-02-01

    The thioredoxin system protects against oxidative stress through the reversible oxidation of the thioredoxin active center dithiol to a disulphide. The genome of Oenococcus oeni PSU-1 contains three thioredoxin genes (trxA1, trxA2, trxA3), one thioredoxin reductase (trxB) and one ferredoxin reductase (fdr) which, until recently, was annotated as a second thioredoxin reductase. For the first time, the entire thioredoxin system in several O. oeni strains isolated from wine has been analysed. Comparisons at the DNA and protein levels have been undertaken between sequences from O. oeni and other genera and species, and the genera Leuconostoc and Lactobacillus were found to present the highest similarities. The gene most frequently absent from a collection of 34 strains and the sequences annotated in the NCBI database was trxA1. Moreover, phylogenetic analysis suggested that this gene was horizontally transferred from Lactobacillus to O. oeni. Strain-dependent expression profiles were determined in rich and in wine-like media. General over-expression was detected after inoculation into wine-like medium, with trxA3 being the most highly expressed gene. The increased transcriptional levels of the thioredoxin genes are indicative of the crucial role of this system in the O. oeni response to wine harsh conditions.

  16. Diversity and Abundance of Ammonia-Oxidizing Archaea in Hydrothermal Vent Chimneys of the Juan de Fuca Ridge▿ †

    PubMed Central

    Wang, Shufang; Xiao, Xiang; Jiang, Lijing; Peng, Xiaotong; Zhou, Huaiyang; Meng, Jun; Wang, Fengping

    2009-01-01

    The abundance and diversity of archaeal ammonia monooxygenase subunit A (amoA) genes from hydrothermal vent chimneys at the Juan de Fuca Ridge were investigated. The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments. PMID:19395559

  17. Investigation of the Solubility and Enzymatic Activity of a Thioredoxin-Gelonin Fusion Protein

    DTIC Science & Technology

    1997-05-01

    tosyl-L-lysine chloromethyl ketone TPCK N -tosyl-L-phenylalanine chloromethyl ketone Tris tris( hydroxymethyl )aminomethane trxA gene for thioredoxin UV...synthesis inhibition assay and the RIP- specific N -glycosidase assay. Thioredoxin-gelonin did not exhibit any enzymatic activity in either assay, even at...Inhibition of Purified Gelonin-XOMA ........... 61 Figure 13: UV Photograph of the Polyacrylamide Gel - N -Glycosidase Activity of Purified Gelonin-XOMA

  18. Novel molecular insights into the function and the antioxidative stress response of a Peroxiredoxin Q protein from cyanobacteria.

    PubMed

    Tailor, Vijay; Ballal, Anand

    2017-01-31

    The Peroxiredoxin Q (PrxQ) proteins are thiol-based peroxidases that are important for maintaining redox homeostasis in several organisms. Activity of PrxQs is mediated by two cysteines, peroxidatic (Cp) and resolving (Cr), in association with a reducing partner. A PrxQ, Alr3183, from the cyanobacterium, Anabaena PCC 7120, was characterized in this study. Alr3183, which required thioredoxin A (TrxA) for peroxidase activity, was an intramolecular disulfide bond-containing monomeric protein. However, Alr3183 lacking Cp (Alr3183C46S) or Cr (Alr3183C51S) formed intermolecular disulfide linkages and was dimeric. Alr3183C46S was completely inactive, while Alr3183C51S required higher concentration of TrxA for peroxidase activity. Surface plasmon resonance analysis showed that unlike Alr3183 or Alr3183C46S, Alr3183C51S bound rather poorly to TrxA. Also, compared to the oxidized protein, the DTT-treated (reduced) Alr3183 displayed decreased interaction with TrxA. In vivo, Alr3183 was found to be induced in response to γ-radiation. On exposure to H2O2, Anabaena strain over-expressing Alr3183 showed reduced formation of ROS, intact photosynthetic pigments and consequently better survival than the wild-type, whereas overproduction of Alr3183C46S did not provide any protection. Significantly, this study (1) reveals the importance of Cr for interaction with thioredoxins and (2) demonstrates that over-expression of PrxQs can protect cyanobacteria from oxidative stresses.

  19. Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal Arctic ocean in summer and winter.

    PubMed

    Christman, Glenn D; Cottrell, Matthew T; Popp, Brian N; Gier, Elizabeth; Kirchman, David L

    2011-03-01

    Ammonia oxidation, the first step in nitrification, is performed by certain Beta- and Gammaproteobacteria and Crenarchaea to generate metabolic energy. Ammonia monooxygenase (amoA) genes from both Bacteria and Crenarchaea have been found in a variety of marine ecosystems, but the relative importance of Bacteria versus Crenarchaea in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal amoA genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial amoA clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal amoA genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal amoA genes were more abundant than betaproteobacterial amoA genes in the first year, but betaproteobacterial amoA was more abundant than archaeal amoA the following year. The ratio of archaeal amoA gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in Crenarchaea at this location. Potential nitrification rates, as well as the total amoA gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing Betaproteobacteria and Crenarchaea.

  20. 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

  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. 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.

  3. 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.

  4. Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia.

    PubMed

    Caffrey, Jane M; Bano, Nasreen; Kalanetra, Karen; Hollibaugh, James T

    2007-11-01

    Nitrification, the oxidation of NH(4)(+) to NO(2)(-) and subsequently to NO(3)(-), plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. The first and rate-limiting step in nitrification is catalyzed by the enzyme ammonia monooxygenase (AmoA). We evaluate the relationships between the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance. This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history.

  5. The Synechocystis PCC6803 MerA-Like Enzyme Operates in the Reduction of Both Mercury and Uranium under the Control of the Glutaredoxin 1 Enzyme

    PubMed Central

    Marteyn, Benoit; Sakr, Samer; Farci, Sandrine; Bedhomme, Mariette; Chardonnet, Solenne; Decottignies, Paulette; Lemaire, Stéphane D.; Cassier-Chauvat, Corinne

    2013-01-01

    In a continuing effort to analyze the selectivity/redundancy of the three glutaredoxin (Grx) enzymes of the model cyanobacterium Synechocystis PCC6803, we have characterized an enzyme system that plays a crucial role in protection against two toxic metal pollutants, mercury and uranium. The present data show that Grx1 (Slr1562 in CyanoBase) selectively interacts with the presumptive mercuric reductase protein (Slr1849). This MerA enzyme plays a crucial role in cell defense against both mercuric and uranyl ions, in catalyzing their NADPH-driven reduction. Like MerA, Grx1 operates in cell protection against both mercury and uranium. The Grx1-MerA interaction requires cysteine 86 (C86) of Grx1 and C78 of MerA, which is critical for its reductase activity. MerA can be inhibited by glutathionylation and subsequently reactivated by Grx1, likely through deglutathionylation. The two Grx1 residues C31, which belongs to the redox active site (CX2C), and C86, which operates in MerA interactions, are both required for reactivation of MerA. These novel findings emphasize the role of glutaredoxins in tolerance to metal stress as well as the evolutionary conservation of the glutathionylation process, so far described mostly for eukaryotes. PMID:23852862

  6. Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat

    PubMed Central

    Fan, Haoxin; Bolhuis, Henk; Stal, Lucas J.

    2015-01-01

    The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate. The composition and abundance of amoA genes seemed to be partly driven by salinity, ammonium, temperature, and the nitrate/nitrite concentration. We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats. PMID:26648931

  7. Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat.

    PubMed

    Biller, Steven J; Mosier, Annika C; Wells, George F; Francis, Christopher A

    2012-01-01

    Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 8000 amoA sequences from the literature and public databases in an effort to understand the ecological factors influencing the distribution and diversity of ammonia-oxidizing archaea (AOA), with a particular focus on sequences from aquatic habitats. This broad survey provides strong statistical support for the hypothesis that different environments contain distinct clusters of AOA amoA sequences, as surprisingly few sequences are found in more than one habitat type. Within aquatic environments, salinity, depth in the water column, and temperature were significantly correlated with the distribution of sequence types. These findings support the existence of multiple distinct aquatic AOA populations in the environment and suggest some possible selective pressures driving the partitioning of AOA amoA diversity.

  8. Quantitative analyses of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fields with different soil types.

    PubMed

    Morimoto, Sho; Hayatsu, Masahito; Takada Hoshino, Yuko; Nagaoka, Kazunari; Yamazaki, Masatsugu; Karasawa, Toshihiko; Takenaka, Makoto; Akiyama, Hiroko

    2011-01-01

    Soil type is one of the key factors affecting soil microbial communities. With regard to ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), however, it has not been determined how soil type affects their community size and soil nitrification activity. Here we quantitatively analyzed the ammonia monooxygenase genes (amoA) of these ammonia oxidizers in fields with three different soil types (Low-humic Andosol [LHA], Gray Lowland Soil [GLS], and Yellow Soil [YS]) under common cropping conditions, and assessed the relationships between soil nitrification activity and the abundance of each amoA. Nitrification activity of LHA was highest, followed by that of GLS and YS; this order was consistent with that for the abundance of AOB amoA. Abundance of AOB amoA showed temporal variation, which was similar to that observed in nitrification activity, and a strong relationship (adjusted R(2)=0.742) was observed between the abundance of AOB amoA and nitrification activity. Abundance of AOA amoA also exhibited a significant relationship (adjusted R(2)=0.228) with nitrification activity, although this relationship was much weaker. Our results indicate that soil type affects the community size of AOA and AOB and the resulting nitrification activity, and that AOB are major contributors to nitrification in soils, while AOA are partially responsible.

  9. amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China

    PubMed Central

    Yang, Jian; Jiang, Hongchen; Dong, Hailiang; Wang, Huanye; Wu, Geng; Hou, Weiguo; Liu, Weiguo; Zhang, Chuanlun; Sun, Yongjuan; Lai, Zhongping

    2013-01-01

    All known ammonia-oxidizing archaea (AOA) belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase) and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of amoA gene-encoding archaea (AEA) in freshwater lakes have been well-studied, little is known about AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol were investigated in nine Qinghai–Tibetan lakes with a salinity range from freshwater to salt-saturation (salinity: 325 g L-1). The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L-1. The archaeal amoA gene diversity in Tibetan lakes was different from those in other lakes worldwide, suggesting Tibetan lakes (high elevation, strong ultraviolet, and dry climate) may host a unique AEA population of different evolutionary origin from those in other lakes. Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed. Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai–Tibetan hypersaline lakes. PMID:24273535

  10. Responses of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater.

    PubMed

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

    2010-04-01

    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.

  11. Geochemical Anomalies and Rock Coatings on Mars: Significance to MSR

    NASA Astrophysics Data System (ADS)

    Clark, B. C.; Gellert, R.

    2016-08-01

    Mars rover missions [Spirit (MER-A), Opportunity (MER-B), Curiosity (MSL)] have discovered unexpected geochemical extremes from aqueous alteration. Coatings and certain trace elements show large enrichment's well beyond magmatic differentiation.

  12. Tensor networks from kinematic space

    DOE PAGES

    Czech, Bartlomiej; Lamprou, Lampros; McCandlish, Samuel; ...

    2016-07-20

    We point out that the MERA network for the ground state of a 1+1-dimensional conformal field theory has the same structural features as kinematic space — the geometry of CFT intervals. In holographic theories kinematic space becomes identified with the space of bulk geodesics studied in integral geometry. We argue that in these settings MERA is best viewed as a discretization of the space of bulk geodesics rather than of the bulk geometry itself. As a test of this kinematic proposal, we compare the MERA representation of the thermofield-double state with the space of geodesics in the two-sided BTZ geometry,more » obtaining a detailed agreement which includes the entwinement sector. In conclusion, we discuss how the kinematic proposal can be extended to excited states by generalizing MERA to a broader class of compression networks.« less

  13. Tensor networks from kinematic space

    SciTech Connect

    Czech, Bartlomiej; Lamprou, Lampros; McCandlish, Samuel; Sully, James

    2016-07-20

    We point out that the MERA network for the ground state of a 1+1-dimensional conformal field theory has the same structural features as kinematic space — the geometry of CFT intervals. In holographic theories kinematic space becomes identified with the space of bulk geodesics studied in integral geometry. We argue that in these settings MERA is best viewed as a discretization of the space of bulk geodesics rather than of the bulk geometry itself. As a test of this kinematic proposal, we compare the MERA representation of the thermofield-double state with the space of geodesics in the two-sided BTZ geometry, obtaining a detailed agreement which includes the entwinement sector. In conclusion, we discuss how the kinematic proposal can be extended to excited states by generalizing MERA to a broader class of compression networks.

  14. Community analysis of a mercury hot spring supports occurrence of domain-specific forms of mercuric reductase.

    PubMed

    Simbahan, Jessica; Kurth, Elizabeth; Schelert, James; Dillman, Amanda; Moriyama, Etsuko; Jovanovich, Stevan; Blum, Paul

    2005-12-01

    Mercury is a redox-active heavy metal that reacts with active thiols and depletes cellular antioxidants. Active resistance to the mercuric ion is a widely distributed trait among bacteria and results from the action of mercuric reductase (MerA). Protein phylogenetic analysis of MerA in bacteria indicated the occurrence of a second distinctive form of MerA among the archaea, which lacked an N-terminal metal recruitment domain and a C-terminal active tyrosine. To assess the distribution of the forms of MerA in an interacting community comprising members of both prokaryotic domains, studies were conducted at a naturally occurring mercury-rich geothermal environment. Geochemical analyses of Coso Hot Springs indicated that mercury ore (cinnabar) was present at concentrations of parts per thousand. Under high-temperature and acid conditions, cinnabar may be oxidized to the toxic form Hg2+, necessitating mercury resistance in resident prokaryotes. Culture-independent analysis combined with culture-based methods indicated the presence of thermophilic crenarchaeal and gram-positive bacterial taxa. Fluorescence in situ hybridization analysis provided quantitative data for community composition. DNA sequence analysis of archaeal and bacterial merA sequences derived from cultured pool isolates and from community DNA supported the hypothesis that both forms of MerA were present. Competition experiments were performed to assess the role of archaeal merA in biological fitness. An essential role for this protein was evident during growth in a mercury-contaminated environment. Despite environmental selection for mercury resistance and the proximity of community members, MerA retains the two distinct prokaryotic forms and avoids genetic homogenization.

  15. 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

  16. Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California.

    PubMed

    Wankel, Scott D; Mosier, Annika C; Hansel, Colleen M; Paytan, Adina; Francis, Christopher A

    2011-01-01

    Ammonia oxidation-the microbial oxidation of ammonia to nitrite and the first step in nitrification-plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing betaproteobacteria (β-AOB). Sediments were examined from four sites in Elkhorn Slough, a small agriculturally impacted coastal California estuary that opens into Monterey Bay. Using an intact sediment core flowthrough incubation system, we observed significant correlations among NO(3)(-), NO(2)(-), NH(4)(+), and PO(4)(3+) fluxes, indicating a tight coupling of sediment biogeochemical processes. (15)N-based measurements of nitrification rates revealed higher rates at the less impacted, lower-nutrient sites than at the more heavily impacted, nutrient-rich sites. Quantitative PCR analyses revealed that β-AOB amoA (encoding ammonia monooxygenase subunit A) gene copies outnumbered AOA amoA gene copies by factors ranging from 2- to 236-fold across the four sites. Sites with high nitrification rates primarily contained marine/estuarine Nitrosospira-like bacterial amoA sequences and phylogenetically diverse archaeal amoA sequences. Sites with low nitrification rates were dominated by estuarine Nitrosomonas-like amoA sequences and archaeal amoA sequences similar to those previously described in soils. This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments.

  17. An in vivo pathway for disulfide bond isomerization in Escherichia coli.

    PubMed

    Rietsch, A; Belin, D; Martin, N; Beckwith, J

    1996-11-12

    Biochemical studies have shown that the periplasmic protein disulfide oxidoreductase DsbC can isomerize aberrant disulfide bonds. Here we present the first evidence for an in vivo role of DsbC in disulfide bond isomerization. Furthermore, our data suggest that the enzymes DsbA and DsbC play distinct roles in the cell in disulfide bond formation and isomerization, respectively. We have shown that mutants in dsbC display a defect in disulfide bond formation specific for proteins with multiple disulfide bonds. The defect can be complemented by the addition of reduced dithiothreitol to the medium, suggesting that absence of DsbC results in accumulation of misoxidized proteins. Mutations in the dipZ and trxA genes have similar phenotypes. We propose that DipZ, a cytoplasmic membrane protein with a thioredoxin-like domain, and thioredoxin, the product of the trxA gene, are components of a pathway for maintaining DsbC active as a protein disulfide bond isomerase.

  18. Tricksy business: transcriptome analysis reveals the involvement of thioredoxin A in redox homeostasis, oxidative stress, sulfur metabolism, and cellular differentiation in Bacillus subtilis.

    PubMed

    Smits, Wiep Klaas; Dubois, Jean-Yves F; Bron, Sierd; van Dijl, Jan Maarten; Kuipers, Oscar P

    2005-06-01

    Thioredoxins are important thiol-reactive proteins. Most knowledge about this class of proteins is derived from proteome studies, and little is known about the global transcriptional response of cells to various thioredoxin levels. In Bacillus subtilis, thioredoxin A is encoded by trxA and is essential for viability. In this study, we report the effects of minimal induction of a strain carrying an IPTG (isopropyl-beta-D-thiogalactopyranoside)-inducible trxA gene (ItrxA) on transcription levels, as determined by DNA macroarrays. The effective depletion of thioredoxin A leads to the induction of genes involved in the oxidative stress response (but not those dependent on PerR), phage-related functions, and sulfur utilization. Also, several stationary-phase processes, such as sporulation and competence, are affected. The majority of these phenotypes are rescued by a higher induction level of ItrxA, leading to an approximately wild-type level of thioredoxin A protein. A comparison with other studies shows that the effects of thioredoxin depletion are distinct from, but show some similarity to, oxidative stress and disulfide stress. Some of the transcriptional effects may be linked to thioredoxin-interacting proteins. Finally, thioredoxin-linked processes appear to be conserved between prokaryotes and eukaryotes.

  19. [Effects of continuous cropping of vegetables on ammonia oxidizers community structure].

    PubMed

    Meng, De-Long; Yang, Yang; Wu, Yan-Zheng; Wu, Min-Na; Qin, Hong-Ling; Zhu, Yi-Jun; Wei, Wen-Xue

    2012-04-01

    Investigations were conducted on the effects of intensive application of chemical fertilizers in crop production on soil nitrifier communities and the relationship between nitrifier communities and soil nitrification ability. Two series of vegetable soils were selected from Huangxing, Changsha, reflecting continuous vegetable cropping with about 20 years and new vegetable field with only about 2 years vegetable growing history. In each series five independent topsoils (0-20 cm) were sampled and each soil was a mixture of 10 cores randomly taken in the same field. Terminal restriction fragment length polymorphism (T-RFLP) and quantity PCR (Q-PCR) were used to determine the composition and abundance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities. Results indicated that long-term and continuous vegetable cropping obviously changed the compositions of both AOB and AOA amoA gene, soil pH and Olsen-P content were the dominant factors affecting the composition of AOB amoA. In the vegetable soils, although the copy number of AOA amoA gene was about 5 times higher than AOB amoA gene, no significant correlation was detected between AOA amoA gene abundance and soil nitrification rate. It was not sure whether long-term and continuous vegetable cropping could shift the abundance of AOB and AOA, but it resulted in the enrichment of some dominant AOB species and increase of soil nitrification potential (PNF).

  20. Effects of sponge bleaching on ammonia-oxidizing Archaea: distribution and relative expression of ammonia monooxygenase genes associated with the barrel sponge Xestospongia muta.

    PubMed

    López-Legentil, Susanna; Erwin, Patrick M; Pawlik, Joseph R; Song, Bongkeun

    2010-10-01

    Sponge-mediated nitrification is an important process in the nitrogen cycle, however, nothing is known about how nitrification and symbiotic Archaea may be affected by sponge disease and bleaching events. The giant barrel sponge Xestospongia muta is a prominent species on Caribbean reefs that contains cyanobacterial symbionts, the loss of which results in two types of bleaching: cyclic, a recoverable condition; and fatal, a condition associated with the disease-like sponge orange band (SOB) syndrome and sponge death. Terminal restriction fragment length polymorphism (TRFLP) analyses, clone libraries, and relative mRNA quantification of ammonia monooxygenase genes (amoA) were performed using a RNA transcript-based approach to characterize the active ammonia-oxidizing Archaea (AOA) community present in bleached, non-bleached, and SOB tissues of cyclically and fatally bleached sponges. We found that non-bleached and cyclically bleached tissues of X. muta harbored a unique Crenarchaeota community closely related to those reported for other sponges. In contrast, bleached tissue from the most degraded sponge contained a Crenarchaeota community that was more similar to those found in sediment and sand. Although there were no significant differences in amoA expression among the different tissues, amoA expression was higher in the most deteriorated tissues. Results suggest that a shift in the Crenarchaeota community precedes an increase in amoA gene expression in fatally bleached sponges, while cyclic bleaching did not alter the AOA community structure and its amoA gene expression.

  1. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools

    NASA Technical Reports Server (NTRS)

    Sakano, Y.; Kerkhof, L.; Janes, H. W. (Principal Investigator)

    1998-01-01

    Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria.

  2. High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA).

    PubMed

    Oregaard, Gunnar; Sørensen, Søren J

    2007-09-01

    DNA was extracted from different depth soils (0-5, 45-55 and 90-100 cm below surface) sampled at Lower East Fork Poplar Creek floodplain (LEFPCF), Oak Ridge (TN, USA). The presence of merA genes, encoding the mercuric reductase, the key enzyme in detoxification of mercury in bacteria, was examined by PCR targeting Actinobacteria, Firmicutes or beta/gamma-Proteobacteria. beta/gamma-Proteobacteria merA genes were successfully amplified from all soils, whereas Actinobacteria were amplified only from surface soil. merA clone libraries were constructed and sequenced. beta/gamma-Proteobacteria sequences revealed high diversity in all soils, but limited vertical similarity. Less than 20% of the operational taxonomic units (OTU) (DNA sequences > or = 95% identical) were shared between the different soils. Only one of the 62 OTU was > or = 95% identical to a GenBank sequence, highlighting that cultivated bacteria are not representative of what is found in nature. Fewer merA sequences were obtained from the Actinobacteria, but these were also diverse, and all were different from GenBank sequences. A single clone was most closely related to merA of alpha-Proteobacteria. An alignment of putative merA genes of genome sequenced mainly marine alpha-Proteobacteria was used for design of merA primers. PCR amplification of soil alpha-Proteobacteria isolates and sequencing revealed that they were very different from the genome-sequenced bacteria (only 62%-66% identical at the amino-acid level), although internally similar. In light of the high functional diversity of mercury resistance genes and the limited vertical distribution of shared OTU, we discuss the role of horizontal gene transfer as a mechanism of bacterial adaptation to mercury.

  3. Crenarchaeota and Their Role in the Nitrogen Cycle in a Subsurface Radioactive Thermal Spring in the Austrian Central Alps▿

    PubMed Central

    Weidler, Gerhard W.; Gerbl, Friedrich W.; Stan-Lotter, Helga

    2008-01-01

    Previous results from a 16S rRNA gene library analysis showed high diversity within the prokaryotic community of a subterranean radioactive thermal spring, the “Franz-Josef-Quelle” (FJQ) in Bad Gastein, Austria, as well as evidence for ammonia oxidation by crenarchaeota. This study reports further characterization of the community by denaturing gradient gel electrophoresis (DGGE) analysis, fluorescence in situ hybridization (FISH), and semiquantitative nitrification measurements. DGGE bands from three types of samples (filtered water, biofilms on glass slides, and naturally grown biofilms), including samples collected at two distinct times (January 2005 and July 2006), were analyzed. The archaeal community consisted mainly of Crenarchaeota of the soil-subsurface-freshwater group (group 1.1b) and showed a higher diversity than in the previous 16S rRNA gene library analysis, as was also found for crenarchaeal amoA genes. No bacterial amoA genes were detected. FISH analysis of biofilms indicated the presence of archaeal cells with an abundance of 5.3% (±4.5%) in the total 4′,6-diamidino-2-phenylindole (DAPI)-stained community. Microcosm experiments of several weeks in duration showed a decline of ammonium that correlated with an increase of nitrite, the presence of crenarchaeal amoA genes, and the absence of bacterial amoA genes. The data suggested that only ammonia-oxidizing archaea (AOA) perform the first step of nitrification in this 45°C environment. The crenarchaeal amoA gene sequences grouped within a novel cluster of amoA sequences from the database, originating from geothermally influenced environments, for which we propose the designation “thermal spring” cluster and which may be older than most AOA from soils on earth. PMID:18723663

  4. 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.

  5. Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils.

    PubMed

    Zhang, Li-Mei; Hu, Hang-Wei; Shen, Ju-Pei; He, Ji-Zheng

    2012-05-01

    Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.

  6. Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps.

    PubMed

    Weidler, Gerhard W; Gerbl, Friedrich W; Stan-Lotter, Helga

    2008-10-01

    Previous results from a 16S rRNA gene library analysis showed high diversity within the prokaryotic community of a subterranean radioactive thermal spring, the "Franz-Josef-Quelle" (FJQ) in Bad Gastein, Austria, as well as evidence for ammonia oxidation by crenarchaeota. This study reports further characterization of the community by denaturing gradient gel electrophoresis (DGGE) analysis, fluorescence in situ hybridization (FISH), and semiquantitative nitrification measurements. DGGE bands from three types of samples (filtered water, biofilms on glass slides, and naturally grown biofilms), including samples collected at two distinct times (January 2005 and July 2006), were analyzed. The archaeal community consisted mainly of Crenarchaeota of the soil-subsurface-freshwater group (group 1.1b) and showed a higher diversity than in the previous 16S rRNA gene library analysis, as was also found for crenarchaeal amoA genes. No bacterial amoA genes were detected. FISH analysis of biofilms indicated the presence of archaeal cells with an abundance of 5.3% (+/-4.5%) in the total 4',6-diamidino-2-phenylindole (DAPI)-stained community. Microcosm experiments of several weeks in duration showed a decline of ammonium that correlated with an increase of nitrite, the presence of crenarchaeal amoA genes, and the absence of bacterial amoA genes. The data suggested that only ammonia-oxidizing archaea (AOA) perform the first step of nitrification in this 45 degrees C environment. The crenarchaeal amoA gene sequences grouped within a novel cluster of amoA sequences from the database, originating from geothermally influenced environments, for which we propose the designation "thermal spring" cluster and which may be older than most AOA from soils on earth.

  7. Effects of chlorimuron-ethyl application with or without urea fertilization on soil ammonia-oxidizing bacteria and archaea.

    PubMed

    Tan, Huanbo; Xu, Mingkai; Li, Xinyu; Zhang, Huiwen; Zhang, Chenggang

    2013-09-15

    Chlorimuron-ethyl (CE) has been widely used in modern agriculture, but little is known regarding the influence of CE on ammonia-oxidizing bacteria (AOB) and archaea (AOA) populations in soils. In this study, microcosm incubation of aquic brown soil was conducted for 60 d. Associated changes in the population sizes of AOB and AOA in response to CE application with or without urea fertilization were examined via quantitative real-time PCR (qPCR) assays of the ammonia monooxygenase gene (amoA). The half-life of CE ranged from 11.80 d to 14.54 d in the tested soil. Compared to the untreated control, the application of CE alone had no strong effects on soil pH, and urea fertilization temporarily increased soil pH in the first 7 days. The abundance of the AOA amoA gene was greater than the abundance of the AOB amoA gene in all treatments, but both were significantly suppressed by CE application in a dose-dependent manner. Urea fertilization generally increased AOB and AOA amoA gene abundances, except that the AOA amoA gene level was slightly reduced at the early stage of the incubation period. AOB and AOA preferred different N levels for growth, with AOB only growing significantly at high NH4(+) levels and AOA growing substantially at low NH₄(+) levels. The stimulation effects of urea fertilization on AOA and AOB amoA gene abundances were strongly suppressed by the CE application. This study indicated that the CE application substantially suppressed soil nitrification via inhibiting the AOB and AOA population regardless of urea fertilization, which resulted in significant changes in the soil NH₄(+)-N and NO₃(-)-N levels. Furthermore, AOB and AOA inhabiting separate ecological niches with different NH₄(+) levels played various roles in N cycling.

  8. 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.

  9. Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean—from the Equator to the Bay of Bengal

    PubMed Central

    Wang, Jing; Kan, Jinjun; Zhang, Xiaodong; Xia, Zhiqiang; Zhang, Xuecheng; Qian, Gang; Miao, Yanyi; Leng, Xiaoyun; Sun, Jun

    2017-01-01

    Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments. PMID:28360898

  10. Mercury induced community tolerance in microbial biofilms is related to pollution gradients in a long-term polluted river.

    PubMed

    Kovac Virsek, Manca; Hubad, Barbara; Lapanje, Ales

    2013-11-15

    The net toxicity of different forms of mercury, in the long-term during their transformation processes, leads to the selection of resistant bacterial cells and this result in community tolerance which is pollution induced. Accordingly, based on profiles of a bacterial community structure, analysis of Hg resistant culturable bacteria and quantification of merA genes, we assessed development of pollution induced community tolerance in a mercury-polluted gradient in the Idrijca River. TTGE analysis did not show effects of mercury pollution to bacterial community diversity, while quantification of merA genes showed that merA genes can be correlated precisely (R(2)=0.83) with the total concentration of mercury in the biofilm microbial communities in the pollution gradient.

  11. A rapid electrochemical procedure for the detection of Hg(0) produced by mercuric-reductase: application for monitoring Hg-resistant bacteria activity.

    PubMed

    Battistel, Dario; Baldi, Franco; Marchetto, Davide; Gallo, Michele; Daniele, Salvatore

    2012-10-02

    In this work, gold microelectrodes are employed as traps for the detection of volatilized metallic mercury produced by mercuric reductase (MerA) extracted from an Hg-resistant Pseudomonas putida strain FB1. The enzymatic reduction of Hg (II) to Hg (0) was induced by NADPH cofactor added to the samples. The amount of Hg(0) accumulated on the gold microelectrode surface was determined by anodic stripping voltammetry (ASV) after transferring the gold microelectrode in an aqueous solution containing 0.1 M HNO(3) + 1 M KNO(3). Electrochemical measurements were combined with spectrofluorometric assays of NADPH consumption to derive an analytical expression for the detection of a relative MerA activity of different samples with respect to that of P. putida. The method developed here was employed for the rapid determination of MerA produced by bacteria harbored in soft tissues of clams (Ruditapes philippinarum), collected in high Hg polluted sediments of Northern Adriatic Sea in Italy.

  12. Microbial pathways for the mobilization of mercury as Hg(O) in anoxic subsurface environments

    SciTech Connect

    Barkay, Tamar

    2005-06-01

    The goal of our project which was initiated in June 2005 is focused on the presence of merA in microbial communities of anoxic environments and the effect of anaerobic respiratory pathways on MR expression and activities. The following progress has been made to date: PCR primers were designed to span the known phylogenetic range of merA genes of Gram-negative bacteria. In control experiments, these primers successfully amplified a 288 bp region at the 3? end of previously characterized merA genes from Shewanella putrefaciens pMERPH, Acidithiobacillus ferrooxidans, Pseudomonas stutzeri pPB, Tn5041, Pseudomonas sp. K-62, and Serratia marcescens pDU1358.

  13. MIMOS II on MER One Year of Mossbauer Spectroscopy on the Surface of Mars: From Jarosite at Meridiani Planum to Goethite at Gusev Crater

    NASA Technical Reports Server (NTRS)

    Klingelhoefer, G.; Rodionov, D. S.; Morris, R. V.; Schroeder, C.; deSouza, P. A.; Ming, D. W.; Yen, A. S.; Bernhardt, B.; Renz, F.; Fleischer, I.

    2005-01-01

    The miniaturized Mossbauer (MB) spectrometer MIMOS II [1] is part of the Athena payload of NASA s twin Mars Exploration Rovers "Spirit" (MER-A) and "Opportunity" (MER-B). It determines the Fe-bearing mineralogy of Martian soils and rocks at the Rovers respective landing sites, Gusev crater and Meridiani Planum. Both spectrometers performed successfully during first year of operation. Total integration time is about 49 days for MERA (79 samples) and 34 days for MER-B (85 samples). For curiosity it might be interesting to mention that the total odometry of the oscillating part of the MB drive exceeds 35 km for both rovers.

  14. Ammonia‐oxidizing Bacteria of the N itrosospira cluster 1 dominate over ammonia‐oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre

    PubMed Central

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

    2015-01-01

    Summary 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 N itrososphaera and N itrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the N itrosospira 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

  15. Long-term impacts of disturbance on nitrogen-cycling bacteria in a New England salt marsh.

    PubMed

    Bernhard, Anne E; Dwyer, Courtney; Idrizi, Adrian; Bender, Geoffrey; Zwick, Rachel

    2015-01-01

    Recent studies on the impacts of disturbance on microbial communities indicate communities show differential responses to disturbance, yet our understanding of how different microbial communities may respond to and recover from disturbance is still rudimentary. We investigated impacts of tidal restriction followed by tidal restoration on abundance and diversity of denitrifying bacteria, ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in New England salt marshes by analyzing nirS and bacterial and archaeal amoA genes, respectively. TRFLP analysis of nirS and betaproteobacterial amoA genes revealed significant differences between restored and undisturbed marshes, with the greatest differences detected in deeper sediments. Additionally, community patterns indicated a potential recovery trajectory for denitrifiers. Analysis of archaeal amoA genes, however, revealed no differences in community composition between restored and undisturbed marshes, but we detected significantly higher gene abundance in deeper sediment at restored sites. Abundances of nirS and betaproteobacterial amoA genes were also significantly greater in deeper sediments at restored sites. Porewater ammonium was significantly higher at depth in restored sediments compared to undisturbed sediments, suggesting a possible mechanism driving some of the community differences. Our results suggest that impacts of disturbance on denitrifying and ammonia-oxidizing communities remain nearly 30 years after restoration, potentially impacting nitrogen-cycling processes in the marsh. We also present data suggesting that sampling deeper in sediments may be critical for detecting disturbance effects in coastal sediments.

  16. 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.

  17. Ammonia and nitrite oxidation in the Eastern Tropical North Pacific

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. Effect of heavy metals on nitrification activity as measured by RNA- and DNA-based function-specific assays

    EPA Science Inventory

    Heavy metals can inhibit nitrification, a key process for nitrogen removal in wastewater treatment. The transcriptional responses of functional genes (amoA, hao, nirK and norB) were measured in conjunction with specific oxygen uptake rate (sOUR) for nitrifying enrichment cultures...

  19. Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea

    PubMed Central

    Horak, Rachel E A; Qin, Wei; Schauer, Andy J; Armbrust, E Virginia; Ingalls, Anitra E; Moffett, James W; Stahl, David A; Devol, Allan H

    2013-01-01

    Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis–Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l−1 was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used 15NH4+ dilution technique. PMID:23657360

  20. Emergence of Competitive Dominant Ammonia-Oxidizing Bacterial Populations in a Full-Scale Industrial Wastewater Treatment Plant

    PubMed Central

    Layton, Alice C.; Dionisi, Hebe; Kuo, H.-W.; Robinson, Kevin G.; Garrett, Victoria M.; Meyers, Arthur; Sayler, Gary S.

    2005-01-01

    Ammonia-oxidizing bacterial populations in an industrial wastewater treatment plant were investigated with amoA and 16S rRNA gene real-time PCR assays. Nitrosomonas nitrosa initially dominated, but over time RI-27-type ammonia oxidizers, also within the Nitrosomonas communis lineage, increased from below detection to codominance. This shift occurred even though nitrification remained constant. PMID:15691975

  1. Archaeal nitrification in the ocean

    PubMed Central

    Wuchter, Cornelia; Abbas, Ben; Coolen, Marco J. L.; Herfort, Lydie; van Bleijswijk, Judith; Timmers, Peer; Strous, Marc; Teira, Eva; Herndl, Gerhard J.; Middelburg, Jack J.; Schouten, Stefan; Sinninghe Damsté, Jaap S.

    2006-01-01

    Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean, but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that Crenarchaeota may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and showed that its abundance, and not that of bacteria, correlates with ammonium oxidation to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit (amoA) is correlated with a decline in ammonium concentrations and with the abundance of Crenarchaeota. Remarkably, the archaeal amoA abundance was 1–2 orders of magnitude higher than those of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also 1–3 orders of magnitude higher than those of bacterial amoA. Our data thus suggest a major role for Archaea in oceanic nitrification. PMID:16894176

  2. Impact of different bioenergy crops on N-cycling bacterial and archaeal communities in soil.

    PubMed

    Mao, Yuejian; Yannarell, Anthony C; Davis, Sarah C; Mackie, Roderick I

    2013-03-01

    Biomass production for bioenergy may change soil microbes and influence ecosystem properties. To explore the impact of different bioenergy cropping systems on soil microorganisms, the compositions and quantities of soil microbial communities (16S rRNA gene) and N-cycling functional groups (nifH, bacterial amoA, archaeal amoA and nosZ genes) were assessed under maize, switchgrass and Miscanthus x giganteus at seven sites representing a climate gradient (precipitation and temperature) in Illinois, USA. Overall, the site-to-site variation in community composition surpassed the variation due to plant type, and microbial communities under each crop did not converge on a 'typical' species assemblage. Fewer than 5% of archaeal amoA, bacterial amoA, nifH and nosZ OTUs were significantly different among these crops, but the largest differences observed at each site were found between maize and the two perennial grasses. Quantitative PCR revealed that the abundance of the nifH gene was significantly higher in the perennial grasses than in maize, and we also found significantly higher total N in the perennial grass soils than in maize. Thus, we conclude that cultivation of these perennial grasses, instead of maize, as bioenergy feedstocks can improve soil ecosystem nitrogen sustainability by increasing the population size of N-fixing bacteria.

  3. 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.

  4. Population ecology of nitrifying archaea and bacteria in the Southern California Bight.

    PubMed

    Beman, J Michael; Sachdeva, Rohan; Fuhrman, Jed A

    2010-05-01

    Marine Crenarchaeota are among the most abundant microbial groups in the ocean, and although relatively little is currently known about their biogeochemical roles in marine ecosystems, recognition that Crenarchaeota posses ammonia monooxygenase (amoA) genes and may act as ammonia-oxidizing archaea (AOA) offers another means of probing the ecology of these microorganisms. Here we use a time series approach combining quantification of archaeal and bacterial ammonia oxidizers with bacterial community fingerprints and biogeochemistry, to explore the population and community ecology of nitrification. At multiple depths (150, 500 and 890 m) in the Southern California Bight sampled monthly from 2003 to 2006, AOA were enumerated via quantitative PCR of archaeal amoA and marine group 1 Crenarchaeota 16S rRNA genes. Based on amoA genes, AOA were highly variable in time - a consistent feature of marine Crenarchaeota- however, average values were similar at different depths and ranged from 2.20 to 2.76 x 10(4) amoA copies ml(-1). Archaeal amoA genes were correlated with Crenarchaeota 16S rRNA genes (r(2) = 0.79) and the slope of this relationship was 1.02, demonstrating that the majority of marine group 1 Crenarchaeota present over the dates and depths sampled possessed amoA. Two AOA clades were specifically quantified and compared with betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) amoA genes at 150 m; these AOA groups were found to strongly co-vary in time (r(2) = 0.70, P < 0.001) whereas AOA : beta-AOB ratios ranged from 13 to 5630. Increases in the AOA : beta-AOB ratio correlated with the accumulation of nitrite (r(2) = 0.87, P < 0.001), and may be indicative of differences in substrate affinities and activities leading to periodic decoupling between ammonia and nitrite oxidation. These data capture a dynamic nitrogen cycle in which multiple microbial groups appear to be active participants.

  5. 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

  6. Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands.

    PubMed

    Sims, Atreyee; Horton, John; Gajaraj, Shashikanth; McIntosh, Steve; Miles, Randall J; Mueller, Ryan; Reed, Robert; Hu, Zhiqiang

    2012-09-01

    Ammonia-oxidizing organisms play an important role in wetland water purification and nitrogen cycling. We determined soil nitrification rates and investigated the seasonal and spatial distributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in three freshwater wetlands by using specific primers targeting the amoA genes of AOA and AOB and real-time quantitative polymerase chain reaction (qPCR). The nitrifying potentials of wetland soils ranged from 1.4 to 4.0 μg g(-1) day(-1). The specific rates of ammonia oxidation activity by AOA and AOB at the Bee Hollow wetlands were 1.9 fmol NH(3) cell(-1) day(-1) and 36.8 fmol NH(3) cell(-1) day(-1), respectively. Soil nitrification potential was positively correlated with both archaeal and bacterial amoA abundance. However, the gene copies of AOA amoA were higher than those of AOB amoA by at least an order of magnitude in wetland soils and water in both summer and winter over a three year study period. AOB were more sensitive to low temperature than AOA. The amoA gene copy ratios of AOA to AOB in top soils (0-10 cm) ranged from 19 ± 4 to 100 ± 11 among the wetland sites. In contrast, the ratio of the wetland boundary soil was 10 ± 2, which was significantly lower than that of the wetland soils (P < 0.001). The NH(4)(+)-N concentrations in wetland water were lower than 2 mg/L throughout the study. The results suggest that ammonium concentration is a major factor influencing AOA and AOB population in wetlands, although other factors such as temperature, dissolved oxygen, and soil organic matter are involved. AOA are more persistent and more abundant than AOB in the nutrient-depleted oligotrophic wetlands. Therefore, ratio of AOA amoA gene copies to AOB amoA gene copies may serve as a new biological indicator for wetland condition assessment and wetland restoration applications.

  7. Thioredoxin-thioredoxin reductase system of Streptomyces clavuligerus: sequences, expression, and organization of the genes.

    PubMed Central

    Cohen, G; Yanko, M; Mislovati, M; Argaman, A; Schreiber, R; Av-Gay, Y; Aharonowitz, Y

    1993-01-01

    The genes that encode thioredoxin and thioredoxin reductase of Streptomyces clavuligerus were cloned, and their DNA sequences were determined. Previously, we showed that S. clavuligerus possesses a disulfide reductase with broad substrate specificity that biochemically resembles the thioredoxin oxidoreductase system and may play a role in the biosynthesis of beta-lactam antibiotics. It consists consists of two components, a 70-kDa NADPH-dependent flavoprotein disulfide reductase with two identical subunits and a 12-kDa heat-stable protein general disulfide reductant. In this study, we found, by comparative analysis of their predicted amino acid sequences, that the 35-kDa protein is in fact thioredoxin reductase; it shares 48.7% amino acid sequence identity with Escherichia coli thioredoxin reductase, the 12-kDa protein is thioredoxin, and it shares 28 to 56% amino acid sequence identity with other thioredoxins. The streptomycete thioredoxin reductase has the identical cysteine redox-active region--Cys-Ala-Thr-Cys--and essentially the same flavin adenine dinucleotide- and NADPH dinucleotide-binding sites as E. coli thioredoxin reductase and is partially able to accept E. coli thioredoxin as a substrate. The streptomycete thioredoxin has the same cysteine redox-active segment--Trp-Cys-Gly-Pro-Cys--that is present in virtually all eucaryotic and procaryotic thioredoxins. However, in vivo it is unable to donate electrons to E. coli methionine sulfoxide reductase and does not serve as a substrate in vitro for E. coli thioredoxin reductase. The S. clavuligerus thioredoxin (trxA) and thioredoxin reductase (trxB) genes are organized in a cluster. They are transcribed in the same direction and separated by 33 nucleotides. In contrast, the trxA and trxB genes of E. coli, the only other organism in which both genes have been characterized, are physically widely separated. Images PMID:8349555

  8. Redox Activation of the Universally Conserved ATPase YchF by Thioredoxin 1

    PubMed Central

    Hannemann, Liya; Suppanz, Ida; Ba, Qiaorui; MacInnes, Katherine; Drepper, Friedel; Warscheid, Bettina

    2016-01-01

    Abstract Aims: YchF/Ola1 are unconventional members of the universally conserved GTPase family because they preferentially hydrolyze ATP rather than GTP. These ATPases have been associated with various cellular processes and pathologies, including DNA repair, tumorigenesis, and apoptosis. In particular, a possible role in regulating the oxidative stress response has been suggested for both bacterial and human YchF/Ola1. In this study, we analyzed how YchF responds to oxidative stress and how it potentially regulates the antioxidant response. Results: Our data identify a redox-regulated monomer–dimer equilibrium of YchF as a key event in the functional cycle of YchF. Upon oxidative stress, the oxidation of a conserved and surface-exposed cysteine residue promotes YchF dimerization, which is accompanied by inhibition of the ATPase activity. No dimers were observed in a YchF mutant lacking this cysteine. In vitro, the YchF dimer is dissociated by thioredoxin 1 (TrxA) and this stimulates the ATPase activity. The physiological significance of the YchF-thioredoxin 1 interaction was demonstrated by in vivo cross-linking, which validated this interaction in living cells. This approach also revealed that both the ATPase domain and the helical domain of YchF are in contact with TrxA. Innovation: YchF/Ola1 are the first redox-regulated members of the universally conserved GTPase family and are inactivated by oxidation of a conserved cysteine residue within the nucleotide-binding motif. Conclusion: Our data provide novel insights into the regulation of the so far ill-defined YchF/Ola1 family of proteins and stipulate their role as negative regulators of the oxidative stress response. Antioxid. Redox Signal. 24, 141–156. PMID:26160547

  9. Differential Adaptive Response and Survival of Salmonella enterica Serovar Enteritidis Planktonic and Biofilm Cells Exposed to Benzalkonium Chloride▿

    PubMed Central

    Mangalappalli-Illathu, Anil K.; Vidović, Sinisa; Korber, Darren R.

    2008-01-01

    This study examined the adaptive response and survival of planktonic and biofilm phenotypes of Salmonella enterica serovar Enteritidis adapted to benzalkonium chloride (BC). Planktonic cells and biofilms were continuously exposed to 1 μg ml−1 of BC for 144 h. The proportion of BC-adapted biofilm cells able to survive a lethal BC treatment (30 μg ml−1) was significantly higher (4.6-fold) than that of BC-adapted planktonic cells. Similarly, there were 18.3-fold more survivors among the BC-adapted biofilm cells than among their nonadapted (i.e., without prior BC exposure) cell counterparts at the lethal BC concentration, and this value was significantly higher than the value for BC-adapted planktonic cells versus nonadapted cells (3.2-fold). A significantly higher (P < 0.05) proportion of surviving cells was noticed among BC-adapted biofilm cells relative to BC-adapted planktonic cells following a 10-min heat shock at 55°C. Fatty acid composition was significantly influenced by phenotype (planktonic cells or biofilm) and BC adaptation. Cell surface roughness of biofilm cells was also significantly greater (P < 0.05) than that of planktonic cells. Key proteins upregulated in BC-adapted planktonic and biofilm cells included CspA, TrxA, Tsf, YjgF, and a probable peroxidase, STY0440. Nine and 17 unique proteins were upregulated in BC-adapted planktonic and biofilm cells, respectively. These results suggest that enhanced biofilm-specific upregulation of 17 unique proteins, along with the increased expression of CspA, TrxA, Tsf, YjgF, and a probable peroxidase, phenotype-specific alterations in cell surface roughness, and a shift in fatty acid composition conferred enhanced survival to the BC-adapted biofilm cell population relative to their BC-adapted planktonic cell counterparts. PMID:18663028

  10. Integrating top-down and bottom-up nanomanufacturing: Design of nucleation and growth processes from electrolytes

    NASA Astrophysics Data System (ADS)

    Kitayaporn, Sathana

    2011-07-01

    The integration of self-propagating material growth (bottom-up) with tool-directed patterning (top-down) has great potential for minimizing the cost and reducing the time needed for manufacturing nanoscale products. This requires new molecules, algorithms, and growth processes. We describe a process called "orchestrated structure evolution" (OSE) in which one "seeds" specific locations and allows a material to spontaneously grow from these sites into the desired final pattern. Software-reconfigurable seed patterning is ideal for manufacturing flexibility, but direct-write tools are often slow: combining them with bottom-up growth is a strategy for reducing patterning times. Seeds are any nucleation initiator (nanoelectrodes, proteins, catalyst, etc.) that can be patterned using tools such as electron-beam lithography (EBL) or dip-pen nanolithography. Here, we explore the OSE concept using nanoelectrode seeds patterned with EBL and engineered Thioredoxin A (TrxA) as protein seeds. For the case of nanoelectrode seeds, we use electrodeposition to initiate copper and nickel growth that propagates into a continuous patterned film. We evaluate the trade-off between reduced pattern time and pattern degradation, and predict seed-scale interactions governing growth rate and composition using Voronoi diagrams and modified Green's function calculations. The work combines experiments and theory for a wide range of pattern length scales, driving forces, seed densities, compositions and geometries. For the case of protein seeds, we use ZnO-binding derivatives of TrxA to understand how proteins may serve as nucleation initiators for ZnO crystal growth. Our studies include thermodynamics prediction of zinc-compatible biological buffers, adsorption isotherms, and electrodeposition of protein-modified ZnO. We show that electrolyte engineering is a critical part of the process, and that the electrolyte stability and prevalence of key species must be matched with protein stability

  11. Biofabrication of ZnS:Mn luminescent nanocrystals using histidine, hexahistidine, and His-tagged proteins: a comparison study

    PubMed Central

    Zhou, Weibin; Baneyx, François

    2013-01-01

    The ubiquitous hexahistidine purification tag has been used to conjugate proteins to the shell of CdSe:ZnS quantum dots (QDs) due to its affinity for surface-exposed Zn2+ ions but little attention has been paid to the potential of His-tagged proteins for mineralizing luminescent ZnS nanocrystals. Here, we compare the ability of free histidine, a His tag peptide, His-tagged thioredoxin (TrxA, a monomeric protein), and N- and C-terminally His-tagged versions of Hsp31 (a homodimeric protein) to support the synthesis of Mn-doped ZnS nanocrystals from aqueous precursors under mild conditions of pH (8.2) and temperature (37°C). We find that: (1) it is possible to produce poor quality QDs when histidine is used at high (8 mM) concentration; (2) an increase in local histidine concentration through repetition of the amino acid as a His tag decreases the amount of needed reagent ≈10-fold and improves optical properties; (3) fusion of the same His tag to TrxA allows for ZnS:Mn QDs mineralization at micromolar concentrations; and (4) doubling the local hexahistidine concentration by exploiting Hsp31 dimerization further improves nanocrystal luminescence with the brightest particles obtained when His tags are spatially co-localized at the Hsp31 N-termini. Although hexahistidine tracts are not as efficient as combinatorially selected ZnS binding peptides at QD synthesis, it should be possible to use the large number of available His-tagged proteins and the synthesis approach described herein to produce luminescent nanoparticles whose protein shell carries a broad range of functions. PMID:25013361

  12. Physiological state, growth mode, and oxidative stress play a role in Cd(II)-mediated inhibition of Nitrosomonas europaea 19718.

    PubMed

    Chandran, Kartik; Love, Nancy G

    2008-04-01

    The goal of this study was to determine the impact of physiological growth states (batch exponential and batch stationary growth) and growth modes (substrate-limited chemostat, substrate-sufficient exponential batch, and substrate-depleted stationary batch growth) on several measures of growth and responses to Cd(II)-mediated inhibition of Nitrosomonas europaea strain 19718. The specific oxygen uptake rate (sOUR) was the most sensitive indicator of inhibition among the different responses analyzed, including total cell abundance, membrane integrity, intracellular 16S rRNA/DNA ratio, and amoA expression. This observation remained true irrespective of the physiological state, the growth mode, or the mode of Cd(II) exposure. Based on the sOUR, a strong time-dependent exacerbation of inhibition (in terms of an inhibition coefficient [K(i)]) in exponential batch cultures was observed. Long-term inhibition levels (based on K(i) estimates) in metabolically active chemostat and exponential batch cultures were also especially severe and comparable. In contrast, the inhibition level in stationary-phase cultures was 10-fold lower and invariable with exposure time. Different strategies for surviving substrate limitation (a 10-fold increase in amoA expression) and starvation (the retention of 16S rRNA levels) in N. europaea cultures were observed. amoA expression was most negatively impacted by Cd(II) exposure in the chemostat cultures, was less impacted in exponential batch cultures, and was least impacted in stationary batch cultures. Although the amoA response was consistent with that of the sOUR, the amoA response was not as strong. The intracellular 16S rRNA/DNA ratio, as determined by fluorescence in situ hybridization, also did not uniformly correlate with the sOUR under conditions of inhibition or no inhibition. Finally, Cd(II)-mediated inhibition of N. europaea was attributed partially to oxidative stress.

  13. Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment.

    PubMed

    Stopnisek, Nejc; Gubry-Rangin, Cécile; Höfferle, Spela; Nicol, Graeme W; Mandic-Mulec, Ines; Prosser, James I

    2010-11-01

    Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and "deep peat" lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

  14. 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

  15. Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea.

    PubMed

    Hu, Anyi; Jiao, Nianzhi; Zhang, Chuanlun L

    2011-10-01

    Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO(2) fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the "shallow" cluster was exclusively derived from epipelagic water and the "deep" cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.

  16. 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.

  17. Energy Drinks and Food Bars: Power or Hype?

    MedlinePlus

    ... Loss Surgery? A Week of Healthy Breakfasts Shyness Energy Drinks and Food Bars: Power or Hype? KidsHealth > ... nutritivas: ¿Energía o mera exageración? The Buzz on Energy Foods Energy drinks and nutrition bars often make ...

  18. Final Report - Molecular Mechanisms of Bacterial Mercury Transformation - UCSF

    SciTech Connect

    Miller, Susan M.

    2014-04-24

    The bacterial mercury resistance (mer) operon functions in Hg biogeochemistry and bioremediation by converting reactive inorganic Hg(II) and organic [RHg(II)]1+ mercurials to relatively inert monoatomic mercury vapor, Hg(0). Its genes regulate operon expression (MerR, MerD, MerOP), import Hg(II) (MerT, MerP, and MerC), and demethylate (MerB) and reduce (MerA) mercurials. We focus on how these components interact with each other and with the host cell to allow cells to survive and detoxify Hg compounds. Understanding how this ubiquitous detoxification system fits into the biology and ecology of its bacterial host is essential to guide interventions that support and enhance Hg remediation. In the current overall project we focused on two aspects of this system: (1) investigations of the energetics of Hg(II)-ligand binding interactions, and (2) both experimental and computational approaches to investigating the molecular mechanisms of Hg(II) acquisition by MerA and intramolecular transfer of Hg(II) prior to reduction within the MerA enzyme active site. Computational work was led by Prof. Jeremy Smith and took place at the University of Tennessee, while experimental work on MerA was led by Prof. Susan Miller and took place at the University of California San Francisco.

  19. Designing Systems for Many Possible Futures. An RSC-based Method for Affordable Concept Selection (RMACS) with Multi-Era Analysis

    SciTech Connect

    Schaffner, Michael

    2014-06-01

    The current downward trend in funding for U.S. defense systems seems to be on a collision course with the state of the practice in systems engineering, which typically results in the increased pace and scale of capabilities and resultantly increased cost of complex national defense systems. Recent advances in the state of the art in systems engineering methodology can be leveraged to address this growing challenge. The present work leverages advanced constructs and methods for early-phase conceptual design of complex systems, when committed costs are still low and management influence is still high. First, a literature review is presented of the topics relevant to this work, including approaches to the design of affordable systems, assumptions and methods of exploratory modeling, and enabling techniques to help mitigate the computational challenges involved. The types, purposes, and limits of early-phase, exploratory models are then elucidated. The RSC-based Method for Affordable Concept Selection (RMACS) is described, which comprises nine processes in the three main thrusts of information gathering, evaluation, and analysis. The method is then applied to a naval ship case example, described as the Next-Generation Combat Ship, with representational information outputs and discussions of affordability with respect to each process. The ninth process, Multi-Era Analysis (MERA), is introduced and explicated, including required and optional informational components, temporal and change-related considerations, required and optional activities involved, and the potential types of outputs from the process. The MERA process is then applied to a naval ship case example similar to that of the RMACS application, but with discrete change options added to enable a tradespace network. The seven activities of the MERA process are demonstrated, with the salient outputs of each given and discussed. Additional thoughts are presented on MERA and RMACS, and 8 distinct areas are

  20. Microbes in mercury-enriched geothermal springs in western North America.

    PubMed

    Geesey, Gill G; Barkay, Tamar; King, Sue

    2016-11-01

    Because geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction

  1. Engineering a root-specific, repressor-operator gene complex.

    PubMed

    Kim, Tehryung; Balish, Rebecca S; Heaton, Andrew C P; McKinney, Elizabeth C; Dhankher, Om Parkash; Meagher, Richard B

    2005-11-01

    Strong, tissue-specific and genetically regulated expression systems are essential tools in plant biotechnology. An expression system tool called a 'repressor-operator gene complex' (ROC) has diverse applications in plant biotechnology fields including phytoremediation, disease resistance, plant nutrition, food safety, and hybrid seed production. To test this concept, we assembled a root-specific ROC using a strategy that could be used to construct almost any gene expression pattern. When a modified E. coli lac repressor with a nuclear localization signal was expressed from a rubisco small subunit expression vector, S1pt::lacIn, LacIn protein was localized to the nuclei of leaf and stem cells, but not to root cells. A LacIn repressible Arabidopsis actin expression vector A2pot was assembled containing upstream bacterial lacO operator sequences, and it was tested for organ and tissue specificity using beta-glucuronidase (GUS) and mercuric ion reductase (merA) gene reporters. Strong GUS enzyme expression was restricted to root tissues of A2pot::GUS/S1pt::lacIn ROC plants, while GUS activity was high in all vegetative tissues of plants lacking the repressor. Repression of shoot GUS expression exceeded 99.9% with no evidence of root repression, among a large percentage of doubly transformed plants. Similarly, MerA was strongly expressed in the roots, but not the shoots of A2pot::merA/S1pt::lacIn plants, while MerA levels remained high in both shoots and roots of plants lacking repressor. Plants with MerA expression restricted to roots were approximately as tolerant to ionic mercury as plants constitutively expressing MerA in roots and shoots. The superiority of this ROC over the previously described root-specific tobacco RB7 promoter is demonstrated.

  2. Seasonal dynamics of ammonia/ammonium-oxidizing prokaryotes in oxic and anoxic wetland sediments of subtropical coastal mangrove.

    PubMed

    Wang, Yong-Feng; Feng, Yao-Yu; Ma, Xiaojun; Gu, Ji-Dong

    2013-09-01

    Mangrove wetlands are an important ecosystem in tropical and subtropical regions, and the sediments may contain both oxic and anoxic zones. In this study, ammonia/ammonium-oxidizing prokaryotes (AOPs) in yellow and black sediments with vegetation and non-vegetated sediments in a mangrove wetland of subtropical Hong Kong were investigated in winter and summer. The phylogenetic diversity of anammox bacterial 16S rRNA genes and archaeal and bacterial amoA genes (encoding ammonia monooxygenase alpha-subunit) were analyzed using PCR amplification and denaturing gradient gel electrophoresis to reveal their community structures. Quantitative PCR was also used to detect their gene abundances. The results showed that seasonality had little effect, but sediment type had a noticeable influence on the community structures and abundances of anammox bacteria. For ammonia-oxidizing archaea (AOA), seasonality had a small effect on their community structures, but a significant effect on their abundances: AOA amoA genes were significantly higher in winter than in summer. In winter, the vegetated yellow sediments had lower AOA amoA genes than the other types of sediments, but in summer, the vegetated yellow sediments had higher AOA amoA genes than the other types of sediments. Sediment type had no apparent effect on AOA community structures in winter. In summer, however, the vegetated yellow sediments showed obviously different AOA community structures from the other types of sediments. For ammonia-oxidizing bacteria (AOB), seasonality had a significant effect on their community structures and abundances: AOB amoA genes in winter were apparently higher than in summer, and AOB community structures were different between winter and summer. Sediment type had little effect on AOB community structures, but had a noticeable effect on the abundances: AOB amoA genes of the vegetated yellow sediments were obviously lower than the black ones in both seasons. This study has demonstrated that

  3. Imbalance between vertical nitrate flux and nitrate assimilation on a continental shelf: Implications of nitrification

    NASA Astrophysics Data System (ADS)

    Shiozaki, Takuhei; Furuya, Ken; Kurotori, Hiroyuki; Kodama, Taketoshi; Takeda, Shigenobu; Endoh, Takahiro; Yoshikawa, Yutaka; Ishizaka, Joji; Matsuno, Takeshi

    2011-10-01

    The nitrate assimilation rate and diapycnal nitrate flux were simultaneously determined on the continental shelf of the East China Sea (ECS). Further, the archaeal amoA gene was quantified to examine the potential distribution of nitrification activity. Nitrate assimilation rates and distribution of the archaeal amoA gene were also investigated in the Philippine Sea and in the Kuroshio Current. At all the stations, while the surface nitrate was depleted (<0.1 μM), active nitrate assimilation was observed with mean rates of 1400, 270, and 96 μmolN m-2 d-1 in the ECS, the Philippine Sea, and the Kuroshio Current, respectively. Archaeal amoA was observed at shallower light depths, namely at or above 10% light depth, in the ECS than in other regions, suggesting that nitrification occurred within the euphotic zone in the ECS, especially on the shelf. Moreover, a station on the continental shelf of the ECS exhibited a considerable discrepancy between the nitrate assimilation rate (1500 μmolN m-2 d-1) and vertical nitrate flux (98 μmolN m-2 d-1). Here, 6.7 ± 3.1 × 103 and 2.5 ± 0.7 × 105 copies mL-1 of archaeal amoA were detected at 10% and 1% light depths relative to the surface, respectively. Thus nitrification within the euphotic zone would be attributed at least in part to the observed discrepancy between nitrate assimilation and vertical flux. These observations imply that the assumption of a direct relationship between new production, export production, and measured nitrate assimilation is misplaced, particularly regarding the continental shelf of the ECS.

  4. Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire.

    PubMed

    Yeager, Chris M; Northup, Diana E; Grow, Christy C; Barns, Susan M; Kuske, Cheryl R

    2005-05-01

    This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH(3)-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.

  5. 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

  6. 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

  7. 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

  8. Niche specialization of terrestrial archaeal ammonia oxidizers.

    PubMed

    Gubry-Rangin, Cécile; Hai, Brigitte; Quince, Christopher; Engel, Marion; Thomson, Bruce C; James, Phillip; Schloter, Michael; Griffiths, Robert I; Prosser, James I; Nicol, Graeme W

    2011-12-27

    Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5 ≤ pH <7), or alkalinophilic (pH ≥ 7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.

  9. Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters

    PubMed Central

    Tolar, Bradley B; Ross, Meredith J; Wallsgrove, Natalie J; Liu, Qian; Aluwihare, Lihini I; Popp, Brian N; Hollibaugh, James T

    2016-01-01

    There are few measurements of nitrification in polar regions, yet geochemical evidence suggests that it is significant, and chemoautotrophy supported by nitrification has been suggested as an important contribution to prokaryotic production during the polar winter. This study reports seasonal ammonia oxidation (AO) rates, gene and transcript abundance in continental shelf waters west of the Antarctic Peninsula, where Thaumarchaeota strongly dominate populations of ammonia-oxidizing organisms. Higher AO rates were observed in the late winter surface mixed layer compared with the same water mass sampled during summer (mean±s.e.: 62±16 versus 13±2.8 nm per day, t-test P<0.0005). AO rates in the circumpolar deep water did not differ between seasons (21±5.7 versus 24±6.6 nm per day; P=0.83), despite 5- to 20-fold greater Thaumarchaeota abundance during summer. AO rates correlated with concentrations of Archaea ammonia monooxygenase (amoA) genes during summer, but not with concentrations of Archaea amoA transcripts, or with ratios of Archaea amoA transcripts per gene, or with concentrations of Betaproteobacterial amoA genes or transcripts. The AO rates we report (<0.1–220 nm per day) are ~10-fold greater than reported previously for Antarctic waters and suggest that inclusion of Antarctic coastal waters in global estimates of oceanic nitrification could increase global rate estimates by ~9%. Chemoautotrophic carbon fixation supported by AO was 3–6% of annualized phytoplankton primary production and production of Thaumarchaeota biomass supported by AO could account for ~9% of the bacterioplankton production measured in winter. Growth rates of thaumarchaeote populations inferred from AO rates averaged 0.3 per day and ranged from 0.01 to 2.1 per day. PMID:27187795

  10. An Analysis of Contractor Logistical Support For Nondevelopmental Items

    DTIC Science & Technology

    1993-03-01

    prgecn no. ISMo . work Uft A~&moa 11. TITLE (kxlude Security Cimuahotion) An Analysis of Contractor Logmucal Support for Nu•developmental talme. 12...for Nondevelopmental Items (NDI). NDI acquisition capitalizes on the use of comnmer•il ostaof-the- art * technologies while providing DOD with effective...for Nondevelopmental Items (NDI). NDI acquisition capitalizes on the use of commercial "state-of-the- art " technologies while providing DOD with

  11. Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on ammonia oxidizers and N2O emissions in a grazed pasture soil.

    PubMed

    Dai, Yu; Di, Hong J; Cameron, Keith C; He, Ji-Zheng

    2013-11-01

    Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) are important drivers of a key step of the nitrogen cycle - nitrification, which affects the production of the potent greenhouse gas, nitrous oxide (N2O). A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of AOB and AOA and on N2O emissions in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100 kg N ha(-1) and animal urine at 300 and 600 kg N ha(-1). DCD was applied to some of the N treatments at 10 kg ha(-1). The results showed that the AOB amoA gene copy numbers were greater than those of AOA. The highest ratio of the AOB to AOA amoA gene copy numbers was 106.6 which occurred in the urine-N 600 treatment. The AOB amoA gene copy numbers increased with increasing nitrogen application rates. DCD had a significant impact in reducing the AOB amoA gene copy numbers especially in the high nitrogen application rates. N2O emissions increased with the N application rates. DCD had the most significant effect in reducing the daily and total N2O emissions in the highest nitrogen application rate. The greatest reduction of total N2O emissions by DCD was 69% in the urine-N 600 treatment. The reduction in the N2O emission factor by DCD ranged from 58% to 83%. The N2O flux and NO3(-)-N concentrations were significantly correlated to the growth of AOB, rather than AOA. This study confirms the importance of AOB in nitrification and the effect of DCD in inhibiting AOB growth and in decreasing N2O emissions in grazed pasture soils under field conditions.

  12. 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.

  13. Ammonia-oxidizing Crenarchaeota and nitrification inside the tissue of a colonial ascidian.

    PubMed

    Martínez-García, Manuel; Stief, Peter; Díaz-Valdés, Marta; Wanner, Gerhard; Ramos-Esplá, Alfonso; Dubilier, Nicole; Antón, Josefa

    2008-11-01

    Marine Crenarchaeota represent an abundant component of the oceanic microbiota that play an important role in the global nitrogen cycle. Here we report the association of the colonial ascidian Cystodytes dellechiajei with putative ammonia-oxidizing Crenarchaeota that could actively be involved in nitrification inside the animal tissue. As shown by 16S rRNA gene analysis, the ascidian-associated Crenarchaeota were phylogenetically related to Nitrosopumilus maritimus, the first marine archaeon isolated in pure culture that grows chemolithoautotrophically oxidizing ammonia to nitrite aerobically. Catalysed reporter deposition (CARD)-FISH revealed that the Crenarchaeota were specifically located inside the tunic tissue of the colony, where moreover the expression of amoA gene was detected. The amoA gene encodes the alpha-subunit of ammonia monooxygenase, which is involved in the first step of nitrification, the oxidation of ammonia to nitrite. Sequencing of amoA gene showed that they were phylogenetically related to amoA genes of N. maritimus and other putative ammonia-oxidizing marine Crenarchaeota. In order to track the suspected nitrification activity inside the ascidian colony under in vivo conditions, microsensor profiles were measured through the tunic tissue. Net NO(x) production was detected in the tunic layer 1200-1800 microm with rates of 58-90 nmol cm(-3) h(-1). Oxygen and pH microsensor profiles showed that the layer of net NO(x) production coincided with O(2) concentrations of 103-116 microM and pH value of 5.2. Together, molecular and microsensor data indicate that Crenarchaeota could oxidize ammonia to nitrite aerobically, and thus be involved in nitrification inside the ascidian tissue.

  14. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California.

    PubMed

    Beman, J Michael; Popp, Brian N; Francis, Christopher A

    2008-04-01

    Nitrification plays an important role in marine biogeochemistry, yet efforts to link this process to the microorganisms that mediate it are surprisingly limited. In particular, ammonia oxidation is the first and rate-limiting step of nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), although mounting evidence indicates that marine Crenarchaeota are capable of ammonia oxidation, and they are among the most abundant microbial groups in the ocean. Here, we have directly quantified ammonia oxidation rates by 15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California. Based on markedly different archaeal amoA sequence types in the upper water column (60 m) and oxygen minimum zone (OMZ; 450 m), novel amoA PCR primers were designed to specifically target and quantify 'shallow' (group A) and 'deep' (group B) clades. These primers recovered extensive variability with depth. Within the OMZ, AOA were most abundant where nitrification may be coupled to denitrification. In the upper water column, group A tracked variations in nitrogen biogeochemistry with depth and between basins, whereas AOB were present in relatively low numbers or undetectable. Overall, 15NH4+ oxidation rates were remarkably well correlated with AOA group A amoA gene copies (r2=0.90, P<0.001), and with 16S rRNA gene copies from marine Crenarchaeota (r2=0.85, P<0.005). These findings represent compelling evidence for an archaeal role in oceanic nitrification.

  15. Niche partitioning of marine group I Crenarchaeota in the euphotic and upper mesopelagic zones of the East China Sea.

    PubMed

    Hu, Anyi; Jiao, Nianzhi; Zhang, Rui; Yang, Zao

    2011-11-01

    Marine group I Crenarchaeota (MGI) represents a ubiquitous and numerically predominant microbial population in marine environments. An understanding of the spatial dynamics of MGI and its controlling mechanisms is essential for an understanding of the role of MGI in energy and element cycling in the ocean. In the present study, we investigated the diversity and abundance of MGI in the East China Sea (ECS) by analysis of crenarchaeal 16S rRNA gene, the ammonia monooxygenase gene amoA, and the biotin carboxylase gene accA. Quantitative PCR analyses revealed that these genes were higher in abundance in the mesopelagic than in the euphotic zone. In addition, the crenarchaeal amoA gene was positively correlated with the copy number of the MGI 16S rRNA gene, suggesting that most of the MGI in the ECS are nitrifiers. Furthermore, the ratios of crenarchaeal accA to amoA or to MGI 16S rRNA genes increased from the euphotic to the mesopelagic zone, suggesting that the role of MGI in carbon cycling may change from the epipelagic to the mesopelagic zones. Denaturing gradient gel electrophoretic profiling of the 16S rRNA genes revealed depth partitioning in MGI community structures. Clone libraries of the crenarchaeal amoA and accA genes showed both "shallow" and "deep" groups, and their relative abundances varied in the water column. Ecotype simulation analysis revealed that MGI in the upper ocean could diverge into special ecotypes associated with depth to adapt to the light gradient across the water column. Overall, our results showed niche partitioning of the MGI population and suggested a shift in their ecological functions between the euphotic and mesopelagic zones of the ECS.

  16. 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

  17. Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea

    PubMed Central

    Lam, Phyllis; Jensen, Marlene M.; Lavik, Gaute; McGinnis, Daniel F.; Müller, Beat; Schubert, Carsten J.; Amann, Rudolf; Thamdrup, Bo; Kuypers, Marcel M. M.

    2007-01-01

    Active expression of putative ammonia monooxygenase gene subunit A (amoA) of marine group I Crenarchaeota has been detected in the Black Sea water column. It reached its maximum, as quantified by reverse-transcription quantitative PCR, exactly at the nitrate maximum or the nitrification zone modeled in the lower oxic zone. Crenarchaeal amoA expression could explain 74.5% of the nitrite variations in the lower oxic zone. In comparison, amoA expression by γ-proteobacterial ammonia-oxidizing bacteria (AOB) showed two distinct maxima, one in the modeled nitrification zone and one in the suboxic zone. Neither the amoA expression by crenarchaea nor that by β-proteobacterial AOB was significantly elevated in this latter zone. Nitrification in the suboxic zone, most likely microaerobic in nature, was verified by 15NO2− and 15N15N production in 15NH4+ incubations with no measurable oxygen. It provided a direct local source of nitrite for anammox in the suboxic zone. Both ammonia-oxidizing crenarchaea and γ-proteobacterial AOB were important nitrifiers in the Black Sea and were likely coupled to anammox in indirect and direct manners respectively. Each process supplied about half of the nitrite required by anammox, based on 15N-incubation experiments and modeled calculations. Because anammox is a major nitrogen loss in marine suboxic waters, such nitrification–anammox coupling potentially occurring also in oceanic oxygen minimum zones would act as a short circuit connecting regenerated ammonium to direct nitrogen loss, thus reducing the presumed direct contribution from deep-sea nitrate. PMID:17420469

  18. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops.

    PubMed

    Mao, Yuejian; Yannarell, Anthony C; Mackie, Roderick I

    2011-01-01

    Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.

  19. 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.

  20. Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils.

    PubMed

    Jung, Jaejoon; Yeom, Jinki; Kim, Jisun; Han, Jiwon; Lim, Hyoun Soo; Park, Hyun; Hyun, Seunghun; Park, Woojun

    2011-12-01

    The microbial community (bacterial, archaeal, and fungi) and eight genes involved in the nitrogen biogeochemical cycle (nifH, nitrogen fixation; bacterial and archaeal amoA, ammonia oxidation; narG, nitrate reduction; nirS, nirK, nitrite reduction; norB, nitric oxide reduction; and nosZ, nitrous oxide reduction) were quantitatively assessed in this study, via real-time PCR with DNA extracted from three Antarctic soils. Interestingly, AOB amoA was found to be more abundant than AOA amoA in Antarctic soils. The results of microcosm studies revealed that the fungal and archaeal communities were diminished in response to warming temperatures (10 °C) and that the archaeal community was less sensitive to nitrogen addition, which suggests that those two communities are well-adapted to colder temperatures. AOA amoA and norB genes were reduced with warming temperatures. The abundance of only the nifH and nirK genes increased with both warming and the addition of nitrogen. NirS-type denitrifying bacteria outnumbered NirK-type denitrifiers regardless of the treatment used. Interestingly, dramatic increases in both NirS and NirK-types denitrifiers were observed with nitrogen addition. NirK types increase with warming, but NirS-type denitrifiers tend to be less sensitive to warming. Our findings indicated that the Antarctic microbial nitrogen cycle could be dramatically altered by temperature and nitrogen, and that warming may be detrimental to the ammonia-oxidizing archaeal community. To the best of our knowledge, this is the first report to investigate genes associated with each process of the nitrogen biogeochemical cycle in an Antarctic terrestrial soil environment.

  1. Seasonal changes in surface albedo of Himalayan glaciers from MODIS data and links with the annual mass balance

    NASA Astrophysics Data System (ADS)

    Brun, F.; Dumont, M.; Wagnon, P.; Berthier, E.; Azam, M. F.; Shea, J. M.; Sirguey, P.; Rabatel, A.; Ramanathan, Al.

    2015-02-01

    Few glaciological field data are available on glaciers in the Hindu Kush-Karakoram-Himalayan (HKH) region, and remote sensing data are thus critical for glacier studies in this region. The main objectives of this study are to document, using satellite images, the seasonal changes of surface albedo for two Himalayan glaciers, Chhota Shigri Glacier (Himachal Pradesh, India) and Mera Glacier (Everest region, Nepal), and to reconstruct the annual mass balance of these glaciers based on the albedo data. Albedo is retrieved from Moderate Resolution Imaging Spectroradiometer (MODIS) images, and evaluated using ground based measurements. At both sites, we find high coefficients of determination between annual minimum albedo averaged over the glacier (AMAAG) and glacier-wide annual mass balance (Ba) measured with the glaciological method (R2 = 0.75). At Chhota Shigri Glacier, the relation between AMAAG found at the end of the ablation season and Ba suggests that AMAAG can be used as a proxy for the maximum snow line altitude or equilibrium line altitude (ELA) on winter-accumulation-type glaciers in the Himalayas. However, for the summer-accumulation-type Mera Glacier, our approach relied on the hypothesis that ELA information is preserved during the monsoon. At Mera Glacier, cloud obscuration and snow accumulation limits the detection of albedo during the monsoon, but snow redistribution and sublimation in the post-monsoon period allows for the calculation of AMAAG. Reconstructed Ba at Chhota Shigri Glacier agrees with mass balances previously reconstructed using a positive degree-day method. Reconstructed Ba at Mera Glacier is affected by heavy cloud cover during the monsoon, which systematically limited our ability to observe AMAAG at the end of the melting period. In addition, the relation between AMAAG and Ba is constrained over a shorter time period for Mera Glacier (6 years) than for Chhota Shigri Glacier (11 years). Thus the mass balance reconstruction is less robust

  2. The Mercury Resistance Operon: From an Origin in a Geothermal Environment to an Efficient Detoxification Machine

    PubMed Central

    Boyd, Eric S.; Barkay, Tamar

    2012-01-01

    Mercuric mercury (Hg[II]) is a highly toxic and mobile element that is likely to have had a pronounced and adverse effect on biology since Earth’s oxygenation ∼2.4 billion years ago due to its high affinity for protein sulfhydryl groups, which upon binding destabilize protein structure and decrease enzyme activity, resulting in a decreased organismal fitness. The central enzyme in the microbial mercury detoxification system is the mercuric reductase (MerA) protein, which catalyzes the reduction of Hg(II) to volatile Hg(0). In addition to MerA, mer operons encode for proteins involved in regulation, Hg binding, and organomercury degradation. Mer-mediated approaches have had broad applications in the bioremediation of mercury-contaminated environments and industrial waste streams. Here, we examine the composition of 272 individual mer operons and quantitatively map the distribution of mer-encoded functions on both taxonomic SSU rRNA gene and MerA phylogenies. The results indicate an origin and early evolution of MerA among thermophilic bacteria and an overall increase in the complexity of mer operons through evolutionary time, suggesting continual gene recruitment and evolution leading to an improved efficiency and functional potential of the Mer detoxification system. Consistent with a positive relationship between the evolutionary history and topology of MerA and SSU rRNA gene phylogenies (Mantel R = 0.81, p < 0.01), the distribution of the majority of mer functions, when mapped on these phylograms, indicates an overall tendency to inherit mer-encoded functions through vertical descent. However, individual mer functions display evidence of a variable degree of vertical inheritance, with several genes exhibiting strong evidence for acquisition via lateral gene transfer and/or gene loss. Collectively, these data suggest that (i) mer has evolved from a simple system in geothermal environments to a widely distributed and more complex and efficient

  3. 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

  4. Population dynamics of ammonia-oxidizing bacteria in an aerated submerged biofilm reactor for micropolluted raw water pretreatment.

    PubMed

    Qin, Ying-Ying; Zhang, Xiao-Wen; Ren, Hong-Qiang; Li, Dao-Tang; Yang, Hong

    2008-05-01

    Population dynamics of ammonia-oxidizing bacteria (AOB) in a full-scale aerated submerged biofilm reactor for micropolluted raw water pretreatment was investigated using molecular techniques for a period of 1 year. The ammonia monooxygenase (amoA) gene fragments were amplified from DNA and RNA extracts of biofilm samples. Denaturing gradient gel electrophoresis (DGGE) profile based on the amoA messenger RNA approach exhibited a more variable pattern of temporal dynamics of AOB communities than the DNA-derived approach during the study. Phylogenetic analysis of excised DGGE bands revealed three AOB groups affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage, and an unknown Nitrosomonas group. The population size of betaproteobacterial AOB, quantified with 16S ribosomal RNA gene real-time polymerase chain reaction assay, ranged from 6.63 x 10(5) to 2.67 x 10(9) cells per gram of dry biofilm and corresponded to 0.23-1.8% of the total bacterial fraction. Quantitative results of amoA gene of the three specific AOB groups revealed changes in competitive dominance between AOB of the N. oligotropha lineage and N. communis lineage. Water temperature is shown to have major influence on AOB population size in the reactor by the statistic analysis, and a positive correlation between AOB cell numbers and ammonia removal efficiency is suggested (r = 0.628, P < 0.05).

  5. High-Throughput Analysis of Ammonia Oxidiser Community Composition via a Novel, amoA-Based Functional Gene Array

    PubMed Central

    Abell, Guy C. J.; Robert, Stan S.; Frampton, Dion M. F.; Volkman, John K.; Rizwi, Farhan; Csontos, József; Bodrossy, Levente

    2012-01-01

    Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition. PMID:23284709

  6. 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.

  7. Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar.

    PubMed

    Frey, Beat; Pesaro, Manuel; Rüdt, Andreas; Widmer, Franco

    2008-06-01

    We assessed the effects of phytoextraction on the dynamics of Pseudomonas spp. and ammonia-oxidizing bacterial populations in a heavy metal (HM) polluted soil. Hybrid poplars were grown in two-compartment root containers with a medium history (> 4 years) of HM pollution for 13 weeks. Bulk and poplar rhizosphere soils were analysed by denaturing gradient gel electrophoresis (DGGE) of Pseudomonas (sensu stricto) 16S rRNA and amoA gene fragments. DGGE patterns revealed that Pseudomonas and amoA-containing populations in the contaminated soils were markedly different from those in the uncontaminated soils. Pseudomonas and amoA profiles appeared to be stable over time in the bulk soils. In contrast, contaminated rhizosphere soils revealed a clear shift of populations with removal of HM becoming similar or at least shifted to the populations of the uncontaminated soils. The effect of phytoextraction was, however, not evident in the bulk samples, which still contained large amounts of HM. Cloning and sequencing of dominant DGGE bands revealed that Pseudomonas were phylogenetically related to the Pseudomonas fluorescens cluster and the amoA sequences to Nitrosospira spp. At the last sampling, major prominent band sequences from contaminated rhizosphere soils were identical to sequences obtained from uncontaminated rhizosphere soils, indicating that the populations were dominated by the same phylotypes. This study suggests that two taxonomically different populations are able to recover after the relief of HM stress by phytoextraction practices, whereas bulk microbial activities still remained depressed.

  8. 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

  9. 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.

  10. Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea.

    PubMed

    Dang, Hongyue; Luan, Xi-Wu; Chen, Ruipeng; Zhang, Xiaoxia; Guo, Lizhong; Klotz, Martin G

    2010-06-01

    The ecological characteristics of amoA-encoding archaea (AEA) in deep-sea sediments are largely unsolved. This paper aimed to study the diversity, structure, distribution and abundance of the archaeal community and especially its AEA components in the cold seep surface sediments of the Okhotsk Sea, a marginal sea harboring one of the largest methane hydrate reservoirs in the world. Diverse archaeal 16S rRNA gene sequences were identified, with the majority being related to sequences from other cold seep and methane-rich sediment environments. However, the AEA diversity and abundance were quite low as revealed by amoA gene analyses. Correlation analysis indicates that the abundance of the archaeal amoA genes was correlated with the sediment organic matter content. Thus, it is possible that the amoA-carrying archaea here might utilize organic matter for a living. The affiliation of certain archaeal amoA sequences to the GenBank sequences originally obtained from deep-sea hydrothermal vent environments indicated that the related AEA either have a wide range of temperature adaptation or they have a thermophilic evolutionary history in the modern cold deep-sea sediments of the Okhotsk Sea. The dominance of ammonia-oxidizing bacteria over AEA may indicate that bacteria play a significant role in nitrification in the Okhotsk Sea cold seep sediments.

  11. Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene.

    PubMed

    Offre, Pierre; Prosser, James I; Nicol, Graeme W

    2009-10-01

    Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

  12. Identification and quantification of bacteria and archaea responsible for ammonia oxidation in different activated sludge of full-scale wastewater treatment plants.

    PubMed

    Sinthusith, Nutpornnapat; Terada, Akihiko; Hahn, Martha; Noophan, Pongsak Lek; Munakata-Marr, Junko; Figueroa, Linda A

    2015-01-01

    In this study, the abundance and sequences of the amoA gene in ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were defined in three wastewater treatment plants using activated sludge with biological nitrogen removal in different countries: Thailand, United States of America (USA), and Japan. Quantitative real-time polymerase chain reaction (PCR) and PCR coupled with denaturing gradient gel electrophoresis were used to find the comparative abundance and identity of AOB and AOA. The conditions at the Phuket WWTP in Thailand promoted the dominance of AOA amoA genes over AOB amoA genes, while conditions at the WWTPs in Japan and USA promoted growth of AOB. Three parameters that may have contributed to the AOA dominance in Phuket were longer SRT, higher temperature, and higher pH. The Phuket WWTP is a unique system that can be used to better understand the conditions that promote AOA growth and dominance over AOB. In addition, analysis of operational data in conjunction with AOA and AOB community structure from the Phuket WWTP may elucidate advantages of AOA in meeting stricter treatment standards.

  13. 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.

  14. 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

    2015-08-04

    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.

  15. Effects of copper on the abundance and diversity of ammonia oxidizers during dairy cattle manure composting.

    PubMed

    Yin, Yanan; Song, Wen; Gu, Jie; Zhang, Kaiyu; Qian, Xun; Zhang, Xin; Zhang, Yajun; Li, Yang; Wang, Xiaojuan

    2016-12-01

    This study investigated the effects of adding Cu(II) at two exposure levels (50 and 500mgkg(-1), i.e., Cu50 and Cu500 treatments, respectively) on the activity of ammonia-oxidizing microorganisms during dairy cattle manure composting. The results showed that the pH, NH4(+)-N, NO3(-)-N, and potential ammonia oxidation values were inhibited significantly by the addition of Cu(II). Furthermore, the abundances of the ammonia-oxidizing archaea (AOA) amoA gene and ammonia-oxidizing bacteria (AOB) amoA gene were determined by quantitative PCR, and their compositions were evaluated by denaturing gradient gel electrophoresis (DGGE). AOA was the dominant ammonia oxidizing microorganism, of which the abundance was much higher than AOB during composting. Cu50 and Cu500 had significant inhibitory effects on the abundance of the amoA gene. The DGGE profile and statistical analysis showed that Cu(II) changed the AOA and AOB community structure and diversity, where Nitrosomonas and Crenarchaeota dominated throughout the composting process.

  16. 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.

  17. 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.

  18. 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.

  19. Response of ammonia oxidizing bacteria and archaea to acute zinc stress and different moisture regimes in soil.

    PubMed

    Vasileiadis, Sotirios; Coppolecchia, Damiano; Puglisi, Edoardo; Balloi, Annalisa; Mapelli, Francesca; Hamon, Rebecca E; Daffonchio, Daniele; Trevisan, Marco

    2012-11-01

    Ammonia oxidation has been intensively studied for its sensitivity to environmental shifts and stresses. However, acute stress effects on the occurrence and composition of ammonia oxidizing bacteria (AOB) and archaea (AOA) based on expression of related molecular markers in complex soil environments have been to an extent overlooked, particularly concerning transient but commonly occurring environmental changes like soil moisture shifts. The present study investigates the responses of AOB and AOA to moisture shifts and high Zn soil content. AmoA gene copies and transcripts of AOB and AOA along with potential nitrification activity were measured in a soil microcosm approach for investigating the referred environmental shifts. Moisture change from 87 to 50 % of the water holding capacity caused a ~99 % reduction of AOB but not of AOA amoA transcripts that did not change significantly. Increasing applied zinc concentrations resulted in a reduction of potential nitrification rates and negatively affected studied gene expressions of both AOB and AOA, with AOB being more responsive. Both 16 S rRNA and amoA transcripts of AOB had an inverse relation to the applied zinc, indicating a gradual loss in total cell activity. Our results suggest the existence of pronounced differences between AOB and AOA concerning ammonia oxidation activity.

  20. Impacts of Edaphic Factors on Communities of Ammonia-Oxidizing Archaea, Ammonia-Oxidizing Bacteria and Nitrification in Tropical Soils

    PubMed Central

    de Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.

    2014-01-01

    Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 105 to 106 copies archaeal amoA g−1 soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity. PMID:24586878

  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. Manure fertilization alters the population of ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea in a paddy soil.

    PubMed

    Wang, Yu; Zhu, Guibing; Song, Liyan; Wang, Shanyun; Yin, Chengqing

    2014-03-01

    Manure fertilizers are widely used in agriculture and highly impacted the soil microbial communities such as ammonia oxidizers. However, the knowledge on the communities of archaeal versus bacterial ammonia oxidizers in paddy soil affected by manure fertilization remains largely unknown, especially for a long-term influence. In present work, the impact of manure fertilization on the population of ammonia oxidizers, related potential nitrification rates (PNRs) and the key factors manipulating the impact were investigated through studying two composite soil cores (long-term fed with manure fertilization versus undisturbed). Moreover, soil incubated with NH(4)(+) for 5 weeks was designed to verify the field research. The results showed that the copy numbers of bacterial amoA gene in the manure fed soil were significant higher than those in the unfed soil (p < 0.05), suggesting a clear stimulating effect of long-term manure fertilization on the population of ammonia-oxidizing bacteria (AOB). The detected PNRs in the manure fed soil core (14-218 nmol L(-1)  N g(-1)  h(-1)) were significant higher than those in the unfed soil core (5-72 nmol L(-1)  N g(-1)  h(-1) ; p < 0.05). Highly correlations between the PNRs and the bacterial amoA gene copies rather than archaeal amoA gene were observed, indicating strong nitrification capacity related to bacterial ammonia oxidizers. The NH(4)(+) -N significantly correlated to the abundance of AOB (p < 0.01) and explained 96.1% of the environmental variation, showing the NH(4)(+) -N was the main factor impacting the population of AOB. The incubation experiment demonstrated a clear increase of the bacterial amoA gene abundance (2.0 × 10(6) to 8.4 × 10(6)  g(-1) d.w.s. and 1.6 × 10(4) to 4.8 × 10(5)  g(-1) d.w.s.) in both soil but not for the archaeal amoA gene, in agreement with the field observation. Overall, our results suggested that manure fertilization promoted the

  3. A defect in holographic interpretations of tensor networks

    NASA Astrophysics Data System (ADS)

    Czech, Bartlomiej; Nguyen, Phuc H.; Swaminathan, Sivaramakrishnan

    2017-03-01

    We initiate the study of how tensor networks reproduce properties of static holographic space-times, which are not locally pure anti-de Sitter. We consider geometries that are holographically dual to ground states of defect, interface and boundary CFTs and compare them to the structure of the requisite MERA networks predicted by the theory of minimal updates. When the CFT is deformed, certain tensors require updating. On the other hand, even identical tensors can contribute differently to estimates of entanglement entropies. We interpret these facts holographically by associating tensor updates to turning on non-normalizable modes in the bulk. In passing, we also clarify and complement existing arguments in support of the theory of minimal updates, propose a novel ansatz called rayed MERA that applies to a class of generalized interface CFTs, and analyze the kinematic spaces of the thin wall and AdS3-Janus geometries.

  4. Memetic algorithms for ligand expulsion from protein cavities

    NASA Astrophysics Data System (ADS)

    Rydzewski, J.; Nowak, W.

    2015-09-01

    Ligand diffusion through a protein interior is a fundamental process governing biological signaling and enzymatic catalysis. A complex topology of channels in proteins leads often to difficulties in modeling ligand escape pathways by classical molecular dynamics simulations. In this paper, two novel memetic methods for searching the exit paths and cavity space exploration are proposed: Memory Enhanced Random Acceleration (MERA) Molecular Dynamics (MD) and Immune Algorithm (IA). In MERA, a pheromone concept is introduced to optimize an expulsion force. In IA, hybrid learning protocols are exploited to predict ligand exit paths. They are tested on three protein channels with increasing complexity: M2 muscarinic G-protein-coupled receptor, enzyme nitrile hydratase, and heme-protein cytochrome P450cam. In these cases, the memetic methods outperform simulated annealing and random acceleration molecular dynamics. The proposed algorithms are general and appropriate in all problems where an accelerated transport of an object through a network of channels is studied.

  5. Microbial DNA records historical delivery of anthropogenic mercury

    PubMed Central

    Poulain, Alexandre J; Aris-Brosou, Stéphane; Blais, Jules M; Brazeau, Michelle; Keller, Wendel (Bill); Paterson, Andrew M

    2015-01-01

    Mercury (Hg) is an anthropogenic pollutant that is toxic to wildlife and humans, but the response of remote ecosystems to globally distributed Hg is elusive. Here, we use DNA extracted from a dated sediment core to infer the response of microbes to historical Hg delivery. We observe a significant association between the mercuric reductase gene (merA) phylogeny and the timing of Hg deposition. Using relaxed molecular clock models, we show a significant increase in the scaled effective population size of the merA gene beginning ~200 years ago, coinciding with the Industrial Revolution and a coincident strong signal for positive selection acting on residues in the terminal region of the mercuric reductase. This rapid evolutionary response of microbes to changes in the delivery of anthropogenic Hg indicates that microbial genomes record ecosystem response to pollutant deposition in remote regions. PMID:26057844

  6. Functions, Evolution, and Application of the Supramolecular Machines of Hg Detoxification

    SciTech Connect

    Miller, Susan M.

    2009-11-27

    The bacterial mercury resistance (mer) operon functions in Hg biogeochemistry and bioremediation by converting reactive inorganic [Hg(II)] and organic [RHg(I)] mercurials to relatively inert monoatomic mercury vapor, Hg(0). Its genes regulate expression (MerR, MerD, MerOP), import Hg(II) (MerT, MerP, and MerC), and demethylate (MerB) and reduce (MerA) mercurials. We focus on how these components interact with each other and with the host cell to allow cells to survive and detoxify Hg compounds. Understanding how this ubiquitous detoxification system fits into the biology and ecology of its bacterial host is essential to guide interventions that support and enhance Hg remediation. At a more basic level, studies of interactions between the metal ion trafficking proteins in this pathway provide insights into general mechanisms used by proteins in pathways involved in trafficking of other metal ions in cells of all types of organisms, including pathways for essential metal ions such as Cu and Zn and other toxic metal ions such as Cd. In this project we focused on investigations of proteins from mer operons found in gamma-proteobacteria with specific objectives to use biophysical and biochemical approaches to detect and define (1) interactions between the structural components of the key detoxifying mer operon enzyme, mercuric ion reductase (MerA), (2) interactions between the components of MerA and the other mer operon enzyme, organomercurial lyase (MerB), and (3) to investigate the structure and interactions of integral membrane transport proteins, MerT and MerC, with MerA.

  7. Long-Term Stability of Mercury-Reducing Microbial Biofilm Communities Analyzed by 16S-23S rDNA Interspacer Region Polymorphism.

    PubMed

    Canstein, H.F.; Li, Y.; Felske, A.; Wagner-Döbler, I.

    2001-12-01

    The composition of mercury-reducing communities in two bioreactors retaining Hg(II) from chloralkali electrolysis wastewater for 485 days was analyzed based on effluent community DNA. Packed bed bioreactors with lava chips as carrier of the biofilm were inoculated with nine Hg(II)-resistant isolates that belonged to the alpha and gamma subdivisions of the proteobacteria. A rapid DNA-fingerprinting method was applied, using the intergenic spacer region (ISR) of the 16S-23S rDNA for analysis of the community composition. This allowed discrimination of the inoculum strains down to subspecies level. A merA specific PCR permitted the discrimination of the community's merA genes. During the 485 days of operation, the bioreactors were exposed to various physical stresses (mixing, gas bubbles, temperature increase up to 41 degrees C, increased flow velocity) and repeated high mercury inflow concentrations, resulting in reduced bioreactor performance and decreased culturable cell numbers in the reactor effluent. Nevertheless, the composition of the microbial community remained rather stable throughout the investigated time period. Of the inoculum strains, two could be detected throughout, whereas three were sometimes present with varying periods of nondetection. Two inoculum strains were only detected within the first month. Two strains of gamma-proteobacteria that were able to reduce ionic mercury invaded the bioreactor community. They did not outcompete established strains and had no negative effect on the Hg(II)-retention activity of the bioreactors. The community comprised diverse merA genes. The abundance of merA genes matched the abundance of their respective strains as confirmed by ISR community analysis. The continuously high selection pressure for mercury resistance maintained a stable and highly active mercury-reducing microbial community within the bioreactors.

  8. The STRONG STAR Multidisciplinary PTSD Research Consortium

    DTIC Science & Technology

    2011-09-01

    inhibitor cocktail using motorized pestles in 1.5 ml microtubes (RPI, Mount prospect, IL, USA ). All steps were conducted at 4 °C. After 30 min...test began. Behavi or was recorded using a CCD ca mera mounted above the cage and stored to video files for offline scoring and analysis . The...20 subjects. *Pɘ.05, significantly different from No CAPS. *P,0.001, significantly different from No CAPS. Molecular biological analysis

  9. Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607

    NASA Astrophysics Data System (ADS)

    Schiering, N.; Kabsch, W.; Moore, M. J.; Distefano, M. D.; Walsh, C. T.; Pai, E. F.

    1991-07-01

    SEVERAL hundred million tons of toxic mercurials are dispersed in the biosphere1. Microbes can detoxify organo-mercurials and mercury salts through sequential action of two enzymes, organomercury lyase2 and mercuric ion reductase (MerA) 3-5. The latter, a homodimer with homology to the FAD-dependent disulphide oxidoreductases6, catalyses the reaction NADPH + Hg(II) --> NADP+ + H+Hg(0), one of the very rare enzymic reactions with metal substrates. Human glutathione reductase7,8 serves as a reference molecule for FAD-dependent disulphide reductases and between its primary structure9 and that of MerA from Tn501 (Pseudomonas), Tn21 (Shigella), pI258 (Staphylococcus) and Bacillus, 25-30% of the residues have been conserved10,11. All MerAs have a C-terminal extension about 15 residues long but have very varied N termini. Although the enzyme from Streptomyces lividans has no addition, from Pseudomonas aeruginosa Tn5Ol and Bacillus sp. strain RC607 it has one and two copies respectively of a domain of 80-85 residues, highly homologous to MerP, the periplasmic component of proteins encoded by the mer operon11. These domains can be proteolytically cleaved off without changing the catalytic efficiency3. We report here the crystal structure of MerA from the Gram-positive bacterium Bacillus sp. strain RC607. Analysis of its complexes with nicotinamide dinucleotide substrates and the inhibitor Cd(II) reveals how limited structural changes enable an enzyme to accept as substrate what used to be a dangerous inhibitor. Knowledge of the mode of mercury ligation is a prerequisite for understanding this unique detoxification mechanism.

  10. Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607.

    PubMed

    Schiering, N; Kabsch, W; Moore, M J; Distefano, M D; Walsh, C T; Pai, E F

    1991-07-11

    Several hundred million tons of toxic mercurials are dispersed in the biosphere. Microbes can detoxify organo-mercurials and mercury salts through sequential action of two enzymes, organomercury lyase and mercuric ion reductase (MerA). The latter, a homodimer with homology to the FAD-dependent disulphide oxidoreductases, catalyses the reaction NADPH + Hg(II)----NADP+ + H+ + Hg(0), one of the very rare enzymic reactions with metal substrates. Human glutathione reductase serves as a reference molecule for FAD-dependent disulphide reductases and between its primary structure and that of MerA from Tn501 (Pseudomonas), Tn21 (Shigella), p1258 (Staphylococcus) and Bacillus, 25-30% of the residues have been conserved. All MerAs have a C-terminal extension about 15 residues long but have very varied N termini. Although the enzyme from Streptomyces lividans has no addition, from Pseudomonas aeruginosa Tn501 and Bacillus sp. strain RC607 it has one and two copies respectively of a domain of 80-85 residues, highly homologous to MerP, the periplasmic component of proteins encoded by the mer operon. These domains can be proteolytically cleaved off without changing the catalytic efficiency. We report here the crystal structure of MerA from the Gram-positive bacterium Bacillus sp. strain RC607. Analysis of its complexes with nicotinamide dinucleotide substrates and the inhibitor Cd(II) reveals how limited structural changes enable an enzyme to accept as substrate what used to be a dangerous inhibitor. Knowledge of the mode of mercury ligation is a prerequisite for understanding this unique detoxification mechanism.

  11. Towards a better understanding of Martian surface processes: zooming in for a quantitative assessment of key geomorphological features from super-resolution HiRISE images in comparison to overlapping rover Navcam image

    NASA Astrophysics Data System (ADS)

    Tao, Y.; Muller, J.-P.

    2015-10-01

    We have performed a quantitative study on automatically detected geomorphological features from MRO HiRISE orthorectified image st 25cm, a 5cm super-resolution resolved HiRISE image and MER-A Navcam orthorectified image to demonstrate one of the advantages of using our novel Gotcha- PDE-TV (GPT) super-resolution restoration (SRR) technique to better understand Martian surface processes.

  12. Mercury Reduction and Methyl Mercury Degradation by the Soil Bacterium Xanthobacter autotrophicus Py2

    PubMed Central

    Petrus, Amanda K.; Rutner, Colin; Liu, Songnian; Wang, Yingjiao

    2015-01-01

    Two previously uncharacterized potential broad-spectrum mercury (Hg) resistance operons (mer) are present on the chromosome of the soil Alphaproteobacteria Xanthobacter autotrophicus Py2. These operons, mer1 and mer2, contain two features which are commonly found in mer operons in the genomes of soil and marine Alphaproteobacteria, but are not present in previously characterized mer operons: a gene for the mercuric reductase (MerA) that encodes an alkylmercury lyase domain typical of those found on the MerB protein, and the presence of an additional gene, which we are calling merK, with homology to glutathione reductase. Here, we demonstrate that Py2 is resistant to 0.2 μM inorganic mercury [Hg(II)] and 0.05 μM methylmercury (MeHg). Py2 is capable of converting MeHg and Hg(II) to elemental mercury [Hg(0)], and reduction of Hg(II) is induced by incubation in sub toxic concentrations of Hg(II). Transcription of the merA genes increased with Hg(II) treatment, and in both operons merK resides on the same polycistronic mRNA as merA. We propose the use of Py2 as a model system for studying the contribution of mer to Hg mobility in soil and marine ecosystems. PMID:26341208

  13. High efficiency preparation of bioactive human alpha-defensin 6 in Escherichia coli Origami(DE3)pLysS by soluble fusion expression.

    PubMed

    Wang, Aiping; Su, Yongping; Wang, Song; Shen, Mingqiang; Chen, Fang; Chen, Mo; Ran, Xinze; Cheng, Tianmin; Wang, Junping

    2010-08-01

    Human alpha-defensin 6 (HD(6)), a small cysteine-rich cationic peptide specially expressed in epithelial cells of digestive tract, may play a crucial role in mucosal immunity. This is the first report on efficient production of bioactive HD(6) through a gene-engineering approach in Escherichia coli. The recombinant plasmid pET32a-omHD(6) was primarily constructed by inserting a PCR fragment encoding mature HD(6) peptide (mHD(6)) preceded by an enterokinase recognition sequence into the expression vector pET32a(+), in frame with the upstream thioredoxin (TrxA) gene. Under optimized expression conditions, a high percentage (>60%) of soluble TrxA-omHD(6) fusion protein was obtained with a yield of about 1.69 g/l, and the theoretical productivity of recombinant mHD(6) (rmHD(6)) reached 0.38 g/l. A feasible three-step purification strategy involving nickel-sepharose chromatography, enterokinase-cleavage and cation exchange chromatography was developed to purify rmHD(6), followed by characteristic identifications by Western blot, mass spectrometry and sequencing. About 102 mg/l of rmHD(6) with its intact N-terminal amino acid sequence was finally achieved. The in vitro experiments showed that rmHD(6) possesses high potency to inhibit herpes simplex virus-2 infection. This work settles substantial foundation for further functional study of HD(6).

  14. Salmonella Rapidly Regulates Membrane Permeability To Survive Oxidative Stress

    PubMed Central

    van der Heijden, Joris; Reynolds, Lisa A.; Deng, Wanyin; Mills, Allan; Scholz, Roland; Imami, Koshi; Foster, Leonard J.; Duong, Franck

    2016-01-01

    ABSTRACT The outer membrane (OM) of Gram-negative bacteria provides protection against toxic molecules, including reactive oxygen species (ROS). Decreased OM permeability can promote bacterial survival under harsh circumstances and protects against antibiotics. To better understand the regulation of OM permeability, we studied the real-time influx of hydrogen peroxide in Salmonella bacteria and discovered two novel mechanisms by which they rapidly control OM permeability. We found that pores in two major OM proteins, OmpA and OmpC, could be rapidly opened or closed when oxidative stress is encountered and that the underlying mechanisms rely on the formation of disulfide bonds in the periplasmic domain of OmpA and TrxA, respectively. Additionally, we found that a Salmonella mutant showing increased OM permeability was killed more effectively by treatment with antibiotics. Together, these results demonstrate that Gram-negative bacteria regulate the influx of ROS for defense against oxidative stress and reveal novel targets that can be therapeutically targeted to increase bacterial killing by conventional antibiotics. PMID:27507830

  15. Functional characterisation of the peroxiredoxin gene family members of Synechococcus elongatus PCC 7942.

    PubMed

    Stork, Tina; Laxa, Miriam; Dietz, Marina S; Dietz, Karl-Josef

    2009-02-01

    The genome of Synechococcus elongatus PCC 7942 encodes six peroxiredoxins (Prx). Single genes are present each for a 1-Cys Prx and a 2-Cys Prx, while four genes code for PrxQ-like proteins (prxQ-A1, -A2, -A3 and B). Their transcript accumulation varies with growth conditions in a gene-specific manner (Stork et al. in J Exp Bot 56:3193-3206, 2005). To address their functional properties, members of the prx gene family were produced as recombinant proteins and analysed for their peroxide detoxification capacity and quaternary structure by size exclusion chromatography. Independent of the reduction state, the 2-Cys Prx separated as oligomer, the 1-Cys Prx as dimer and the PrxQ-A1 as monomer. PrxQ-A2 was inactive in our assays, 1-Cys Prx activity was unaffected by addition of TrxA, while all others were stimulated to a variable extent by addition of E. coli thioredoxin. Sensitivity towards cumene hydroperoxide treatment of E. coli BL21 cells expressing the cyanobacterial PrxQ-A1 to A3 proteins was greatly reduced, while expression of the other Prx had no effect. The study shows differentiation of Prx functions in S. elongatus PCC 7942 which is discussed in relation to potential roles in site- and stress-specific defence.

  16. Components of glycine reductase from Eubacterium acidaminophilum. Cloning, sequencing and identification of the genes for thioredoxin reductase, thioredoxin and selenoprotein PA.

    PubMed

    Lübbers, M; Andreesen, J R

    1993-10-15

    The genes encoding thioredoxin reductase (trxB), thioredoxin (trxA), protein PA of glycine reductase (grdA) and the first 23 amino acids of the large subunit of protein PC of glycine reductase (grdC) belonging to the reductive deamination systems present in Eubacterium acidaminophilum were cloned and sequenced. The proteins were products of closely linked genes with 314 codons (thioredoxin reductase), 110 codons (thioredoxin), and 158 codons (protein PA). The protein previously called 'atypically small lipoamide dehydrogenase' or 'electron transferring flavoprotein' could now conclusively be identified as a thioredoxin reductase (subunit mass of 34781 Da) by the alignment with the enzyme of Escherichia coli showing the same typical order of the corresponding domains. The thioredoxin (molecular mass of 11742 Da) deviated considerably from the known consensus sequence, even in the most strongly conserved redox-active segment WCGPC that was now GCVPC. The selenocysteine of protein PA (molecular mass of 16609 Da) was encoded by TGA. The protein was highly similar to those of Clostridium purinolyticum and Clostridium sticklandii involved in glycine reductase. Thioredoxin reductase and thioredoxin of E. acidaminophilum could be successfully expressed in E. coli.

  17. Cloning and characterization of metallothionein gene (HcMT) from Halostachys caspica and its expression in E. coli.

    PubMed

    Liu, Zhongyuan; Meng, Hongen; Abdulla, Hasiyatihan; Zhang, Fuchun; Mao, Xinfang

    2016-07-10

    Halostachys caspica is a short shrub distributed in the semi-arid and saline-alkali area, which evolved various mechanisms for modulating salt and metal level. In the present study, a Type 2 metallothionein (HcMT) gene was cloned from the salt induced suppression subtractive hybridization (SSH) cDNA library of H.caspica. Quantitative real time PCR (qRT-PCR) analysis indicated that HcMT gene was up-regulated under the stress of Cu(2+), Zn(2+) and Cd(2+), and the tolerance of E. coli strain harboring with the recombinant HcMT (pET-32a-HcMT) to Cu(2+), Zn(2+) and Cd(2+) was enhanced compared to strain with control vector (pET-32a). Moreover, the purified TrxA-HcMT fusion protein from E. coli cells grown in the presence of 0.3mM CuSO4, 0.3mM ZnSO4, or 0.1mM CdCl2 could bind more metal ions than TrxA alone. The predicted 3D structure showed that HcMT could form a single metal-thiolate cluster, which confers the ability to bind five divalent metal ions through fourteen cysteine residues. These data indicate that HcMT may be involved in processes of metal tolerance in H. caspica and could be employed as a potential candidate for heavy metal phytoremediation.

  18. 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.

  19. 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.

  20. Restoration of taxonomic and functional genes after bioaugmentation of petroleum contaminated soil.

    PubMed

    Wu, Zuojun; Zou, Liangdong; Lu, Diannan; Liu, Zheng

    2011-10-01

    Soil microbial ecosystems are responsive to environmental changes that underpin the biological functions of the soil. The present study was conducted to profile variations in the microbial ecological system of remediated soil (R) and petroleum contaminated soil (P) based on comparisons with soil that had not been contaminated (N), using a cloning library of taxonomic genes (16S rRNA gene for bacteria and 18S rRNA gene for eukaryotes) and functional genes (nifH, amoA and narG). The results showed that N and R had a similar distribution in both the taxonomic genes and functional genes for bacteria and eukaryotes, which were dominated by Proteobacteria and Arthropoda, respectively. Phylogenetic analysis based on the nifH gene showed that the sequences from the three soils were clustered into six taxonomic groups, Actinobacteridae, and Alpha-, Beta-, Gamma- and Delta-proteobacteria, as well as an unclassified group. Evaluation of the amoA gene revealed that all sequences derived from the three samples belonged to Betaproteobacteria. The R and N soil had similar Shannon-Wiener diversity index (H') values, both of which were significantly higher than that of the P soil. The most abundant bacterial phylotype identified in the N and R soils were the same and were related to an uncultured bacterial clone (GAN-SB17, FN423475). None of the narG genes were found in the P soil. Similar results in terms of distribution, composition and the related index were obtained for nifH and amoA. These parameters may comprise a biological ecology index that may be applied to aid the design, implementation and evaluation of soil bioremediation.

  1. Quantitative analyses of ammonia-oxidizing Archaea and bacteria in the sediments of four nitrogen-rich wetlands in China.

    PubMed

    Wang, Shanyun; Wang, Yu; Feng, Xiaojuan; Zhai, Liming; Zhu, Guibing

    2011-04-01

    With the rapid development of ammonia-synthesizing industry, the ammonia-nitrogen pollution in wetlands acting as the sink of point and diffuse pollution has been increased dramatically. Most of ammonia-nitrogen is oxidized at least once by ammonia-oxidizing prokaryotes to complete the nitrogen cycle. Current research findings have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex wetlands environment, it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea or Bacteria as implied by specific high abundance. In this research, the abundance and composition of Archaea and Bacteria in sediments of four kinds of wetlands with different nitrogen concentration were investigated by using quantitative real-time polymerase chain reaction, cloning, and sequencing approaches based on amoA genes. The results indicated that AOA distributed widely in wetland sediments, and the phylogenetic tree revealed that archaeal amoA functional gene sequences from wetlands sediments cluster as two major evolutionary branches: soil/sediment and sediment/water. The bacteria functionally dominated microbial ammonia oxidation in different wetlands sediments on the basis of molecule analysis, potential nitrification rate, and soil chemistry. Moreover, the factors influencing AOA and AOB abundances with environmental indicator were also analyzed, and the results addressed the copy numbers of archaeal and bacterial amoA functional gene having the higher correlation with pH and ammonia concentration. The pH had relatively great negative impact on the abundance of AOA and AOB, while ammonia concentration showed positive impact on AOB abundance only. These findings could be fundamental to improve understanding of the importance of AOB and AOA in nitrogen and other nutrients cycle in wetland ecosystems.

  2. 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

  3. Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters.

    PubMed

    Kalanetra, Karen M; Bano, Nasreen; Hollibaugh, James T

    2009-09-01

    We compared abundance, distributions and phylogenetic composition of Crenarchaeota and ammonia-oxidizing Archaea (AOA) in samples collected from coastal waters west of the Antarctic Peninsula during the summers of 2005 and 2006, with samples from the central Arctic Ocean collected during the summer of 1997. Ammonia-oxidizing Archaea and Crenarchaeota abundances were estimated from quantitative PCR measurements of amoA and 16S rRNA gene abundances. Crenarchaeota and AOA were approximately fivefold more abundant at comparable depths in the Antarctic versus the Arctic Ocean. Crenarchaeota and AOA were essentially absent from the Antarctic Summer Surface Water (SSW) water mass (0-45 m depth). The ratio of Crenarchaeota 16S rRNA to archaeal amoA gene abundance in the Winter Water (WW) water mass (45-105 m depth) of the Southern Ocean was much lower (0.15) than expected and in sharp contrast to the ratio (2.0) in the Circumpolar Deep Water (CDW) water mass (105-3500 m depth) immediately below it. We did not observe comparable segregation of this ratio by depth or water mass in Arctic Ocean samples. A ubiquitous, abundant and polar-specific crenarchaeote was the dominant ribotype in the WW and important in the upper halocline of the Arctic Ocean. Our data suggest that this organism does not contain an ammonia monooxygenase gene. In contrast to other studies where Crenarchaeota populations apparently lacking amoA genes are found in bathypelagic waters, this organism appears to dominate in well-defined, ammonium-rich, near-surface water masses in polar oceans.

  4. Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California.

    PubMed

    Beman, J Michael; Steele, Joshua A; Fuhrman, Jed A

    2011-07-01

    Microorganisms remineralize and respire half of marine primary production, yet the niches occupied by specific microbial groups, and how these different groups may interact, are poorly understood. In this study, we identify co-occurrence patterns for marine Archaea and specific bacterial groups in the chlorophyll maximum of the Southern California Bight. Quantitative PCR time series of marine group 1 (MG1) Crenarchaeota 16S rRNA genes varied substantially over time but were well-correlated (r(2)=0.94, P<0.001) with ammonia monooxygenase subunit A (amoA) genes, and were more weakly related to 16S rRNA genes for all Archaea (r(2)=0.39), indicating that other archaeal groups (for example, Euryarchaeota) were numerically important. These data sets were compared with variability in bacterial community composition based on automated ribosomal intergenic spacer analysis (ARISA). We found that archaeal amoA gene copies and a SAR11 (or Pelagibacter) group Ib operational taxonomic unit (OTU) displayed strong co-variation through time (r(2)=0.55, P<0.05), and archaeal amoA and MG1 16S rRNA genes also co-occurred with two SAR86 and two Bacteroidetes OTUs. The relative abundance of these groups increased and decreased in synchrony over the course of the time series, and peaked during periods of seasonal transition. By using a combination of quantitative and relative abundance estimates, our findings show that abundant microbial OTUs-including the marine Crenarchaeota, SAR11, SAR86 and the Bacteroidetes-co-occur non-randomly; they consequently have important implications for our understanding of microbial community ecology in the sea.

  5. Nitrification and denitrification gene abundances in swine wastewater anaerobic lagoons.

    PubMed

    Ducey, Thomas F; Shriner, Anthony D; Hunt, Patrick G

    2011-01-01

    Although anaerobic lagoons are used globally for livestock waste treatment, their detailed microbial cycling ofN is only beginning to become understood. Within this cycling, nitrification can be performed by organisms that produce the enzyme ammonia monooxygenase. For denitrification, the reduction of nitrite to nitric oxide can be catalyzed by two forms of nitrite reductases, and N,O can be reduced by nitrous oxide reductase encoded by the gene nosZ The objectives of this investigation were to (i) quantify the abundance of the amoA, nirK, nirS, and nosZ genes; (ii) evaluate the influence of environmental conditions on their abundances; and (iii) evaluate their abundance relative to denitrification enzyme activity (DEA). Samples were analyzed via real-time quantitative polymerase chain reaction and collected from eight typical, commercial anaerobic, swine wastewater lagoons located in the Carolinas. The four genes assayed in this study were present in all eight lagoons. Their abundances relative to total bacterial populations were 0.04% (amoA), 1.33% (nirS), 5.29% (nirK), and 0.27% (nosZ). When compared with lagoon chemical characteristics, amoA and nirK correlated with several measured variables. Neither nirS nor nosZ correlated with any measured environmental variables. Although no gene measured in this study correlated with actual or potential DEA, nosZ copy numbers did correlate with the disparity between actual and potential DEA. Phylogenetic analysis ofnosZdid not reveal any correlations to DEA rates. As with other investigations, analyses of these genes provide useful insight while revealing the underlying greater complexity of N cycling within swine waste lagoons.

  6. Environmental Shaping of Sponge Associated Archaeal Communities

    PubMed Central

    Turque, Aline S.; Batista, Daniela; Silveira, Cynthia B.; Cardoso, Alexander M.; Vieira, Ricardo P.; Moraes, Fernando C.; Clementino, Maysa M.; Albano, Rodolpho M.; Paranhos, Rodolfo; Martins, Orlando B.; Muricy, Guilherme

    2010-01-01

    Background Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood. Methodology/Principal Findings We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA) gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA) generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum. Conclusion/Significance The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition of their associated

  7. Thaumarchaeotal Signature Gene Distribution in Sediments of the Northern South China Sea: an Indicator of the Metabolic Intersection of the Marine Carbon, Nitrogen, and Phosphorus Cycles?

    PubMed Central

    Zhou, Haixia; Yang, Jinying; Ge, Huangmin; Jiao, Nianzhi; Luan, Xiwu; Klotz, Martin G.

    2013-01-01

    Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of hcd genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA genes. When the pore water PO43− concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA gene abundance significantly correlated with the sediment pore water NO2− concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments. PMID:23335759

  8. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring.

    PubMed

    Hatzenpichler, Roland; Lebedeva, Elena V; Spieck, Eva; Stoecker, Kilian; Richter, Andreas; Daims, Holger; Wagner, Michael

    2008-02-12

    The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification. In this study, a moderately thermophilic (46 degrees C) ammonia-oxidizing enrichment culture, which had been seeded with biomass from a hot spring, was screened for ammonia oxidizers. Although gene sequences for crenarchaeotal 16S rRNA and two subunits of the ammonia monooxygenase (amoA and amoB) were detected via PCR, no hints for known ammonia-oxidizing bacteria were obtained. Comparative sequence analyses of these gene fragments demonstrated the presence of a single operational taxonomic unit and thus enabled the assignment of the amoA and amoB sequences to the respective 16S rRNA phylotype, which belongs to the widely distributed group I.1b (soil group) of the Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH combined with microautoradiography (MAR) demonstrated metabolic activity of this archaeon in the presence of ammonium. This finding was corroborated by the detection of amoA gene transcripts in the enrichment. CARD-FISH/MAR showed that the moderately thermophilic AOA is highly active at 0.14 and 0.79 mM ammonium and is partially inhibited by a concentration of 3.08 mM. The enriched AOA, which is provisionally classified as "Candidatus Nitrososphaera gargensis," is the first described thermophilic ammonia oxidizer and the first member of the crenarchaeotal group I.1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA.

  9. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

    PubMed

    Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

    2016-01-01

    Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.

  10. 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.

  11. 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.

  12. 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

  13. Thaumarchaeotal signature gene distribution in sediments of the northern South China Sea: an indicator of the metabolic intersection of the marine carbon, nitrogen, and phosphorus cycles?

    PubMed

    Dang, Hongyue; Zhou, Haixia; Yang, Jinying; Ge, Huangmin; Jiao, Nianzhi; Luan, Xiwu; Zhang, Chuanlun; Klotz, Martin G

    2013-04-01

    Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of hcd genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA genes. When the pore water PO4(3-) concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA gene abundance significantly correlated with the sediment pore water NO2(-) concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.

  14. Diversity, Abundance, and Potential Activity of Nitrifying and Nitrate-Reducing Microbial Assemblages in a Subglacial Ecosystem ▿ †

    PubMed Central

    Boyd, Eric S.; Lange, Rachel K.; Mitchell, Andrew C.; Havig, Jeff R.; Hamilton, Trinity L.; Lafrenière, Melissa J.; Shock, Everett L.; Peters, John W.; Skidmore, Mark

    2011-01-01

    Subglacial sediments sampled from beneath Robertson Glacier (RG), Alberta, Canada, were shown to harbor diverse assemblages of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Although archaeal amoA genes were detected, they were less abundant and less diverse than bacterial amoA, suggesting that bacteria are the predominant nitrifiers in RG sediments. Maximum nitrification and nitrate reduction rates in microcosms incubated at 4°C were 280 and 18.5 nmol of N per g of dry weight sediment per day, respectively, indicating the potential for these processes to occur in situ. Geochemical analyses of subglacial sediment pore waters and bulk subglacial meltwaters revealed low concentrations of inorganic and organic nitrogen compounds. These data, when coupled with a C/N atomic ratio of dissolved organic matter in subglacial pore waters of ∼210, indicate that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence of N limitation and the detection of nifH, we were unable to detect biological nitrogen fixation activity in subglacial sediments. Collectively, the results presented here suggest a role for nitrification and nitrate reduction in sustaining microbial life in subglacial environments. Considering that ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of Earth at times in the past, the demonstration of nitrification and nitrate reduction in subglacial environments furthers our understanding of the potential for these environments to contribute to global biogeochemical cycles on glacial-interglacial timescales. PMID:21622799

  15. Diversity, abundance, and potential activity of nitrifying and nitrate-reducing microbial assemblages in a subglacial ecosystem.

    PubMed

    Boyd, Eric S; Lange, Rachel K; Mitchell, Andrew C; Havig, Jeff R; Hamilton, Trinity L; Lafrenière, Melissa J; Shock, Everett L; Peters, John W; Skidmore, Mark

    2011-07-01

    Subglacial sediments sampled from beneath Robertson Glacier (RG), Alberta, Canada, were shown to harbor diverse assemblages of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Although archaeal amoA genes were detected, they were less abundant and less diverse than bacterial amoA, suggesting that bacteria are the predominant nitrifiers in RG sediments. Maximum nitrification and nitrate reduction rates in microcosms incubated at 4°C were 280 and 18.5 nmol of N per g of dry weight sediment per day, respectively, indicating the potential for these processes to occur in situ. Geochemical analyses of subglacial sediment pore waters and bulk subglacial meltwaters revealed low concentrations of inorganic and organic nitrogen compounds. These data, when coupled with a C/N atomic ratio of dissolved organic matter in subglacial pore waters of ~210, indicate that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence of N limitation and the detection of nifH, we were unable to detect biological nitrogen fixation activity in subglacial sediments. Collectively, the results presented here suggest a role for nitrification and nitrate reduction in sustaining microbial life in subglacial environments. Considering that ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of Earth at times in the past, the demonstration of nitrification and nitrate reduction in subglacial environments furthers our understanding of the potential for these environments to contribute to global biogeochemical cycles on glacial-interglacial timescales.

  16. Distribution patterns of ammonia-oxidizing bacteria and anammox bacteria in the freshwater marsh of Honghe wetland in Northeast China.

    PubMed

    Lee, Kwok-Ho; Wang, Yong-Feng; Zhang, Guo-Xia; Gu, Ji-Dong

    2014-12-01

    Community characteristics of aerobic ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria in Honghe freshwater marsh, a Ramsar-designated wetland in Northeast China, were analyzed in this study. Samples were collected from surface and low layers of sediments in the Experimental, Buffer, and Core Zones in the reserve. Community structures of AOB were investigated using both 16S rRNA and amoA (encoding for the α-subunit of the ammonia monooxygenase) genes. Majority of both 16S rRNA and amoA gene-PCR amplified sequences obtained from the samples in the three zones affiliated with Nitrosospira, which agreed with other wetland studies. A relatively high richness of β-AOB amoA gene detected in the freshwater marsh might suggest minimal external pressure was experienced, providing a suitable habitat for β-AOB communities. Anammox bacteria communities were assessed using both 16S rRNA and hzo (encoding for hydrazine oxidoreductase) genes. However, PCR amplification of the hzo gene in all samples failed, suggesting that the utilization of hzo biomarker for detecting anammox bacteria in freshwater marsh might have serious limitations. Results with 16S rRNA gene showed that Candidatus Kuenenia was detected in only the Experimental Zone, whereas Ca. Scalindua including different lineages was observed in both the Buffer and Experimental Zones but not the Core Zone. These results indicated that both AOB and anammox bacteria have specific distribution patterns in the ecosystem corresponding to the extent of anthropogenic impact.

  17. Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges.

    PubMed

    Radax, Regina; Hoffmann, Friederike; Rapp, Hans Tore; Leininger, Sven; Schleper, Christa

    2012-04-01

    The association of archaea with marine sponges was first described 15 years ago and their role in the nitrification process in Mediterranean and tropical sponges has been suggested. Here we explore the occurrence and abundance of potential ammonia-oxidizing archaea (AOA) in four morphologically different cold-water sponges (Phakellia ventilabrum, Geodia barretti, Antho dichotoma and Tentorium semisuberites) from the sublittoral and upper bathyal zone [Correction added on 30 December 2011, after first online publication on 19 December 2011: The term 'mesopelagic zone' has been replaced.] of the Norwegian coast, and relate them to nitrification rates determined in laboratory incubations. Net nitrification rates, calculated from the sum of nitrite and nitrate release during 24 h, were up to 1880 nmol N cm(-3) day(-1); i.e. comparable with those measured in Mediterranean sponges. Furthermore, a high abundance of archaeal cells was determined by fluorescence in situ hybridizations (CARD-FISH) and quantitative PCR, targeting archaeal amoA genes (encoding the alpha subunit of ammonia monooxygenase). AmoA genes as well as amoA transcripts were either exclusively detectable from archaea or were orders of magnitudes higher in abundance than their bacterial counterparts. Phylogenetic analyses of AOA and bacterial nitrite oxidizers (genus Nitrospira) confirmed the presence of specific populations of nitrifying microorganisms in the sponge mesohyl, which either were affiliated with groups detected earlier in marine sponges or were typical inhabitants of cold- and deep-water environments. Estimated cell-specific nitrification rates for P. ventilabrum were 0.6 to 6 fmol N archaeal cell(-1) day(-1), thus comparable with planktonic organisms. Our results identify AOA as the major drivers of nitrification in four cold-water sponges, and indicate that these archaea may be considered as a relevant factor in nitrogen cycling in ocean regions with high sponge biomass.

  18. 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

  19. 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.

  20. 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

  1. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

    PubMed

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-11-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

  2. Transcriptional response of nitrifying communities to wetting of dry soil.

    PubMed

    Placella, Sarah A; Firestone, Mary K

    2013-05-01

    The first rainfall following a severe dry period provides an abrupt water potential change that is both an acute physiological stress and a defined stimulus for the reawakening of soil microbial communities. We followed the responses of indigenous communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and nitrite-oxidizing bacteria to the addition of water to laboratory incubations of soils taken from two California annual grasslands following a typically dry Mediterranean summer. By quantifying transcripts for a subunit of bacterial and archaeal ammonia monooxygenases (amoA) and a bacterial nitrite oxidoreductase (nxrA) in soil from 15 min to 72 h after water addition, we identified transcriptional response patterns for each of these three groups of nitrifiers. An increase in quantity of bacterial amoA transcripts was detectable within 1 h of wet-up and continued until the size of the ammonium pool began to decrease, reflecting a possible role of transcription in upregulation of nitrification after drought-induced stasis. In one soil, the pulse of amoA transcription lasted for less than 24 h, demonstrating the transience of transcriptional pools and the tight coupling of transcription to the local soil environment. Analysis of 16S rRNA using a high-density microarray suggested that nitrite-oxidizing Nitrobacter spp. respond in tandem with ammonia-oxidizing bacteria while nitrite-oxidizing Nitrospina spp. and Nitrospira bacteria may not. Archaeal ammonia oxidizers may respond slightly later than bacterial ammonia oxidizers but may maintain elevated transcription longer. Despite months of desiccation-induced inactivation, we found rapid transcriptional response by all three groups of soil nitrifiers.

  3. 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

  4. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards* #

    PubMed Central

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-01-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle. PMID:25367788

  5. Distributions, abundances and activities of microbes associated with the nitrogen cycle in riparian and stream sediments of a river tributary.

    PubMed

    Kim, Haryun; Bae, Hee-Sung; Reddy, K Ramesh; Ogram, Andrew

    2016-12-01

    River tributaries are ecologically important environments that function as sinks of inorganic nitrogen. To gain greater insight into the nitrogen cycle (N-cycle) in these environments, the distributions and activities of microbial populations involved in the N-cycle were studied in riparian and stream sediments of the Santa Fe River (SFR) tributaries located in northern Florida, USA. Riparian sediments were characterized by much higher organic matter content, and extracellular enzyme activities, including cellobiohydrolase, β-d-glucosidase, and phenol oxidase than stream sediments. Compared with stream sediments, riparian sediments exhibited significantly higher activities of nitrification, denitrification, dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonia oxidation; correspondingly, with higher copies of amoA (a biomarker for enumerating nitrifiers), nirS and nirK (for denitrifiers), and nrfA (for DNRA bacteria). Among N-cycle processes, denitrification showed the highest activities and the highest concentrations of the corresponding gene (nirK and nirS) copy numbers. In riparian sediments, substantial nitrification activities (6.3 mg-N kg soil(-1)d(-1) average) and numbers of amoA copies (7.3 × 10(7) copies g soil(-1) average) were observed, and nitrification rates correlate with denitrification rates. The guild structures of denitrifiers and nitrifiers in riparian sediments differed significantly from those found in stream sediments, as revealed by analysis of nirS and archaeal amoA sequences. This study shows that riparian sediments serve as sinks for inorganic nitrogen loads from non-point sources of agricultural runoff, with nitrification and denitrification associated with elevated levels of carbon and nitrogen contents and extracellular enzyme activities.

  6. 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.

  7. Interaction of the mechanism-based inactivator acetylene with ammonia monooxygenase of Nitrosomonas europaea.

    PubMed

    Gilch, Stefan; Vogel, Manja; Lorenz, Matthias W; Meyer, Ortwin; Schmidt, Ingo

    2009-01-01

    The ammonia monooxygenase (AMO) of Nitrosomonas europaea is a metalloenzyme that catalyses the oxidation of ammonia to hydroxylamine. We have identified histidine 191 of AmoA as the binding site for the oxidized mechanism-based inactivator acetylene. Binding of acetylene changed the molecular mass of His-191 from 155.15 to 197.2 Da (+42.05), providing evidence that acetylene was oxidized to ketene (CH2CO; 42.04 Da) which binds specifically to His-191. It must be assumed that His-191 is part of the acetylene-activating site in AMO or at least directly neighbours this site.

  8. 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

  9. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

    PubMed Central

    Rughöft, Saskia; Herrmann, Martina; Lazar, Cassandre S.; Cesarz, Simone; Levick, Shaun R.; Trumbore, Susan E.; Küsel, Kirsten

    2016-01-01

    Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our

  10. Biomolecular Mechanisms of Mercury Transfers and Transformations by Proteins of the Mer Operon

    NASA Astrophysics Data System (ADS)

    Miller, S. M.; Hong, B.; Nauss, R.; Momany, C.; Summers, A. O.; Feng, X.; Harwood, I.; Stroud, R.

    2008-12-01

    Aerobic bacteria exhibiting resistance to the toxic effects of Hg(II) and organomercurials [RHg(I), e.g. MeHg(I)] and are widely found in both pristine and mercury contaminated environments. Resistance, afforded by a plasmid- or transposon-associated mer operon, involves an unusual pathway where Hg(II) and organomercurials [RHg(I)] undergo facilitated entry into the bacterial cytoplasm via an integral membrane transport protein (MerT) and are then "detoxified" by the concerted effort of two enzymes, organomercurial lyase (MerB), which catalyzes dealkylation (i.e., demethylation) of RHg(I) to Hg(II) and a hydrocarbon, and mercuric ion reductase (MerA), which catalyzes reduction of Hg(II) to Hg(0) as the ultimate detoxification for the organism. With a widespread distribution, these bacterial transformations play a significant role in the fate of mercury in the environment. Our focus is on elucidation of the molecular mechanisms for the transport and catalytic transformations of RHg(I) and Hg(II) by these proteins and the factors that influence the overall efficiency of the process. Current efforts are focused primarily on elucidating details of RHg(I) binding and dealkylation by MerB as well as the mechanism for transfer of the Hg(II) product to MerA. Key findings include the demonstration of a non-cysteine residue as essential for the catalytic activity and demonstration that direct transfer of Hg(II) to MerA proceeds more rapidly and more completely than transfer to small MW thiols such as cysteines or glutathione. Reuslts of these studies as well as an overview of our current understanding of the whole system will be presented.

  11. Phytoremediation of ionic and methyl mercury pollution

    SciTech Connect

    Meagher, R.B.

    1998-06-01

    'The long-term objective of the research is to manipulate single-gene traits into plants, enabling them to process heavy metals and remediate heavy-metal pollution by resistance, sequestration, removal, and management of these contaminants. The authors are focused on mercury pollution as a case study of this plant genetic engineering approach. The working hypothesis behind this proposal was that transgenic plants expressing both the bacterial organo mercury lyase (merB) and the mercuric ion reductase gene (merA) will: (A) remove the mercury from polluted sites and (B) prevent methyl mercury from entering the food chain. The results from the research are so positive that the technology will undoubtedly be applied in the very near future to cleaning large mercury contaminates sites. Many such sites were not remediable previously due to the excessive costs and the negative environmental impact of conventional mechanical-chemical technologies. At the time this grant was awarded 20 months ago, the authors had successfully engineered a small model plant, Arabidopsis thaliana, to use a highly modified bacterial mercuric ion reductase gene, merA9, to detoxify ionic mercury (Hg(II)), reducing it to much less toxic and volatile metallic Hg(0) (Rugh et al., 1996). Seeds from these plants germinate, grow, and set seed at normal growth rates on levels of Hg(II) that are lethal to normal plants. In assays on transgenic seedlings suspended in a solution of Hg(II), 10 ng of Hg(0) was evolved per min per mg wet weight of plant tissue. At that time, the authors had no information on expression of merA in any other plant species, nor had the authors tested merB in any plant. However, the results were so startlingly positive and well received that they clearly presaged a paradigm shift in the field of environmental remediation.'

  12. Improved Method for Recovery of mRNA from Aquatic Samples and Its Application to Detection of mer Expression

    PubMed Central

    Jeffrey, Wade H.; Nazaret, Sylvie; Von Haven, Robin

    1994-01-01

    Previously described methods for extraction of mRNA from environmental samples may preclude detecting transcripts from genes that were present in low abundance in aquatic bacterial communities. By combining a boiling sodium dodecyl sulfate-diethylpyrocarbonate lysis step with acid-guanidinium extraction, we improved recovery of target mRNA from both pure cultures and environmental samples. The most significant advantage of the new protocol is that it is easily adapted to yield high recovery of mRNA from 142-mm-diameter flat filters and high-capacity cartridge filters. The lysis and extraction procedures are more rapid than previously described methods, and many samples can be handled at once. RNA extracts have been shown to be free of contaminating DNA. The lysis procedure does not damage target mRNA sequences, and mRNA can be detected from fewer than 106 bacterial cells. We used the new method to examine transcripts of genes responsible for detoxification of mercurial compounds. Induction of merA (specifying mercuric reductase) transcripts in stationary-phase Pseudomonas aeruginosa containing Tn501 occurred within 60 s of HgCl2 addition and was proportional to the amount of Hg(II) added. The new technique also allowed the detection of merA transcripts from the microbial community of a mercury-contaminated pond (Reality Lake, Oak Ridge, Tenn.). Significant differences in merA transcript abundance were observed between different locations associated with the lake. The results indicate that the new method is simple and rapid and can be applied to the study of mer gene expression of aquatic communities in their natural habitats. PMID:16349274

  13. Mercury-mediated cross-resistance to tellurite in Pseudomonas spp. isolated from the Chilean Antarctic territory.

    PubMed

    Rodríguez-Rojas, F; Díaz-Vásquez, W; Undabarrena, A; Muñoz-Díaz, P; Arenas, F; Vásquez, C

    2016-01-01

    Mercury salts and tellurite are among the most toxic compounds for microorganisms on Earth. Bacterial mercury resistance is established mainly via mercury reduction by the mer operon system. However, specific mechanisms underlying tellurite resistance are unknown to date. To identify new mechanisms for tellurite detoxification we demonstrate that mercury resistance mechanisms can trigger cross-protection against tellurite to a group of Pseudomonads isolated from the Chilean Antarctic territory. Sequencing of 16S rRNA of four isolated strains resulted in the identification of three Pseudomonads (ATH-5, ATH-41 and ATH-43) and a Psychrobacter (ATH-62) bacteria species. Phylogenetic analysis showed that ATH strains were related to other species previously isolated from cold aquatic and soil environments. Furthermore, the identified merA genes were related to merA sequences belonging to transposons commonly found in isolated bacteria from mercury contaminated sites. Pseudomonas ATH isolates exhibited increased tellurite resistance only in the presence of mercury, especially ATH-43. Determination of the growth curves, minimal inhibitory concentrations and growth inhibition zones showed different tellurite cross-resistance of the ATH strains and suggested a correlation with the presence of a mer operon. On the other hand, reactive oxygen species levels decreased while the thiol content increased when the isolates were grown in the presence of both toxicants. Finally, qPCR determinations of merA, merC and rpoS transcripts from ATH-43 showed a synergic expression pattern upon combined tellurite and mercury treatments. Altogether, the results suggest that mercury could trigger a cell response that confers mercury and tellurite resistance, and that the underlying mechanism participates in protection against oxidative damage.

  14. Phytoremediation of ionic and methyl mercury pollution. 1997 annual progress report

    SciTech Connect

    Meagher, R.B.

    1997-01-01

    'The long-term goal of this research is to manipulate single-gene traits into plants, enabling them to process heavy metals and remediate heavy-metal pollution by resistance, sequestration, removal, and management of these contaminants (Meagher and Rugh, 1996; Meagher et al., 1997). The working hypothesis behind this proposal was that transgenic plants expressing both the bacterial organo mercury lyase (merB) and the mercuric ion reductase gene (merA) will (A) remove the mercury from polluted sites and (B) prevent methyl mercury from entering the food chain. The authors have had a very successful first year either testing aspects of this hypothesis directly or preparing material needed for future experiments. The results are outlined below under goals A and B, which are explicit in this hypothesis. There were less than 10% of the funds remaining in any category as projected in the first 12 month budget at the end of the first year, with the exception of the equipment category which had 25% of the funds remaining ({approximately} $8,000). Much of this remaining equipment money is being spent this week on a mercury vapor analyzer. It might be useful to remember that at the time this grant was awarded, the authors had successfully engineered a small model plant, Arabidopsis thalianat to use a highly modified bacterial mercuric ion reductase gene, merA9, to detoxify ionic mercury (Hg(II)), reducing it to Hg(0) (Rugh et al., 1996). Seeds from these plants germinate, grow, and set seed at normal growth rates on levels of Hg(II) that are lethal to normal plants. In assays on transgenic seedlings suspended in a solution of Hg(II), 10 ng of Hg(0) was evolved per min per mg wet weight of plant tissue. However, at that time, they had no information on expression of merA in any other plant species, nor had they expressed merB in any plant.'

  15. The Mars Exploration Rovers Entry Descent and Landing and the Use of Aerodynamic Decelerators

    NASA Technical Reports Server (NTRS)

    Steltzner, Adam; Desai, Prasun; Lee, Wayne; Bruno, Robin

    2003-01-01

    The Mars Exploration Rovers (MER) project, the next United States mission to the surface of Mars, uses aerodynamic decelerators in during its entry, descent and landing (EDL) phase. These two identical missions (MER-A and MER-B), which deliver NASA s largest mobile science suite to date to the surface of Mars, employ hypersonic entry with an ablative energy dissipating aeroshell, a supersonic/subsonic disk-gap-band parachute and an airbag landing system within EDL. This paper gives an overview of the MER EDL system and speaks to some of the challenges faced by the various aerodynamic decelerators.

  16. Defining the Molecular-Cellular-Field Continuum of Mercury Detoxification

    SciTech Connect

    Miller, Susan M.

    2014-09-04

    Hg is of special interest to DOE due to past use at the Oak Ridge Reservation (ORR). Its facile redox [Hg2+/0] chemistry, bonding to carbon [e.g. MeHg+] and unique physical properties [e.g., Hg0 volatility] underlie a complex global Hg cycle involving biotic and abiotic chemical and physical transport and transformations in soils, sediments, waterways and the atmosphere. Facultative and anaerobic bacteria make MeHg+, which is neurotoxic to wildlife and humans. Sustainable stewardship requires eliminating both MeHg+ and even more toxic Hg2+, which is also the substrate for methylation. The proteins encoded by the mer locus in aerobic and facultative mercury resistant (HgR) bacteria convert soil or waterborne Hg2+ or MeHg+ to less toxic, gaseous Hg0. HgR microbes live in highly Hg-contaminated sites and depress MeHg+ formation >500-fold in such zones. So, enhancing the capacity of natural HgR microbes to remove Hg2+/MeHg+ from wetlands and waterways is a logical component of contaminated site stewardship. To apply enhancement in the field requires knowing how the HgR pathway works including the metabolic demands it makes on the cell, i.e., the entire cell is the relevant catalytic unit. HgR loci occur in metabolically diverse bacteria and unique mer-host co-evolution has been found. In this project we extended our previous studies of mer enzymes in γ-proteobacteria, which are abundant in high Hg areas of the ORR to include studies of mer enzymes from HgR α-proteobacteria and HgR actinobacteria, which also increase in the high Hg regions of the ORR. Specifically, we (1) examined interactions between structural compoenents of MerA and MerB enzymes from γ-proteobacteria, (2) investigated effects of mutations on kinetic efficiency of Hg2+ reduction by γ-proteobacterial MerA, (3) cloned and performed initital characterization of MerA and MerB enzymes from Streptomyces lividans, an actinobacterium, (4) cloned and performed initial characterization of a fused Mer

  17. MGS and Odyssey - relay satellites for the MER mission

    NASA Technical Reports Server (NTRS)

    Esposito, Pasquale B.; Bhat, R.; Demeak, S.; Ardalan, S.; Breeden, J.; Helfrich, C.; Jefferson, D.; Stauch, J.

    2004-01-01

    Both Mars Global Surveyor (MGS) and Odyssey are currently in low altitude, nearly circular and highly inclined orbits about Mars. Thus, they are available adn compartible to serve as relay satellites for the Mars Exploration Rovers (MER) mission. Consequently, the MER project developed requirements for MGS to be overhead for MER-A (Spirit) at Gusev crater, at maximum elevation, mudway between lander separation and initial touchdown; in time, this was specified as 01/04/04. 04:24:55 UTC/SCET with a 30 sec tolerance.

  18. Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments.

    PubMed

    Lage, Melissa D; Reed, Heather E; Weihe, Claudia; Crain, Caitlin M; Martiny, Jennifer B H

    2010-07-01

    Ammonia oxidation is a central process in the nitrogen cycle. Particularly in marine and estuarine environments, few experiments have been conducted to tease apart the factors influencing their abundance and composition. To investigate the effect of nitrogen and phosphorus availability on ammonia-oxidizing bacteria (AOB), we conducted a nutrient enrichment experiment in a Maine salt marsh and sampled sediment communities in three seasons over 2 years. We assessed community composition using terminal restriction fragment length polymorphism analysis and sequencing of cloned fragments of the ammonia monooxygenase (amoA) gene. Almost all of the amoA sequences fell within the marine and estuarine-specific Nitrosospira-like clade. Applied separately, nitrogen and phosphorus significantly altered AOB composition; however, together the nutrients had an interactive effect, and composition did not change. In contrast, nutrient enrichment did not alter AOB abundance. Furthermore, the response of AOB composition to nutrient enrichment varied over time. We conclude that closely related taxa within the marine/estuarine-specific Nitrosospira-like clade vary in their preference for nutrient concentrations, and this preference may depend on other temporally variable abiotic factors. Finally, AOB composition was highly variable within and across years even in untreated plots. Further studies are needed to test how these different aspects of compositional variability in AOB communities influence nitrogen cycling.

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

    PubMed Central

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

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep. PMID:26284035

  20. Short-term effects of TiO2, CeO2, and ZnO nanoparticles on metabolic activities and gene expression of Nitrosomonas europaea.

    PubMed

    Yu, Ran; Fang, Xiaohua; Somasundaran, Ponisseril; Chandran, Kartik

    2015-06-01

    Nanosized TiO2 (n-TiO2), CeO2 (n-CeO2), and ZnO (n-ZnO) and bulk ZnO were chosen for a 4-h exposure study on a model ammonia oxidizing bacterium, Nitrosomonas europaea. n-ZnO displayed the most serious cytotoxicity while n-TiO2 was the least toxic one. The change of cell morphologies, the retardance of specific oxygen uptake rates and ammonia oxidation rates, and the depression of amoA gene expressions under NP stresses were generally observed when the cell densities and membrane integrities were not significantly impaired yet. The TEM imaging and the synchrotron X-ray fluorescence microscopy of the NPs impacted cells revealed the increase of the corresponding intracellular Ti, Ce or Zn contents and suggested the intracellular NP accumulation. The elevation of intracellular S contents accompanied with higher K contents implied the possible activation of thiol-containing glutathione and thioredoxin production for NP stress alleviation. The NP cytotoxicity was not always a function of NP concentration. The 200 mg L(-1) n-TiO2 or n-CeO2 impacted cells displayed the similar ammonia oxidation activities but higher amoA gene expression levels than the 20 mg L(-1) NPs impacted ones. Such phenomenon further indicated the possible establishment of an anti-toxicity mechanism in N. europaea at the genetic level to redeem the weakened AMO activities along with the NP aggregation effects.

  1. 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.

  2. Nitrous Oxide Emissions from Ephemeral Wetland Soils are Correlated with Microbial Community Composition.

    PubMed

    Ma, Wai K; Farrell, Richard E; Siciliano, Steven D

    2011-01-01

    Nitrous oxide (N(2)O) is a greenhouse gas with a global warming potential far exceeding that of CO(2). Soil N(2)O emissions are a product of two microbially mediated processes: nitrification and denitrification. Understanding the effects of landscape on microbial communities, and the subsequent influences of microbial abundance and composition on the processes of nitrification and denitrification are key to predicting future N(2)O emissions. The objective of this study was to examine microbial abundance and community composition in relation to N(2)O associated with nitrification and denitrification processes over the course of a growing season in soils from cultivated and uncultivated wetlands. The denitrifying enzyme assay and [Formula: see text] pool dilution methods were used to compare the rates of denitrification and nitrification and their associated N(2)O emissions. Functional gene composition was measured with restriction fragment length polymorphism profiles and abundance was measured with quantitative polymerase chain reaction. The change in denitrifier nitrous oxide reductase gene (nosZ) abundance and community composition was a good predictor of net soil N(2)O emission. However, neither ammonia oxidizing bacteria ammonia monooxygenase (bacterial amoA) gene abundance nor composition predicted nitrification-associated-N(2)O emissions. Alternative strategies might be necessary if bacterial amoA are to be used as predictive in situ indicators of nitrification rate and nitrification-associated-N(2)O emission.

  3. Enhanced long-term ammonium removal and its ranked contribution of microbial genes associated with nitrogen cycling in a lab-scale multimedia biofilter.

    PubMed

    Wang, Honglei; Ji, Guodong; Bai, Xueyuan

    2015-11-01

    The multimedia biofilter achieved high and stable removal efficiencies for chemical oxygen demand (COD, 62-98%) and NH4(+) (68-98%) without costly aeration. Results revealed that lower CL (less than 13.9gCOD/m(3)d) and ACL (less than 2.8gNH4(+)-N/m(3)d) or a C/N ratio exceeding five was required to reduce NO3(-)-N accumulation and NO/N2O emission. Integrated analyses indicated that the coupling of simultaneous nitrification, anammox and denitrification processes (SNAD) were the primary reason accounted for the enhanced NH4(+)-N treatment performance. NH4(+)-N removal pathways can be ranked as follows: nitrification (amoA, archaeal) (54.6%)>partial denitrification (nirS, nirK) and anammox (37.8%)>anammox and partial denitrification (narG, napA) (12.6%). Specifically, NH4(+)-N removal was significantly inhibited by NO2(-)-N accumulation in the system (-21.6% inhibition). Results from stepwise regression analysis suggested that the NH4(+) removal rate was collectively controlled by amoA, archaeal, anammox, nirS, nirK, narG and napA.

  4. Phylogenetic Diversity of Archaea and the Archaeal Ammonia Monooxygenase Gene in Uranium Mining-Impacted Locations in Bulgaria

    PubMed Central

    Radeva, Galina; Kenarova, Anelia; Bachvarova, Velina; Popov, Ivan; Selenska-Pobell, Sonja

    2014-01-01

    Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity. PMID:24711725

  5. Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe.

    PubMed

    Zhang, Cuijing; Shen, Jupei; Sun, Yifei; Wang, Juntao; Zhang, Limei; Yang, Zhongling; Han, Hongyan; Wan, Shiqiang; He, Jizheng

    2017-03-15

    Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially-mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition. Only the abundance of ammonia-oxidizing bacteria significantly increased by nitrogen addition and decreased by watering. The interactions of watering × warming on the bacterial amoA community and warming × nitrogen addition on the nosZ community were found. Redundancy analysis indicated that the ammonia-oxidizing archaeal community was affected by total N and total carbon, while the community of bacterial amoA and nosZ were significantly affected by soil pH. According to a structural equation modeling analysis, climate change influenced net primary production indirectly by altering microbial abundance and activities. These results indicated that microbial responses to the combination of chronic global change tend to be smaller than expected from single-factor global change manipulations.

  6. Epilithic biofilms as hotspots of in-stream nitrification in a high N loaded urban stream

    NASA Astrophysics Data System (ADS)

    Bernal, S.; Merbt, S. N.; Ribot, M.; Casamayor, E. O.; Martí Roca, E.

    2015-12-01

    Nitrification, the oxidation of ammonia to nitrate, is one of the most important biogeochemical processes in high nitrogen loaded urban streams. The first rate-limiting step of the nitrification process is carried out by ammonia-oxidizing (AO) archaea (AOB) and bacteria (AOB) that live in stream sediments and epilithic biofilms. Yet, the relative contribution of these two stream habitats to whole-reach nitrification is largely unknown. We tested the well-established idea that whole-reach nitrification is mainly driven by AO present in hyporheic sediments because of their relative high active surface area compared to the thin epilithic biofilm interface. To do so, we examined substrata-specific nitrification rates and AO transcripts abundance (amoA gene) in mesocosms and scaled data to whole reach. Further, we compared the scaled data to in situ whole-reach nitrification rates and amoA transcript and gene abundances in a high N loaded urban stream downstream of a waste water treatment plant effluent. Against expectations, whole-reach in-stream nitrification was mainly driven by AOB embedded in biofilms growing on the sediment-facing side (> 60%) and light-exposed side (20%) of stream cobbles. Hyporheic sediments, which were mainly colonized by AOA, accounted for 11% of in situ whole-reach nitrification. Our study points epilithic biofilms as hot spots of nitrification within urban stream ecosystems.

  7. Community shift of ammonia-oxidizing bacteria along an anthropogenic pollution gradient from the Pearl River Delta to the South China Sea.

    PubMed

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

    2012-04-01

    The phylogenetic diversity and abundance of ammonia-oxidizing beta-proteobacteria (beta-AOB) was analyzed along an anthropogenic pollution gradient from the coastal Pearl River Delta to the South China Sea using the ammonia monooxygenase subunit A (amoA) gene. Along the gradient from coastal to the open ocean, the phylogenetic diversity of the dominant genus changed from Nitrosomonas to Nitrosospira, indicating the niche specificity by these two genera as both salinity and anthropogenic influence were major factors involved. The diversity of bacterial amoA gene was also variable along the gradient, with the highest in the deep-sea sediments, followed by the marshes sediments and the lowest in the coastal areas. Within the Nitrosomonas-related clade, four distinct lineages were identified including a putative new one (A5-16) from the different sites over the large geographical area. In the Nitrosospira-related clade, the habitat-specific lineages to the deep-sea and coastal sediments were identified. This study also provides strong support that Nitrosomonas genus, especially Nitrosomonas oligotropha lineage (6a) could be a potential bio-indicator species for pollution or freshwater/wastewater input into coastal environments. A suite of statistical analyses used showed that water depth and temperature were major factors shaping the community structure of beta-AOB in this study area.

  8. 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.

  9. Differential response of nonadapted ammonia-oxidising archaea and bacteria to drying-rewetting stress.

    PubMed

    Thion, Cécile; Prosser, James I

    2014-11-01

    Climate change is expected to increase the frequency of severe drought events followed by heavy rainfall, which will influence growth and activity of soil microorganisms, through osmotic stress and changes in nutrient concentration. There is evidence of rapid recovery of processes and adaptation of communities in soils regularly experiencing drying/rewetting and lower resistance and resilience in nonadapted soils. A microcosm-based study of ammonia-oxidising archaea (AOA) and bacteria (AOB), employing a grassland soil that rarely experiences drought, was used to test this hypothesis and also whether AOB were more resistant and resilient, through greater tolerance of high ammonia concentrations produced during drought and rewetting. Treated soils were dried, incubated for 3 weeks, rewetted, incubated for a further 3 weeks and compared to untreated soils, maintained at a constant moisture content. Nitrate accumulation and AOA and AOB abundance (abundance of respective amoA genes) and community composition (DGGE analysis of AOA amoA and AOB 16S rRNA genes) were poorly adapted to drying-rewetting. AOA abundance and community composition were less resistant than AOB during drought and less resilient after rewetting, at times when ammonium concentration was higher. Data provide evidence for poor adaptation of microbial communities and processes to drying-rewetting in soils with no history of drought and indicate niche differentiation of AOA and AOB associated with high ammonia concentration.

  10. Nitrous Oxide Emissions from Ephemeral Wetland Soils are Correlated with Microbial Community Composition

    PubMed Central

    Ma, Wai K.; Farrell, Richard E.; Siciliano, Steven D.

    2011-01-01

    Nitrous oxide (N2O) is a greenhouse gas with a global warming potential far exceeding that of CO2. Soil N2O emissions are a product of two microbially mediated processes: nitrification and denitrification. Understanding the effects of landscape on microbial communities, and the subsequent influences of microbial abundance and composition on the processes of nitrification and denitrification are key to predicting future N2O emissions. The objective of this study was to examine microbial abundance and community composition in relation to N2O associated with nitrification and denitrification processes over the course of a growing season in soils from cultivated and uncultivated wetlands. The denitrifying enzyme assay and N15O3− pool dilution methods were used to compare the rates of denitrification and nitrification and their associated N2O emissions. Functional gene composition was measured with restriction fragment length polymorphism profiles and abundance was measured with quantitative polymerase chain reaction. The change in denitrifier nitrous oxide reductase gene (nosZ) abundance and community composition was a good predictor of net soil N2O emission. However, neither ammonia oxidizing bacteria ammonia monooxygenase (bacterial amoA) gene abundance nor composition predicted nitrification-associated-N2O emissions. Alternative strategies might be necessary if bacterial amoA are to be used as predictive in situ indicators of nitrification rate and nitrification-associated-N2O emission. PMID:21712943

  11. pH-dominated niche segregation of ammonia-oxidising microorganisms in Chinese agricultural soils.

    PubMed

    Baolan, Hu; Shuai, Liu; Wei, Wang; Lidong, Shen; Liping, Lou; Weiping, Liu; Guangming, Tian; Xiangyang, Xu; Ping, Zheng

    2014-10-01

    Ammonia-oxidising archaea (AOA) are increasingly recognised as the primary mediators of soil ammonia oxidation, particularly in acidic soils. To explore the niche segregation of AOA and ammonia-oxidising bacteria (AOB) and the potential effect of this segregation on nitrification rates and the nitrogen cycle in Chinese agricultural soils, AOA and AOB amoA gene databases were established, and 454 high-throughput sequencing was used to investigate the key factors leading to the niche segregation of these two types of microorganisms. qPCR results demonstrated that there were more functional genes for AOA than for AOB in most of the soils. AOA diversity was higher than AOB diversity in most of the soils with AOA operational taxonomic units (OTU) numbers ranging from 40 to 169 and AOB OTU numbers ranging from 18 to 105. pH was the most important factor influencing the community structure of AOA (P < 0.01) and AOB (P < 0.05), and acidophilic AOA (i.e. Nitrosotalea-related sequences) were dominant in soils with pH values below 6.0. In addition, AOA amoA gene copy numbers were significantly positively correlated with pH (P < 0.05), the ratio of AOA OTU numbers/AOB OTU numbers was significantly negatively correlated with pH (P < 0.05), and the percentage of sequences represented by the Nitrosotalea cluster was significantly negatively correlated with pH (P < 0.01).

  12. Strong influence of medium pH condition on gas-phase biofilter ammonia removal, nitrous oxide generation and microbial communities.

    PubMed

    Yang, Liangcheng; Wang, Xinlei; Funk, Ted L

    2014-01-01

    Effects of pH on gas-phase biofilter performance including NH3 removal efficiency (RE), N2O generation, and microbial communities of ammonia oxidizers and denitrifies, are examined. A two-step experiment was carried out on four biofilters for 130 days. In step 1 with pH 8.0, NH3 REs were 85-95% and N2O concentrations were 0.1-0.4 ppm. In step 2, pH was adjusted to 4.5, 6.0, 8.0, and 9.5 in four biofilters, respectively. The acidified biofilters showed higher NH3 REs than the alkalized biofilters. N2O concentration in biofilters with pH 4.5 and 6.0 was increased to 1.5 and 0.5 ppm, respectively, while no change in the alkalized biofilters. Comparing to communities in step 1, the amoA and nosZ structures were altered when pH was changed to 4.5 and 6.0, but not at 9.5. Abundance of amoA was reduced at pH 4.5, while nosZ abundance was increased with considerably less changes in acidified biofilters compared to alkalized biofilters.

  13. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions.

    PubMed

    Laanbroek, Hendrikus J; Keijzer, Rosalinde M; Verhoeven, Jos T A; Whigham, Dennis F

    2013-01-01

    In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.

  14. Elucidation of major contributors involved in nitrogen removal and transcription level of nitrogen-cycling genes in activated sludge from WWTPs

    PubMed Central

    Che, You; Liang, Peixin; Gong, Ting; Cao, Xiangyu; Zhao, Ying; Yang, Chao; Song, Cunjiang

    2017-01-01

    We investigated nitrogen-cycle bacterial communities in activated sludge from 8 municipal wastewater treatment plants (WWTPs). Redundancy analyses (RDA) showed that temperature was the most significant driving force in shaping microbial community structure, followed by influent NH4+ and total nitrogen (TN). The diversity of ammonia oxidizing and nitrite reducing bacteria were investigated by the construction of amoA, nirS and nirK gene clone libraries. Phylogenetic analysis indicated that Thauera and Mesorhizobium were the predominant nitrite reducing bacteria, and Nitrosomonas was the only detected ammonia oxidizing bacteria in all samples. Quantification of transcription level of nirS and nirK genes indicated that nirS-type nitrite reducing bacteria played the dominant roles in nitrite reduction process. Transcription level of nirS gene positively correlated with influent NH4+ and TN significantly, whereas inversely linked with hydraulic retention time. Temperature had a strong positive correlation to transcription level of amoA gene. Overall, this study deepened our understanding of the major types of ammonia oxidizing and nitrite reducing bacteria in activated sludge of municipal WWTPs. The relationship between transcription level of nitrogen-cycle genes and operational or environmental variables of WWTPs revealed in this work could provide guidance for optimization of operating parameters and improving the performance of nitrogen removal. PMID:28294196

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

    PubMed

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

    2015-01-01

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

  16. Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate.

    PubMed

    Gabarró, J; Hernández-Del Amo, E; Gich, F; Ruscalleda, M; Balaguer, M D; Colprim, J

    2013-12-01

    This study investigates the microbial community dynamics in an intermittently aerated partial nitritation (PN) SBR treating landfill leachate, with emphasis to the nosZ encoding gene. PN was successfully achieved and high effluent stability and suitability for a later anammox reactor was ensured. Anoxic feedings allowed denitrifying activity in the reactor. The influent composition influenced the mixed liquor suspended solids concentration leading to variations of specific operational rates. The bacterial community was low diverse due to the stringent conditions in the reactor, and was mostly enriched by members of Betaproteobacteria and Bacteroidetes as determined by 16S rRNA sequencing from excised DGGE melting types. The qPCR analysis for nitrogen cycle-related enzymes (amoA, nirS, nirK and nosZ) demonstrated high amoA enrichment but being nirS the most relatively abundant gene. nosZ was also enriched from the seed sludge. Linear correlation was found mostly between nirS and the organic specific rates. Finally, Bacteroidetes sequenced in this study by 16S rRNA DGGE were not sequenced for nosZ DGGE, indicating that not all denitrifiers deal with complete denitrification. However, nosZ encoding gene bacteria was found during the whole experiment indicating the genetic potential to reduce N2O.

  17. Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea.

    PubMed

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

    2011-11-01

    In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA and beta-AOB from the coastal marginal areas to the slope in the deep-sea was detected, while the OTU numbers of AOA amoA were more stable than those of the beta-AOB. The OTUs of beta-AOB increased with the distance from the coastal margin areas to the slope in the deep-sea. Beta-AOB showed lower diversity with dominant strains in a polluted area but higher diversity without dominant strains in a clean area. Moreover, the diversity of beta-AOB was correlated with pH values, while no noticeable relationships were established between AOA and physicochemical parameters. Beta-AOB was more sensitive to transect environmental variability and might be a potential indicator for environmental changes. Additionally, the surface sediments surveyed in the South China Sea harboured diverse and distinct AOA and beta-AOB phylotypes different from other environments, suggesting the endemicity of some nitrifying prokaryotes in the South China Sea.

  18. Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids.

    PubMed

    Coolen, Marco J L; Abbas, Ben; van Bleijswijk, Judith; Hopmans, Ellen C; Kuypers, Marcel M M; Wakeham, Stuart G; Sinninghe Damsté, Jaap S

    2007-04-01

    Within the upper 400 m at western, central and eastern stations in the world's largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alpha-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 microM including layers where previously anammox bacteria were described. Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared with the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 microM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared with the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.

  19. Phylogenetic diversity of archaea and the archaeal ammonia monooxygenase gene in uranium mining-impacted locations in Bulgaria.

    PubMed

    Radeva, Galina; Kenarova, Anelia; Bachvarova, Velina; Flemming, Katrin; Popov, Ivan; Vassilev, Dimitar; Selenska-Pobell, Sonja

    2014-01-01

    Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity.

  20. Abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a chinese shallow eutrophic urban lake

    PubMed Central

    Qiu, Shanlian; Chen, Guoyuan; Zhou, Yiyong

    2010-01-01

    The measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a Chinese shallow eutrophic urban lake (Lake Yuehu). Among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 105 cells g-1 dry weight) in sediment significantly. Furthermore, the diversity of ammonia-oxidizing bacteria were determined by means of PCR primers targeting the amoA gene with five gene libraries created and restriction pattern analysis. The 13 restriction patterns were recorded with 4 ones being common among all sampling sites. The 8 restriction patterns including 4 unique ones were found at the site with the highest NH4+ concentrations in interstitial water, while, there were only common patterns without unique ones at the site with the lowest NH4+ concentrations in interstitial water. Phylogenetic analysis showed that the amoA fragments retrieved belong to Nitrosomonas oligotropha & ureae lineage, N. europaea lineage, N. communis lineage and Nitrosospira lineage, most of which were affiliated with the genus Nitrosomonas. The N. oligotropha & ureae-like bacteria were the dominant species. Thus, the abundance and diversity of sediment AOB is closely linked to ammonium status in eutrophic lakes. PMID:24031484

  1. Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil.

    PubMed

    Yang, Liuqing; Zhang, Xiaojun; Ju, Xiaotang

    2017-02-24

    The linkage between N2O emissions and the abundance of nitrifier and denitrifier genes is unclear in the intensively managed calcareous fluvo-aquic soils of the North China Plain. We investigated the abundance of bacterial amoA for nitrification and narG, nirS, nirK, and nosZ for denitrification by in situ soil sampling to determine how the abundance of these genes changes instantly during N fertilization events and is related to high N2O emission peaks. We also investigated how long-term incorporated straw and/or manure affect(s) the abundance of these genes based on a seven-year field experiment. The overall results demonstrate that the long-term application of urea-based fertilizer and/or manure significantly enhanced the number of bacterial amoA gene copies leading to high N2O emission peaks after N fertilizer applications. These peaks contributed greatly to the annual N2O emissions in the crop rotation. A significant correlation between annual N2O emissions and narG, nirS, and nirK gene numbers indicates that the abundance of these genes is related to N2O emission under conditions for denitrification, thus partly contributing to the annual N2O emissions. These findings will help to draw up appropriate measures for mitigation of N2O emissions in this 'hotspot' region.

  2. Relationship of Temporal and Spatial Variabilities of Ammonia-Oxidizing Bacteria to Nitrification Rates in Monterey Bay, California

    PubMed Central

    O'Mullan, G. D.; Ward, B. B.

    2005-01-01

    Temporal and spatial dynamics of ammonia-oxidizing bacteria (AOB) were examined using genes encoding 16S rRNA and ammonia monooxygenase subunit A (AmoA) in Monterey Bay, Calif. Samples were collected from three depths in the water column on four dates at one mid-bay station. Diversity estimators for the two genes showed a strong positive correlation, indicating that overlapping bacterial populations had been sampled by both sets of clone libraries. Some samples that were separated by only 15 m in depth had less genetic similarity than samples that were collected from the same depth months apart. Clone libraries from the Monterey Bay AOB community were dominated by Nitrosospira-like sequences and clearly differentiated from the adjacent AOB community in Elkhorn Slough. Many Monterey Bay clones clustered with previously identified 16S rRNA and amoA groups composed entirely of marine sequences, supporting the hypothesis that these groups are specific to the marine environment and are dominant marine AOB. In addition, novel, phylogenetically distinct groups of AOB sequences were identified and compared to sequences in the database. Only one cluster of gammaproteobacterial AOB was detected using 16S rRNA genes. Although significant genetic variation was detected in AOB populations from both vertical and temporal samples, no significant correlation was detected between diversity and environmental variables or the rate of nitrification. PMID:15691919

  3. 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).

  4. Physiological and transcriptional responses of nitrifying bacteria exposed to copper in activated sludge.

    PubMed

    Ouyang, Fan; Zhai, Hongyan; Ji, Min; Zhang, Hongyang; Dong, Zhao

    2016-01-15

    Cu inhibition of gene transcription in ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were rarely studied simultaneously in activated sludge. In this study, the transcription of amoA (for AOB) and nxrB (for NOB), nitrification efficiencies, AOB and NOB respiratory rates, and Cu distribution were simultaneously investigated. Modeling the relationships among the aforementioned parameters revealed that in complex activated sludge systems, nitrification efficiency was an insensitive parameter for showing Cu inhibition. Respiration activities and gene transcription were sensitive to Cu and positively correlated with each other. The transcription of amoA and nxrB genes indicated that the Cu had different inhibitory effects on AOB and NOB. AOB were more susceptible to Cu toxicity than NOB. Moreover, the degree of Cu inhibition on ammonia oxidation was greater than on nitrite oxidation. The analysis and related modeling results indicate that the inhibitory actions of Cu on nitrifying bacteria could mainly be attributed to intracellular Cu. The findings from this study provide insight into the mechanism of Cu inhibition on nitrification in complex activated sludge systems.

  5. Variability of nitrifying communities in surface coastal waters of the Eastern South Pacific (∼36° S).

    PubMed

    Levipan, Héctor A; Molina, Verónica; Anguita, Cristóbal; Rain-Franco, Angel; Belmar, Lucy; Fernandez, Camila

    2016-08-03

    We report the seasonal and single-diurnal variability of potentially active members of the prokaryote community in coastal surface waters off central Chile and the relationship between nitrifiers and solar radiation by combining 16S cDNA-based pyrosequencing, RT-qPCR of specific gene markers for nitrifiers (amoA, for general AOA, AOA-A, AOA-B, Nitrosopumilus maritimus and beta-AOB; and 16S rRNA gene for Nitrospina-like NOB), and solar irradiance measurements. We also evaluated the effects of artificial UVA-PAR and PAR spectra on nitrifiers by RT-qPCR. All nitrifiers (except AOA-B ecotype) were detected via RT-qPCR but AOA was the only group detected by pyrosequencing. Results showed high variability in their transcriptional levels during the day which could be associated to sunlight intensity thresholds in winter although AOA and Nitrospina-like NOB transcript number were also potentially related with environmental substrate availability. Only N. maritimus amoA transcripts showed a significant negative correlation with solar irradiances in both periods. During spring-summer, Nitrospina transcripts decreased at higher sunlight intensities, whereas the opposite was found during winter under natural (in situ) and artificial light experiments. In summary, a nitrifying community with variable tolerance to solar radiation is responsible for daily nitrification, and was particularly diverse during winter in the study area.

  6. Elucidation of major contributors involved in nitrogen removal and transcription level of nitrogen-cycling genes in activated sludge from WWTPs

    NASA Astrophysics Data System (ADS)

    Che, You; Liang, Peixin; Gong, Ting; Cao, Xiangyu; Zhao, Ying; Yang, Chao; Song, Cunjiang

    2017-03-01

    We investigated nitrogen-cycle bacterial communities in activated sludge from 8 municipal wastewater treatment plants (WWTPs). Redundancy analyses (RDA) showed that temperature was the most significant driving force in shaping microbial community structure, followed by influent NH4+ and total nitrogen (TN). The diversity of ammonia oxidizing and nitrite reducing bacteria were investigated by the construction of amoA, nirS and nirK gene clone libraries. Phylogenetic analysis indicated that Thauera and Mesorhizobium were the predominant nitrite reducing bacteria, and Nitrosomonas was the only detected ammonia oxidizing bacteria in all samples. Quantification of transcription level of nirS and nirK genes indicated that nirS-type nitrite reducing bacteria played the dominant roles in nitrite reduction process. Transcription level of nirS gene positively correlated with influent NH4+ and TN significantly, whereas inversely linked with hydraulic retention time. Temperature had a strong positive correlation to transcription level of amoA gene. Overall, this study deepened our understanding of the major types of ammonia oxidizing and nitrite reducing bacteria in activated sludge of municipal WWTPs. The relationship between transcription level of nitrogen-cycle genes and operational or environmental variables of WWTPs revealed in this work could provide guidance for optimization of operating parameters and improving the performance of nitrogen removal.

  7. Effects of olive mill wastewater on soil carbon and nitrogen cycling.

    PubMed

    Tsiknia, Myrto; Tzanakakis, Vasileios A; Oikonomidis, Dimitris; Paranychianakis, Nikolaos V; Nikolaidis, Nikolaos P

    2014-03-01

    This study investigated the cycling of C and N following application of olive mill wastewater (OMW) at various rates (0, 42, 84, and 168 m(3)/ha). OMW stimulated respiration rate throughout the study period, but an increase in soil organic matter was observed only at the highest rate. Soil phenol content decreased rapidly within 2 weeks following application but neither phenol oxidase and peroxidase activity nor laccase gene copies could explain this response. Soil NH4 (+)-N content increased in response to OMW application rate, while an opposite trend observed for NO3 (-)-N, which attributed to immobilization. This decrease was in accordance with amoA gene copies of archaeal and bacterial ammonia oxidizers in the first days following OMW application. Afterwards, although amoA gene copies and potential nitrification rates recovered to values similar to or higher than those in the non-treated soils, NO3 (-)-N content did not change among the treatments. A corresponding increase in denitrifying gene copies (nirK, nirS, nosZ) during that period indicates that denitrification, stimulated by OMW application rate, was responsible for this effect; a hypothesis consistent with the decrease in total Kjeldahl nitrogen content late in the season. The findings suggest that land application of OMW is a promising practice for OMW management, even at rates approaching the soil water holding capacity.

  8. 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.

  9. 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

  10. Juvenile hormone enhances aversive learning performance in 2-day old worker honey bees while reducing their attraction to queen mandibular pheromone.

    PubMed

    McQuillan, H James; Nakagawa, Shinichi; Mercer, Alison R

    2014-01-01

    Previous studies have shown that exposing young worker bees (Apis mellifera) to queen mandibular pheromone (QMP) reduces their aversive learning performance, while enhancing their attraction to QMP. As QMP has been found to reduce the rate of juvenile hormone (JH) synthesis in worker bees, we examined whether aversive learning in 2-day old workers exposed to QMP from the time of adult emergence could be improved by injecting JH (10 µg in a 2 µl volume) into the haemolymph. We examined in addition, the effects of JH treatment on worker attraction to QMP, and on the levels of expression of amine receptor genes in the antennae, as well as in the mushroom bodies of the brain. We found that memory acquisition and 1-hour memory recall were enhanced by JH. In contrast, JH treatment reduced the bees' attraction towards a synthetic strip impregnated with QMP (Bee Boost). Levels of expression of the dopamine receptor gene Amdop1 were significantly lower in the mushroom bodies of JH-treated bees than in bees treated with vehicle alone (acetone diluted with bee ringer). Expression of the octopamine receptor gene, Amoa1, in this brain region was also affected by JH treatment, and in the antennae, Amoa1 transcript levels were significantly lower in JH-treated bees compared to controls. The results of this study suggest that QMP's effects on JH synthesis may contribute to reducing aversive learning performance and enhancing attraction to QMP in young worker bees.

  11. Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil

    NASA Astrophysics Data System (ADS)

    Yang, Liuqing; Zhang, Xiaojun; Ju, Xiaotang

    2017-02-01

    The linkage between N2O emissions and the abundance of nitrifier and denitrifier genes is unclear in the intensively managed calcareous fluvo-aquic soils of the North China Plain. We investigated the abundance of bacterial amoA for nitrification and narG, nirS, nirK, and nosZ for denitrification by in situ soil sampling to determine how the abundance of these genes changes instantly during N fertilization events and is related to high N2O emission peaks. We also investigated how long-term incorporated straw and/or manure affect(s) the abundance of these genes based on a seven-year field experiment. The overall results demonstrate that the long-term application of urea-based fertilizer and/or manure significantly enhanced the number of bacterial amoA gene copies leading to high N2O emission peaks after N fertilizer applications. These peaks contributed greatly to the annual N2O emissions in the crop rotation. A significant correlation between annual N2O emissions and narG, nirS, and nirK gene numbers indicates that the abundance of these genes is related to N2O emission under conditions for denitrification, thus partly contributing to the annual N2O emissions. These findings will help to draw up appropriate measures for mitigation of N2O emissions in this ‘hotspot’ region.

  12. Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil

    PubMed Central

    Yang, Liuqing; Zhang, Xiaojun; Ju, Xiaotang

    2017-01-01

    The linkage between N2O emissions and the abundance of nitrifier and denitrifier genes is unclear in the intensively managed calcareous fluvo-aquic soils of the North China Plain. We investigated the abundance of bacterial amoA for nitrification and narG, nirS, nirK, and nosZ for denitrification by in situ soil sampling to determine how the abundance of these genes changes instantly during N fertilization events and is related to high N2O emission peaks. We also investigated how long-term incorporated straw and/or manure affect(s) the abundance of these genes based on a seven-year field experiment. The overall results demonstrate that the long-term application of urea-based fertilizer and/or manure significantly enhanced the number of bacterial amoA gene copies leading to high N2O emission peaks after N fertilizer applications. These peaks contributed greatly to the annual N2O emissions in the crop rotation. A significant correlation between annual N2O emissions and narG, nirS, and nirK gene numbers indicates that the abundance of these genes is related to N2O emission under conditions for denitrification, thus partly contributing to the annual N2O emissions. These findings will help to draw up appropriate measures for mitigation of N2O emissions in this ‘hotspot’ region. PMID:28233823

  13. Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation.

    PubMed

    Galand, Pierre E; Lovejoy, Connie; Hamilton, Andrew K; Ingram, R Grant; Pedneault, Estelle; Carmack, Eddy C

    2009-04-01

    Evidence of microbial zonation in the open ocean is rapidly accumulating, but while the distribution of communities is often described according to depth, the other physical factors structuring microbial diversity and function remain poorly understood. Here we identify three different water masses in the North Water (eastern Canadian Arctic), defined by distinct temperature and salinity characteristics, and show that they contained distinct archaeal communities. Moreover, we found that one of the water masses contained an increased abundance of the archaeal alpha-subunit of the ammonia monooxygenase gene (amoA) and accounted for 70% of the amoA gene detected overall. This indicates likely differences in putative biogeochemical capacities among different water masses. The ensemble of our results strongly suggest that the widely accepted view of depth stratification did not explain microbial diversity, but rather that parent water masses provide the framework for predicting communities and potential microbial function in an Arctic marine system. Our results emphasize that microbial distributions are strongly influenced by oceanic circulation, implying that shifting currents and water mass boundaries resulting from climate change may well impact patterns of microbial diversity by displacing whole biomes from their historic distributions. This relocation could have the potential to establish a substantially different geography of microbial-driven biogeochemical processes and associated oceanic production.

  14. Comammox in drinking water systems.

    PubMed

    Wang, Yulin; Ma, Liping; Mao, Yanping; Jiang, Xiaotao; Xia, Yu; Yu, Ke; Li, Bing; Zhang, Tong

    2017-03-20

    The discovery of complete ammonia oxidizer (comammox) has fundamentally upended our perception of the global nitrogen cycle. Here, we reported four metagenome assembled genomes (MAGs) of comammox Nitrospira that were retrieved from metagenome datasets of tap water in Singapore (SG-bin1 and SG-bin2), Hainan province, China (HN-bin3) and Stanford, CA, USA (ST-bin4). Genes of phylogenetically distinct ammonia monooxygenase subunit A (amoA) and hydroxylamine dehydrogenase (hao) were identified in these four MAGs. Phylogenetic analysis based on ribosomal proteins, AmoA, hao and nitrite oxidoreductase (subunits nxrA and nxrB) sequences indicated their close relationships with published comammox Nitrospira. Canonical ammonia-oxidizing microbes (AOM) were also identified in the three tap water samples, ammonia-oxidizing bacteria (AOB) in Singapore's and Stanford's samples and ammonia-oxidizing archaea (AOA) in Hainan's sample. The comammox amoA-like sequences were also detected from some other drinking water systems, and even outnumbered the AOA and AOB amoA-like sequences. The findings of MAGs and the occurrences of AOM in different drinking water systems provided a significant clue that comammox are widely distributed in drinking water systems.

  15. Differential contributions of archaeal ammonia oxidizer ecotypes to nitrification in coastal surface waters.

    PubMed

    Smith, Jason M; Casciotti, Karen L; Chavez, Francisco P; Francis, Christopher A

    2014-08-01

    The occurrence of nitrification in the oceanic water column has implications extending from local effects on the structure and activity of phytoplankton communities to broader impacts on the speciation of nitrogenous nutrients and production of nitrous oxide. The ammonia-oxidizing archaea, responsible for carrying out the majority of nitrification in the sea, are present in the marine water column as two taxonomically distinct groups. Water column group A (WCA) organisms are detected at all depths, whereas Water column group B (WCB) are present primarily below the photic zone. An open question in marine biogeochemistry is whether the taxonomic definition of WCA and WCB organisms and their observed distributions correspond to distinct ecological and biogeochemical niches. We used the natural gradients in physicochemical and biological properties that upwelling establishes in surface waters to study their roles in nitrification, and how their activity--ascertained from quantification of ecotype-specific ammonia monooxygenase (amoA) genes and transcripts--varies in response to environmental fluctuations. Our results indicate a role for both ecotypes in nitrification in Monterey Bay surface waters. However, their respective contributions vary, due to their different sensitivities to surface water conditions. WCA organisms exhibited a remarkably consistent level of activity and their contribution to nitrification appears to be related to community size. WCB activity was less consistent and primarily constrained to colder, high nutrient and low chlorophyll waters. Overall, the results of our characterization yielded a strong, potentially predictive, relationship between archaeal amoA gene abundance and the rate of nitrification.

  16. 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.

  17. Microbial community on oceanic ferro-manganese crusts from Takuyo-Daigo Seamount and Ryusei Seamount

    NASA Astrophysics Data System (ADS)

    Nitahara, S.; Kato, S.; Yamagishi, A.

    2012-12-01

    Background and Purpose Iron and manganese oxide deposits are often found on deep seafloor. Rocks covered with these oxides are called ferro-manganese crusts (Mn crusts), and are ubiquitously distributed on deep seafloor (Rona 2003). Because Mn crusts contain rare metals such as Co, Pt and rare earth element, it can be resources in the future. Mn crusts and microbes on Mn crusts may contribute to material, especially carbon and nitrogen circulation between hydrosphere and lithosphere. Mechanism of Mn crust formation is not completely understood. Wang et al. propose a model that microorganisms associate with initial Mn mineral deposition (Wang et al., 2011). There is a possibility that microbes may contribute to formation of Mn crust relying on their ability to oxidize Fe and Mn. However, there is limited information about diversity, spatial distribution and abundance of microbes on Mn crust surface. Our purpose is to clarify microbial community composition, spatial distribution, diversity and abundance of microbes on Mn crusts collected from Takuyo-Daigo seamount and Ryusei seamount. Method We collected Mn crusts, sediments and ambient seawater from Takuyo-Daigo seamount at the depth of 1200 m, 1419 m, 2209 m and 2991 m during NT09-02 cruise in Feb 2009 and Ryusei seamount at the depth of 1194 m, 2079 m during KY11-02 in Feb 2011 with remotely operated vehicle Hyper-Dolphin (JAMSTEC). Genomic DNA was extracted from each sample using Fast DNA kit for soil (Qbiogene). Partial 16S rRNA gene and amoA gene were amplified by PCR with prokaryote-universal primer set (Uni516F-Uni1407R) and bacterial and archaeal amoA specific primer sets. PCR products were cloned. The nucleotide sequences of randomly selected clones were determined. We performed phylogenetic and statistical analysis to determine microbial community compositions, and estimated diversity indices. We also estimated the copy numbers of 16S rRNA and amoA genes of Bacteria and Archaea by quantitative PCR. Results

  18. Disulfide bond formation in the Escherichia coli cytoplasm: an in vivo role reversal for the thioredoxins.

    PubMed Central

    Stewart, E J; Aslund, F; Beckwith, J

    1998-01-01

    Cytoplasmic proteins do not generally contain structural disulfide bonds, although certain cytoplasmic enzymes form such bonds as part of their catalytic cycles. The disulfide bonds in these latter enzymes are reduced in Escherichia coli by two systems; the thioredoxin pathway and the glutathione/glutaredoxin pathway. However, structural disulfide bonds can form in proteins in the cytoplasm when the gene (trxB) for the enzyme thioredoxin reductase is inactivated by mutation. This disulfide bond formation can be detected by assessing the state of the normally periplasmic enzyme alkaline phosphatase (AP) when it is localized to the cytoplasm. Here we show that the formation of disulfide bonds in cytoplasmic AP in the trxB mutant is dependent on the presence of two thioredoxins in the cell, thioredoxins 1 and 2, the products of the genes trxA and trxC, respectively. Our evidence supports a model in which the oxidized forms of these thioredoxins directly catalyze disulfide bond formation in cytoplasmic AP, a reversal of their normal role. In addition, we show that the recently discovered thioredoxin 2 can perform many of the roles of thioredoxin 1 in vivo, and thus is able to reduce certain essential cytoplasmic enzymes. Our results suggest that the three most effective cytoplasmic disulfide-reducing proteins are thioredoxin 1, thioredoxin 2 and glutaredoxin 1; expression of any one of these is sufficient to support aerobic growth. Our results help to explain how the reducing environment in the cytoplasm is maintained so that disulfide bonds do not normally occur. PMID:9755155

  19. Adaptive Resistance and Differential Protein Expression of Salmonella enterica Serovar Enteritidis Biofilms Exposed to Benzalkonium Chloride▿

    PubMed Central

    Mangalappalli-Illathu, Anil K.; Korber, Darren R.

    2006-01-01

    The development of adaptive resistance of Salmonella enterica serovar Enteritidis ATCC 4931 biofilms following exposure to benzalkonium chloride (BC) either continuously (1 μg ml−1) or intermittently (10 μg ml−1 for 10 min daily) was examined. Biofilms adapted to BC over a 144-h period could survive a normally lethal BC challenge (500 μg ml−1 for 10 min) and then regrow, as determined by increases in biofilm thickness, total biomass, and the ratio of the viable biomass to the nonviable biomass. Exposure of untreated control biofilms to the lethal BC challenge resulted in biofilm erosion and cell death. Proteins found to be up-regulated following BC adaptation were those involved in energy metabolism (TpiA and Eno), amino acid and protein biosynthesis (WrbA, TrxA, RplL, Tsf, Tuf, DsbA, and RpoZ), nutrient binding (FruB), adaptation (CspA), detoxification (Tpx, SodB, and a probable peroxidase), and degradation of 1,2-propanediol (PduJ and PduA). A putative universal stress protein (YnaF) was also found to be up-regulated. Proteins involved in proteolysis (DegQ), cell envelope formation (RfbH), adaptation (UspA), heat shock response (DnaK), and broad regulatory functions (Hns) were found to be down-regulated following adaptation. An overall increase in cellular protein biosynthesis was deduced from the significant up-regulation of ribosomal subunit proteins, translation elongation factors, and amino acid biosynthesis protein and down-regulation of serine endoprotease. The cold shock response, stress response, and detoxification are suggested to play roles in the adaptive resistance of Salmonella serovar Enteritidis biofilms to BC. PMID:16940079

  20. Partitioning of the Linear Chromosome during Sporulation of Streptomyces coelicolor A3(2) Involves an oriC-Linked parAB Locus

    PubMed Central

    Kim, Hyun-Jin; Calcutt, Michael J.; Schmidt, Francis J.; Chater, Keith F.

    2000-01-01

    Candidate partitioning genes (parA and parB) for the linear chromosome of Streptomyces coelicolor were identified by DNA sequencing in a series of seven genes located between rnpA and trxA near the chromosomal replication origin. The most likely translation start point of parB overlapped the parA stop codon, suggestive of coregulation, and transcription analysis suggested that the two genes formed an operon. Deletion of part of parB had no effect on the growth or appearance of colonies but caused a deficiency in DNA partitioning during the multiple septation events involved in converting aerial hyphae into long chains of spores. At least 13% of spore compartments failed to inherit the normal DNA allocation. The same phenotype was obtained with a deletion removing a segment of DNA from both parA and parB. Reinforcing the idea of a special role for the par locus during sporulation, the stronger of two parAB promoters was greatly upregulated at about the time when sporulation septation was maximal in colonies. Three copies of a 14-bp inverted repeat (GTTTCACGTGAAAC) were found in or near the parAB genes, and at least 12 more identical copies were identified within 100 kb of oriC from the growing genome sequence database. Only one perfect copy of the 14-bp sequence was present in approximately 5 Mb of sequence available from the rest of the genome. The 14-bp sequence was similar to sequences identified as binding sites for Spo0J, a ParB homologue from Bacillus subtilis believed to be important for DNA partitioning (D. C.-H. Lin and A. D. Grossman, Cell 92:675–685, 1998). One of these sites encompassed the transcription start point of the stronger parA promoter. PMID:10671452

  1. Adaptive resistance and differential protein expression of Salmonella enterica serovar Enteritidis biofilms exposed to benzalkonium chloride.

    PubMed

    Mangalappalli-Illathu, Anil K; Korber, Darren R

    2006-11-01

    The development of adaptive resistance of Salmonella enterica serovar Enteritidis ATCC 4931 biofilms following exposure to benzalkonium chloride (BC) either continuously (1 microg ml(-1)) or intermittently (10 microg ml(-1) for 10 min daily) was examined. Biofilms adapted to BC over a 144-h period could survive a normally lethal BC challenge (500 microg ml(-1) for 10 min) and then regrow, as determined by increases in biofilm thickness, total biomass, and the ratio of the viable biomass to the nonviable biomass. Exposure of untreated control biofilms to the lethal BC challenge resulted in biofilm erosion and cell death. Proteins found to be up-regulated following BC adaptation were those involved in energy metabolism (TpiA and Eno), amino acid and protein biosynthesis (WrbA, TrxA, RplL, Tsf, Tuf, DsbA, and RpoZ), nutrient binding (FruB), adaptation (CspA), detoxification (Tpx, SodB, and a probable peroxidase), and degradation of 1,2-propanediol (PduJ and PduA). A putative universal stress protein (YnaF) was also found to be up-regulated. Proteins involved in proteolysis (DegQ), cell envelope formation (RfbH), adaptation (UspA), heat shock response (DnaK), and broad regulatory functions (Hns) were found to be down-regulated following adaptation. An overall increase in cellular protein biosynthesis was deduced from the significant up-regulation of ribosomal subunit proteins, translation elongation factors, and amino acid biosynthesis protein and down-regulation of serine endoprotease. The cold shock response, stress response, and detoxification are suggested to play roles in the adaptive resistance of Salmonella serovar Enteritidis biofilms to BC.

  2. [Prokaryotic expression and characterization of two recombinant receptor-binding domain(RBD) proteins of human coronavirus NL63(HcoV-NL63)].

    PubMed

    Chang, Hui; Yi, Yao; Zhao, Min; Zhou, Wei-Min; Zhao, Guo-Xia; Wang, Hui-Juan; Bi, Sheng-Li; Gao, Ji-Min; Liu, Bing; Tan, Wen-Jie

    2013-03-01

    The receptor-binding domain(RBD) protein of HCoV-NL63 is a major target in the development of diagnostic assay and vaccine, it has a pivotal role in receptor attachment, viral entry and membrane fusion. In this study, we prepared 2 purified recombinant HCoV-NL63 RBD proteins using in E. coli system and identified the proteins by Western blotting. We first optimized codon and synthesized the RL (232-684aa)coding gene, then amplified the RL or RS(476-616aa) coding gene via PCR using different primers . The RL or RS coding gene was cloned into the pM48 expression vector fused with TrxA tag. The RBD (RL and RS) of HCoV-NL63 were expressed majorly as inclusion body when expressed in E. coli BL21pLys S under different conditions. The expressed products were purified by affinity chromatography then analyzed by SDS-PAGE and Western blotting. Our results showed that the recombinant RBD proteins were maximally expressed at 37 degrees C with 0. 8mM IPTG induction for 4h. RL or RS protein with 95 % purity was obtained and reacted positively with anti-sera from mice immunized with the recombinant vaccinia virus (Tiantan strain) in which HCoV-NL63 RL or RS protein was expressed. In conclusion, the purified recombinant RBD proteins(RL and RS)derived from E. coli were first prepared in China and they might provide a basis for further exploring biological role and vaccine development of HCoV-NL63.

  3. Selenite Protection of Tellurite Toxicity Toward Escherichia coli

    PubMed Central

    Vrionis, Helen A.; Wang, Siyuan; Haslam, Bronwyn; Turner, Raymond J.

    2015-01-01

    In this work the influence of selenite on metal resistance in Escherichia coli was examined. Both synergistic and antagonistic resistance and toxicities were found upon co exposure with selenite. In wild type cells co-exposure to selenite had little effect on arsenic resistance, decreased resistance to cadmium and mercury but led to a dramatically increased resistance to tellurite of 32-fold. Due to the potential importance of thiol chemistry in metal biochemistry, deletion strains in γ-glutamylcysteine synthetase (key step in glutathione biosynthesis, encoded by gshA), thioredoxin (trxA), glutaredoxin (grxA), glutathione oxidoreductase (gor), and the periplasmic glutathione transporter (cydD) were also evaluated for resistance to various metals in the presence of selenite. The protective effect of selenite on tellurite toxicity was seen in several of the mutants and was pronounced in the gshA mutant were resistance to tellurite was increased up to 1000-fold relative to growth in the absence of selenite. Thiol oxidation studies revealed a faster rate of loss of reduced thiol content in the cell with selenite than with tellurite, indicating differential thiol reactivity. Selenite addition resulted in reactive oxygen species (ROS) production equivalent to levels associated with H2O2 addition. Tellurite addition resulted in considerably lower ROS generation while vanadate and chromate treatment did not increase ROS production above that of background. This work shows increased resistance toward most oxyanions in mutants of thiol redox suggesting that metalloid reaction with thiol components such as glutathione actually enhances toxicity of some metalloids. PMID:26732755

  4. Mars Exploration Rover surface mission flight thermal performance

    NASA Technical Reports Server (NTRS)

    Novak, Keith S.; Phillips, Charles J.; Sunada, Eric T.; Kinsella, Gary M.

    2005-01-01

    NASA launched two rovers in June and July of 2003 as a part of the Mars Exploration Rover (MER) project. MER-A (Spirit) landed on Mars in Gusev Crater at 15 degrees South latitude and 175 degree East longitude on January 4, 2004 (Squyres, et al., Dec. 2004)). MER-B (Opportunity) landed on Mars in Terra Meridiani at 2 degrees South latitude and 354 degrees East longitude on January 25, 2004 (Squyres, et al., August 2004) Both rovers have well exceeded their design lifetime (90 Sols) by more than a factor of 4. Spirit and Opportunity are still healthy and continue to execute their roving science missions at the time of this writing. This paper discusses rover flight thermal performance during the surface missions of both vehicles, covering roughly the time from the MER-A landing in late Southern Summer (Ls = 328, Sol 1A) through the Southern Winter solstice (Ls = 90, Sol 255A) to nearly Southern Vernal equinox (Ls = 160 , Sol 398A).

  5. Displacement of permanent GPS stations during the Lana (July 2001) earthquake

    NASA Astrophysics Data System (ADS)

    Massironi, M.; Caporali, A.

    2003-04-01

    The Mw 4.7, Mo=1.2*10^16 Nm (CSEM) Lana earthquake occurred on July 17, 2001. The epicenter was located in Northern Italy, near Merano (South Tyrol), by 40 seismic stations. The permanent GPS stations MERA, BZRG and TREN were operating within 1, 30 and 50 km respectively from the epicenter. The changes in position of those stations in a two year interval centered at the seismic event could be accurately reconstructed with time resolution of one week to one day using state of the art software (Bernese 4.2, IGS/EUREF processing standards), as these stations are part of the Permanent GPS network of Italy, which is maintained on a weekly basis. The high resolution GPS data show that the coseismic displacement at MERA is fully consistent with the fault plane solution, and that there exist differential velocities and coordinate glitches at epochs different from that of the quake. Although one cannot exclude other, non geophysical reasons for such events in time series of otherwise very stable stations, we consider the occasional deviations from linearity in the time series as indicative of ground motion, and attempt to correlate them with local seismicity, structural geology and with the level of the groundwater.

  6. Revision of the genus Vanenga Schaus, 1928 (Lepidoptera, Mimallonoidea, Mimallonidae) with the description of a new species

    PubMed Central

    St. Laurent, Ryan A.; Herbin, Daniel

    2017-01-01

    Abstract Vanenga Schaus, 1928, like many other Mimallonidae genera being revised in recent years, has not been studied since Schaus (1928) in his revision of the family. This currently monotypic genus is entirely restricted to South America, with no known representatives in Central or North America. Prior to this work, Schaus (1928) and subsequent lists of the family (Gaede 1931, Becker 1996) have mentioned the single species Vanenga mera (Dognin, 1924) described from the Brazilian Amazon (Pará state). In Schaus (1928) this species is listed as occurring in both Amazonia and southeastern Brazil. In completing the present article, numerous “type” specimens have been discovered bearing three different manuscript names associated with the populations of southeastern Brazil and adjacent areas. Despite the fact that these names were written on various labels, the absence of any published descriptions results in them being unavailable (ICZN 1999). Therefore, this distinct southern South American species is now officially recognized and formally described, as well as providing a much more thorough distribution for both Vanenga species, including many new records for Vanenga mera. PMID:28144186

  7. The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study

    DOE PAGES

    Rothenberg, Sarah E.; Keiser, Sharon; Ajami, Nadim J.; ...

    2016-02-01

    The mechanisms by which gut microbiota contribute to methylmercury metabolism remain unclear. Among a cohort of pregnant mothers, the main objectives of our pilot study were to determine 1) associations between gut microbiota and mercury concentrations in biomarkers (stool, hair and cord blood) and 2) the contributions of gut microbial mercury methylation/demethylation to stool methylmercury. Moreover, for pregnant women (36-39 weeks gestation, n=17) donated hair and stool specimens, and cord blood was collected for a subset (n=7). The diversity of gut microbiota was determined using 16S rRNA gene profiling (n=17). For 6 stool samples with highest/lowest methylmercury concentrations, metagenomic wholemore » genome shotgun sequencing was employed to search for one mercury methylation gene (hgcA), and two mer operon genes involved in methylmercury detoxification (merA and merB). There were seventeen bacterial genera that were significantly correlated (increasing or decreasing) with stool methylmercury, stool inorganic mercury, or hair total mercury; however, aside from one genus, there was no overlap between biomarkers. No definitive matches for hgcA or merB, while merA were detected at low concentrations in all six samples. Proportional differences in stool methylmercury were not likely attributed to gut microbiota through methylation/demethylation. Gut microbiota potentially altered methylmercury metabolism using indirect pathways.« less

  8. The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study

    SciTech Connect

    Rothenberg, Sarah E.; Keiser, Sharon; Ajami, Nadim J.; Wong, Matthew C.; Gesell, Jonathan; Petrosino, Joseph F.; Johs, Alexander

    2016-02-01

    The mechanisms by which gut microbiota contribute to methylmercury metabolism remain unclear. Among a cohort of pregnant mothers, the main objectives of our pilot study were to determine 1) associations between gut microbiota and mercury concentrations in biomarkers (stool, hair and cord blood) and 2) the contributions of gut microbial mercury methylation/demethylation to stool methylmercury. Moreover, for pregnant women (36-39 weeks gestation, n=17) donated hair and stool specimens, and cord blood was collected for a subset (n=7). The diversity of gut microbiota was determined using 16S rRNA gene profiling (n=17). For 6 stool samples with highest/lowest methylmercury concentrations, metagenomic whole genome shotgun sequencing was employed to search for one mercury methylation gene (hgcA), and two mer operon genes involved in methylmercury detoxification (merA and merB). There were seventeen bacterial genera that were significantly correlated (increasing or decreasing) with stool methylmercury, stool inorganic mercury, or hair total mercury; however, aside from one genus, there was no overlap between biomarkers. No definitive matches for hgcA or merB, while merA were detected at low concentrations in all six samples. Proportional differences in stool methylmercury were not likely attributed to gut microbiota through methylation/demethylation. Gut microbiota potentially altered methylmercury metabolism using indirect pathways.

  9. Diversity of mercury resistance determinants among Bacillus strains isolated from sediment of Minamata Bay.

    PubMed

    Narita, Masaru; Chiba, Kazuyuki; Nishizawa, Hiroshi; Ishii, Hidenori; Huang, Chieh-Chen; Kawabata, Zen'ichiro; Silver, Simon; Endo, Ginro

    2003-06-06

    Thirty mercury-resistant (Hg R) Bacillus strains were isolated from mercury-polluted sediment of Minamata Bay, Japan. Mercury resistance phenotypes were classified into broad-spectrum (resistant to inorganic Hg(2+) and organomercurials) and narrow-spectrum (resistant to inorganic Hg(2+) and sensitive to organomercurials) groups. Polymerase chain reaction (PCR) product sizes and the restriction nuclease site maps of mer operon regions from all broad-spectrum Hg R Bacillus were identical to that of Bacillus megaterium MB1. On the other hand, the PCR products of the targeted merP (extracellular mercury-binding protein gene) and merA (intracellular mercury reductase protein gene) regions from the narrow-spectrum Hg R Bacillus were generally smaller than those of the B. megaterium MB1 mer determinant. Diversity of gene structure configurations was also observed by restriction fragment length polymorphism (RFLP) profiles of the merA PCR products from the narrow-spectrum Hg R Bacillus. The genetic diversity of narrow-spectrum mer operons was greater than that of broad-spectrum ones.

  10. Potential Noachian-Aged Sites for MER-B

    NASA Astrophysics Data System (ADS)

    Gilmore, M. S.; Tanaka, K. L.

    2001-01-01

    Two Mars Exploration Rovers (MER) are slated for launch in 2003 and will land in the equatorial region of Mars. These rovers are More formidable in both size and instrument complement than the Sojourner rover, potentially allowing greater range. For landing, they will be housed in an airbag system nearly identical to Pathfinder allowing them to land in an area with elevation below 1.3 km, Root Mean Square (RMS) slopes less than 6 degrees, rock abundance less than 20%, and fine component thermal inertia greater than 3-4 cgs units. MER-A may land between 15 S to 5 N and MER-B between 10 S and 10 N. Numerous sites have been identified by the JPL team as meeting the above engineering requirements for the landing of the rovers. Here we focus on a subset of these that lie in Noachian-aged terrain, as defined by Viking-era geologic mapping. This subset is further reduced by the first author's support of the selection (if possible) of a site in the Valles Marineris which can only be reached by MER-A, this study therefore focuses on those Noachian-aged sites that can be reached by MER-B.

  11. Lunar and Planetary Science XXXV: Special Session: Mars Missions

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The session "Special Session: Mars Missions" contained the following reports:Initial Results from the MER Athena Science Investigation at Gusev Crater and Meridiani Planum; Geomorphology of the Mars Exploration Rover (MER-A) Landing Site from Observations by the Spirit Rover; Geology of Meridiani Planum as Inferred from Mars Exploration Rover: Observations;Preliminary Mineralogy and Geochemistry Results at the MER-A Landing Site in Gusev; A First Look at the Mineralogy and Geochemistry of the MER-B Landing Site in Meridiani Planum; Mini-TES Observations of the Gusev and Meridiani Landing Sites; Preliminary Results of the Magnetic Properties Experiments on the Mars Exploration Rovers, Spirit and Opportunity; Pancam Imaging of the Mars Exploration Rover Landing Sites in Gusev Crater and Meridiani Planum; Atmospheric Science with the Mars Exploration Rovers: Things are Looking Up; The Mars Express Mission:Initial Scientific Results from Orbit; The HRSC Experiment in Mars Orbit: First Results; The OMEGA/Mars Express First Results; and SPICAM on Mars Express: First Results and First Observations of Water Ice at South.

  12. Methylmercury degradation by Pseudomonas putida V1.

    PubMed

    Cabral, Lucélia; Yu, Ri-Qing; Crane, Sharron; Giovanella, Patricia; Barkay, Tamar; Camargo, Flávio A O

    2016-08-01

    Environmental contamination of mercury (Hg) has caused public health concerns with focuses on the neurotoxic substance methylmercury, due to its bioaccumulation and biomagnification in food chains. The goals of the present study were to examine: (i) the transformation of methylmercury, thimerosal, phenylmercuric acetate and mercuric chloride by cultures of Pseudomonas putida V1, (ii) the presence of the genes merA and merB in P. putida V1, and (iii) the degradation pathways of methylmercury by P. putida V1. Strain V1 cultures readily degraded methylmercury, thimerosal, phenylmercury acetate, and reduced mercuric chloride into gaseous Hg(0). However, the Hg transformation in LB broth by P. putida V1 was influenced by the type of Hg compounds. The merA gene was detected in P. putida V1, on the other hand, the merB gene was not detected. The sequencing of this gene, showed high similarity (100%) to the mercuric reductase gene of other Pseudomonas spp. Furthermore, tests using radioactive (14)C-methylmercury indicated an uncommon release of (14)CO2 concomitant with the production of Hg(0). The results of the present work suggest that P. putida V1 has the potential to remove methylmercury from contaminated sites. More studies are warranted to determine the mechanism of removal of methylmercury by P. putida V1.

  13. Phytoremediation of Ionic and Methyl Mercury P

    SciTech Connect

    Meagher, Richard B.

    1999-06-01

    Our long-term goal is to enable highly productive plant species to extract, resist, detoxify, and/or sequester toxic heavy metal pollutants as an environmentally friendly alternative to physical remediation methods. We have focused this phytoremediation research on soil and water-borne ionic and methylmercury. Mercury pollution is a serious world-wide problem affecting the health of human and wild-life populations. Methylmercury, produced by native bacteria at mercury-contaminated wetland sites, is a particularly serious problem due to its extreme toxicity and efficient biomagnification in the food chain. We engineered several plant species (e.g., Arabidopsis, tobacco, canola, yellow poplar, rice) to express the bacterial genes, merB and/or merA, under the control of plant regulatory sequences. These transgenic plants acquired remarkable properties for mercury remediation. (1) Transgenic plants expressing merB (organomercury lyase) extract methylmercury from their growth substrate and degrade it to less toxic ionic mercury. They grow on concentrations of methylmercury that kill normal plants and accumulate low levels of ionic mercury. (2) Transgenic plants expressing merA (mercuric ion reductase) extract and electrochemically reduce toxic, reactive ionic mercury to much less toxic and volatile metallic mercury. This metal transformation is driven by the powerful photosynthetic reducing capacity of higher plants that generates excess NADPH using solar energy. MerA plants grow vigorously on levels of ionic mercury that kill control plants. Plants expressing both merB and merA degrade high levels of methylmercury and volatilize metallic mercury. These properties were shown to be genetically stable for several generations in the two plant species examined. Our work demonstrates that native trees, shrubs, and grasses can be engineered to remediate the most abundant toxic mercury pollutants. Building on these data our working hypothesis for the next grant period is that

  14. Metagenomic Analysis of Ammonia-Oxidizing Archaea Affiliated with the Soil Group

    PubMed Central

    Bartossek, Rita; Spang, Anja; Weidler, Gerhard; Lanzen, Anders; Schleper, Christa

    2012-01-01

    Ammonia-oxidizing archaea (AOA) have recently been recognized as a significant component of many microbial communities and represent one of the most abundant prokaryotic groups in the biosphere. However, only few AOA have been successfully cultivated so far and information on the physiology and genomic content remains scarce. We have performed a metagenomic analysis to extend the knowledge of the AOA affiliated with group I.1b that is widespread in terrestrial habitats and of which no genome sequences has been described yet. A fosmid library was generated from samples of a radioactive thermal cave (46°C) in the Austrian Central Alps in which AOA had been found as a major part of the microbial community. Out of 16 fosmids that possessed either an amoA or 16S rRNA gene affiliating with AOA, 5 were fully sequenced, 4 of which grouped with the soil/I.1b (Nitrososphaera-) lineage, and 1 with marine/I.1a (Nitrosopumilus-) lineage. Phylogenetic analyses of amoBC and an associated conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and supported the separation of the soil and marine group. Several putative genes that did not have homologs in currently available marine Thaumarchaeota genomes indicated that AOA of the soil group contain specific genes that are distinct from their marine relatives. Potential cis-regulatory elements around conserved promoter motifs found upstream of the amo genes in sequenced (meta-) genomes differed in marine and soil group AOA. On one fosmid, a group of genes including amoA and amoB were flanked by identical transposable insertion sequences, indicating that amoAB could potentially be co-mobilized in the form of a composite transposon. This might be one of the mechanisms that caused the greater variation in gene order compared to genomes in the marine counterparts. Our findings highlight the genetic diversity within the two major and widespread lineages of Thaumarchaeota. PMID:22723795

  15. Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

    PubMed Central

    Hamilton, Trinity L.; Koonce, Evangeline; Howells, Alta; Havig, Jeff R.; Jewell, Talia; de la Torre, José R.; Peters, John W.

    2014-01-01

    Source waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii” and the putatively nitrogen-fixing (diazotrophic) bacterium Thermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N2 fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increased amoA transcript levels while it suppressed rates of acetylene reduction and decreased nifH transcript levels. Sequencing of amplified nifH and amoA transcripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N2 fixation are closely affiliated with Ca. Nitrosocaldus yellowstonii and T. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such as Ca. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable

  16. Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments

    PubMed Central

    Kong, Angela Y. Y.; Hristova, Krassimira; Scow, Kate M.; Six, Johan

    2011-01-01

    Real-time quantitative PCR assays, targeting part of the ammonia-monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were coupled with 15N pool dilution techniques to investigate the effects of long-term agricultural management practices on potential gross N mineralization and nitrification rates, as well as ammonia-oxidizing bacteria (AOB), denitrifier, and total bacterial community sizes within different soil microenvironments. Three soil microenvironments [coarse particulate organic matter (cPOM; >250 μm), microaggregate (53–250 μm), and silt-and-clay fraction (<53 μm)] were physically isolated from soil samples collected across the cropping season from conventional, low-input, and organic maize-tomato systems (Zea mays L.- Lycopersicum esculentum L.). We hypothesized that (i) the higher N inputs and soil N content of the organic system foster larger AOB and denitrifier communities than in the conventional and low-input systems, (ii) differences in potential gross N mineralization and nitrification rates across the systems correspond with AOB and denitrifier abundances, and (iii) amoA, nosZ, and 16S rRNA gene abundances are higher in the microaggregates than in the cPOM and silt-and-clay microenvironments. Despite 13 years of different soil management and greater soil C and N content in the organic compared to the conventional and low-input systems, total bacterial communities within the whole soil were similar in size across the three systems (~5.15×108 copies g−1 soil). However, amoA gene densities were ~2 times higher in the organic (1.75×108 copies g−1 soil) than the other systems at the start of the season and nosZ gene abundances were ~2 times greater in the conventional (7.65×107 copies g−1 soil) than in the other systems by the end of the season. Because organic management did not consistently lead to larger AOB and denitrifier communities than the other two systems, our first hypothesis was not corroborated. Our second

  17. An Analysis of Thaumarchaeota Populations from the Northern Gulf of Mexico

    PubMed Central

    Tolar, Bradley B.; King, Gary M.; Hollibaugh, James T.

    2013-01-01

    We sampled Thaumarchaeota populations in the northern Gulf of Mexico, including shelf waters under the Mississippi River outflow plume that are subject to recurrent hypoxia. Data from this study allowed us to: (1) test the hypothesis that Thaumarchaeota would be abundant in this region; (2) assess phylogenetic composition of these populations for comparison with other regions; (3) compare the efficacy of quantitative PCR (qPCR) based on primers for 16S rRNA genes (rrs) with primers for genes in the ammonia oxidation (amoA) and carbon fixation (accA, hcd) pathways; (4) compare distributions obtained by qPCR with the relative abundance of Thaumarchaeota rrs in pyrosequenced libraries; (5) compare Thaumarchaeota distributions with environmental variables to help us elucidate the factors responsible for the distributions; (6) compare the distribution of Thaumarchaeota with Nitrite-Oxidizing Bacteria (NOB) to gain insight into the coupling between ammonia and nitrite oxidation. We found up to 108 copies L−1 of Thaumarchaeota rrs in our samples (up to 40% of prokaryotes) by qPCR, with maximum abundance in slope waters at 200–800 m. Thaumarchaeota rrs were also abundant in pyrosequenced libraries and their relative abundance correlated well with values determined by qPCR (r2 = 0.82). Thaumarchaeota populations were strongly stratified by depth. Canonical correspondence analysis using a suite of environmental variables explained 92% of the variance in qPCR-estimated gene abundances. Thaumarchaeota rrs abundance was correlated with salinity and depth, while accA abundance correlated with fluorescence and pH. Correlations of Archaeal amoA abundance with environmental variables were primer-dependent, suggesting differential responses of sub-populations to environmental variables. Bacterial amoA was at the limit of qPCR detection in most samples. NOB and Euryarchaeota rrs were found in the pyrosequenced libraries; NOB distribution was correlated with that of

  18. Transcript Analysis of Multiple Copies of amo (Encoding Ammonia Monooxygenase) and hao (Encoding Hydroxylamine Oxidoreductase) in Nitrosomonas europaea

    PubMed Central

    Hommes, Norman G.; Sayavedra-Soto, Luis A.; Arp, Daniel J.

    2001-01-01

    The genes encoding ammonia monooxygenase (amoCAB), hydroxylamine oxidoreductase (hao), and the c-type cytochrome c-554 (hcy) are present in multiple copies in the genome of Nitrosomonas europaea. The upstream regions of the two copies of amoC, the three copies of hao, and one copy of hcy were cloned and sequenced. Primer extension reactions were done to identify transcription start sites for these genes, as well as for amoA. Putative ς70 promoter sequences were found associated with all but one of the mapped transcription start sites. Primer extensions were done with amoC primers using RNA harvested from cells incubated with and without ammonium. The experiments suggested that N. europaea cells may be able to use different promoters in the presence and absence of ammonium. PMID:11208810

  19. Microbial community structure and occurrence of diverse autotrophic ammonium oxidizing microorganisms in the anammox process.

    PubMed

    Bae, H; Chung, Y-C; Jung, J-Y

    2010-01-01

    The enrichment of anaerobic ammonium oxidizing (anammox) bacteria using an upflow anaerobic sludge bioreactor was successfully conducted for 400 days of continuous operation. The bacterial community structure of anammox bioreactor included Proteobacteria (42%), Chloroflexi (22%), Planctomycetes (20%), Chlorobi (7%), Bacteroidetes (5%), Acidobacteria (2%), and Actinobacteria (2%). All clones of Planctomycetes were affiliated with the anammox bacteria, Planctomycete KSU-1 (AB057453). The presence and diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) were identified by terminal restriction fragment length polymorphism (T-RFLP) based on the amoA gene sequences. The AOB in anammox bioreactor were affiliated with the Nitrosomonas europaea cluster. The T-RFLP result of AOA showed the diverse microbial community structure of AOA with three terminal restriction fragments (T-RFs).

  20. Monoterpenoid-based preparations in beehives affect learning, memory, and gene expression in the bee brain.

    PubMed

    Bonnafé, Elsa; Alayrangues, Julie; Hotier, Lucie; Massou, Isabelle; Renom, Allan; Souesme, Guillaume; Marty, Pierre; Allaoua, Marion; Treilhou, Michel; Armengaud, Catherine

    2017-02-01

    Bees are exposed in their environment to contaminants that can weaken the colony and contribute to bee declines. Monoterpenoid-based preparations can be introduced into hives to control the parasitic mite Varroa destructor. The long-term effects of monoterpenoids are poorly investigated. Olfactory conditioning of the proboscis extension reflex (PER) has been used to evaluate the impact of stressors on cognitive functions of the honeybee such as learning and memory. The authors tested the PER to odorants on bees after exposure to monoterpenoids in hives. Octopamine receptors, transient receptor potential-like (TRPL), and γ-aminobutyric acid channels are thought to play a critical role in the memory of food experience. Gene expression levels of Amoa1, Rdl, and trpl were evaluated in parallel in the bee brain because these genes code for the cellular targets of monoterpenoids and some pesticides and neural circuits of memory require their expression. The miticide impaired the PER to odors in the 3 wk following treatment. Short-term and long-term olfactory memories were improved months after introduction of the monoterpenoids into the beehives. Chronic exposure to the miticide had significant effects on Amoa1, Rdl, and trpl gene expressions and modified seasonal changes in the expression of these genes in the brain. The decrease of expression of these genes in winter could partly explain the improvement of memory. The present study has led to new insights into alternative treatments, especially on their effects on memory and expression of selected genes involved in this cognitive function. Environ Toxicol Chem 2017;36:337-345. © 2016 SETAC.

  1. Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea.

    PubMed

    Bennett, Kristen; Sadler, Natalie C; Wright, Aaron T; Yeager, Chris; Hyman, Michael R

    2016-04-01

    Nitrosomonas europaea is an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2 (-)) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4 (+)-dependent O2 uptake by N. europaea by 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, andde novoprotein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and matrix-assisted laser desorption ionization-tandem time of flight (MALDI-TOF/TOF) analyses also confirmed that the fluorescent 28-kDa polypeptide was AmoA.

  2. Transcription of genes coding for metabolic key functions in Nitrosomonas europaea during aerobic and anaerobic growth.

    PubMed

    Beyer, Sonja; Gilch, Stefan; Meyer, Ortwin; Schmidt, Ingo

    2009-01-01

    Nitrosomonas europaea can grow under conditions of chemolithoautotrophic aerobic (oxygen as oxidant) as well as anaerobic [nitrogen dioxide (NO(2)) as oxidant] nitrification or chemoorganotrophic anaerobic pyruvate-dependent denitrification. In this study, the adaptation of the transcription (mRNA synthesis/concentration) of N. europaea to aerobic and anaerobic growth conditions was evaluated and the transcription of genes coding for metabolic key functions was analyzed: nitrogen and energy metabolism (amoA, hao, rh1, nirK, norB, nsc, aceE, ldhA, ppc, gltA, odhA, coxA), carbon dioxide fixation (cbbL), gluconeogenesis (ppsA), cell growth (ftsZ), and oxidative stress (sodB). During aerobic ammonia oxidation the specific activities of ammonia oxidation, nitrite reduction, and the growth rates correlated with the transcription level of the corresponding genes amoA/hao, nirK/norB/nsc, and cbbL/ftsZ. In anaerobically ammonia-oxidizing cells of N. europaea, the cellular mRNA concentrations of amoA, hao, rh1,coxA, cbbL, ftsZ, and sodB were reduced compared with aerobically nitrifying cells, but the mRNA levels of nirK, norB, and nsc were significantly increased. During anaerobic pyruvate-dependent denitrification, the mRNA abundance of nirK, norB, nsc, aceE, gltA, and odhA was increased, while the concentrations of amoA,hao, rh1, coxAcbbL, ftsZ, and sodB were significantly reduced. Temperature, pH value, and NH(4)(+), O(2), NO, and NO(2) concentrations had comparatively small effects on the transcription of the studied genes.

  3. 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

  4. Communities of Archaea and Bacteria in a Subsurface Radioactive Thermal Spring in the Austrian Central Alps, and Evidence of Ammonia-Oxidizing Crenarchaeota▿

    PubMed Central

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

    2007-01-01

    Scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal Alpine springs, which contain radium 226 and radon 222. A culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the “Franz-Josef-Quelle” in Bad Gastein, Austria, was performed. Four hundred fifteen clones were analyzed. One hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units (OTUs) and 283 with four archaeal OTUs. Rarefaction analysis indicated a high diversity of bacterial sequences, while archaeal sequences were less diverse. The majority of the cloned archaeal 16S rRNA gene sequences belonged to the soil-freshwater-subsurface (1.1b) crenarchaeotic group; other representatives belonged to the freshwater-wastewater-soil (1.3b) group, except one clone, which was related to a group of uncultivated Euryarchaeota. These findings support recent reports that Crenarchaeota are not restricted to high-temperature environments. Most of the bacterial sequences were related to the Proteobacteria (α, β, γ, and δ), Bacteroidetes, and Planctomycetes. One OTU was allied with Nitrospina sp. (δ-Proteobacteria) and three others grouped with Nitrospira. Statistical analyses suggested high diversity based on 16S rRNA gene analyses; the rarefaction plot of archaeal clones showed a plateau. Since Crenarchaeota have been implicated recently in the nitrogen cycle, the spring environment was probed for the presence of the ammonia monooxygenase subunit A (amoA) gene. Sequences were obtained which were related to crenarchaeotic amoA genes from marine and soil habitats. The data suggested that nitrification processes are occurring in the subterranean environment and that ammonia may possibly be an energy source for the resident communities. PMID:17085711

  5. Effects of planting Phragmites australis on nitrogen removal, microbial nitrogen cycling, and abundance of ammonia-oxidizing and denitrifying microorganisms in sediments.

    PubMed

    Toyama, Tadashi; Nishimura, Yoshiko; Ogata, Yuka; Sei, Kazunari; Mori, Kazuhiro; Ike, Michihiko

    2015-10-21

    We examined the effect of planting an emergent aquatic plant (Phragmites australis) on nitrogen removal from sediments using a 42-d pot experiment. The experimental pot systems comprised two types of sediments planted with and without young P. australis. Total nitrogen (total N), total dissolved N, and NH4-N in the sediments decreased markedly after planting. In contrast, those levels decreased only slightly in the unplanted sediments. The decrease in total N in the P. australis-planted sediments was 7-20 times those in the unplanted sediments. Abundances of bacterial 16S rRNA, archaeal 16S rRNA, ammonia-oxidizing bacterial ammonia monooxygenase (amoA), ammonia-oxidizing archaeal amoA, and denitrifying bacterial nitrite reductase (nirK) genes increased significantly in sediments after planting. Phragmites australis appears to have released oxygen and created a repeating cycle of oxidizing and reducing conditions in the sediments. These conditions should promote mineralization of organic N, nitrification, and denitrification in the sediments. Phragmites australis absorbed bioavailable nitrogen generated by microbial nitrogen metabolism. During the 42-d period after planting, 31-44% of total N was removed by microbial nitrogen cycling, and 56-69% was removed via absorption by P. australis. These results suggest that planting P. australis can increase microbial populations and their activities, and that nitrogen removal can be accelerated by the combined functions of P. australis and microorganisms in the sediment. Thus, planting P. australis has considerable potential as an effective remediation technology for eutrophic sediments.

  6. Complete nitrification by a single microorganism

    PubMed Central

    van Kessel, Maartje A.H.J.; Speth, Daan R.; Albertsen, Mads; Nielsen, Per H.; Op den Camp, Huub J.M.; Kartal, Boran; Jetten, Mike S.M.; Lücker, Sebastian

    2016-01-01

    Summary Nitrification is a two-step process where ammonia is considered to first be oxidized to nitrite by ammonia-oxidizing bacteria (AOB) and/or archaea (AOA), and subsequently to nitrate by nitrite-oxidizing bacteria (NOB). Described by Winogradsky already in 18901, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle2. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible and it was postulated that this process could occur under conditions selecting for species with lower growth-rates but higher growth-yields than canonical ammonia-oxidizing microorganisms3. Still, organisms catalysing this process have not yet been discovered. Here, we report the enrichment and initial characterization of two Nitrospira species that encode all enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding on the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle. PMID:26610025

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

    PubMed

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

    2007-01-01

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

  8. The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils

    PubMed Central

    Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

    2016-01-01

    Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations

  9. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions

    PubMed Central

    Laanbroek, Hendrikus J.; Keijzer, Rosalinde M.; Verhoeven, Jos T. A.; Whigham, Dennis F.

    2013-01-01

    In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests. PMID:24312088

  10. 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.

  11. Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico.

    PubMed

    Mills, Heath J; Hunter, Evan; Humphrys, Mike; Kerkhof, Lee; McGuinness, Lora; Huettel, Markus; Kostka, Joel E

    2008-07-01

    Sandy or permeable sediment deposits cover the majority of the shallow ocean seafloor, and yet the associated bacterial communities remain poorly described. The objective of this study was to expand the characterization of bacterial community diversity in permeable sediment impacted by advective pore water exchange and to assess effects of spatial, temporal, hydrodynamic, and geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) was used to analyze nearly 100 sediment samples collected from two northeastern Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic conditions. Communities were described across multiple taxonomic levels using universal bacterial small subunit (SSU) rRNA targets (RNA- and DNA-based) and functional markers for nitrification (amoA) and denitrification (nosZ). Clonal analysis of SSU rRNA targets identified several taxa not previously detected in sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Firmicutes). Sequence diversity was high among the overall bacterial and denitrifying communities, with members of the Alphaproteobacteria predominant in both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did not covary with the other gene targets. TRFLP fingerprinting revealed changes in sequence diversity from the family to species level across sediment depth and study site. The high diversity of facultative denitrifiers was consistent with the high permeability, deeper oxygen penetration, and high rates of aerobic respiration determined in these sediments. The high relative abundance of Gammaproteobacteria in RNA clone libraries suggests that this group may be poised to respond to short-term periodic pulses of growth substrates, and this observation warrants further investigation.

  12. Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave.

    PubMed

    Chen, Yin; Wu, Liqin; Boden, Rich; Hillebrand, Alexandra; Kumaresan, Deepak; Moussard, Hélène; Baciu, Mihai; Lu, Yahai; Colin Murrell, J

    2009-09-01

    Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monooxygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using 13C-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the 'heavy' DNA and sequences related to nitrite-oxidizing bacteria Nitrospira and Candidatus 'Nitrotoga' were also detected in the 'heavy' DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylovorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave. Other sequences detected in the bacterial 16S rRNA clone library included Verrucomicrobia, Firmicutes, Bacteroidetes, alphaproteobacterial Rhodobacterales and gammaproteobacterial Xanthomonadales. Archaeal 16S rRNA sequences retrieved were restricted within two groups, namely the Deep-sea Hydrothermal Vent Euryarchaeota group and the Miscellaneous Crenarchaeotic group. No sequences related to known sulfur-oxidizing archaea, ammonia-oxidizing archaea, methanogens or anaerobic methane-oxidizing archaea were detected in this clone library. The results provided molecular biological evidence to support the hypothesis that Movile Cave is driven by chemolithoautotrophy, mainly through sulfur oxidation by sulfur-oxidizing bacteria and reveal that

  13. Spatial Distribution of Total, Ammonia-Oxidizing, and Denitrifying Bacteria in Biological Wastewater Treatment Reactors for Bioregenerative Life Support

    PubMed Central

    Sakano, Yuko; Pickering, Karen D.; Strom, Peter F.; Kerkhof, Lee J.

    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. PMID:11976099

  14. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

    PubMed Central

    Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A.; McHardy, Alice C.; Embley, T. Martin; Prosser, James I.; Macqueen, Daniel J.

    2015-01-01

    The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400–700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum. PMID:26170282

  15. Microbial N Transformations and N2O Emission after Simulated Grassland Cultivation: Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate (DMPP).

    PubMed

    Duan, Yun-Feng; Kong, Xian-Wang; Schramm, Andreas; Labouriau, Rodrigo; Eriksen, Jørgen; Petersen, Søren O

    2017-01-01

    Grassland cultivation can mobilize large pools of N in the soil, with the potential for N leaching and N2O emissions. Spraying with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) before cultivation was simulated by use of soil columns in which the residue distribution corresponded to plowing or rotovation to study the effects of soil-residue contact on N transformations. DMPP was sprayed on aboveground parts of ryegrass and white clover plants before incorporation. During a 42-day incubation, soil mineral N dynamics, potential ammonia oxidation (PAO), denitrifying enzyme activity (DEA), nitrifier and denitrifier populations, and N2O emissions were investigated. The soil NO3(-) pool was enriched with (15)N to trace sources of N2O. Ammonium was rapidly released from decomposing residues, and PAO was stimulated in soil near residues. DMPP effectively reduced NH4(+) transformation irrespective of residue distribution. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) were both present, but only the AOB amoA transcript abundance correlated with PAO. DMPP inhibited the transcription of AOB amoA genes. Denitrifier genes and transcripts (nirK, nirS, and clades I and II of nosZ) were recovered, and a correlation was found between nirS mRNA and DEA. DMPP showed no adverse effects on the abundance or activity of denitrifiers. The (15)N enrichment of N2O showed that denitrification was responsible for 80 to 90% of emissions. With support from a control experiment without NO3(-) amendment, it was concluded that DMPP will generally reduce the potential for leaching of residue-derived N, whereas the effect of DMPP on N2O emissions will be significant only when soil NO3(-) availability is limiting.

  16. 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.

  17. Revisiting nitrification in the Eastern Tropical South Pacific: A focus on controls

    NASA Astrophysics Data System (ADS)

    Peng, Xuefeng; Fuchsman, Clara A.; Jayakumar, Amal; Warner, Mark J.; Devol, Allan H.; Ward, Bess B.

    2016-03-01

    Nitrification, the oxidation of ammonium (NH4+) to nitrite (NO2-) and to nitrate (NO3-), is a component of the nitrogen (N) cycle internal to the fixed N pool. In oxygen minimum zones (OMZs), which are hotspots for oceanic fixed N loss, nitrification plays a key role because it directly supplies substrates for denitrification and anaerobic ammonia oxidation (anammox), and may compete for substrates with these same processes. However, the control of oxygen and substrate concentrations on nitrification are not well understood. We performed onboard incubations with 15N-labeled substrates to measure rates of NH4+ and NO2- oxidation in the eastern tropical South Pacific (ETSP). The spatial and depth distributions of NH4+ and NO2- oxidation rates were primarily controlled by NH4+ and NO2- availability, oxygen concentration, and light. In the euphotic zone, nitrification was partially photoinhibited. In the anoxic layer, NH4+ oxidation was negligible or below detection, but high rates of NO2- oxidation were observed. NH4+ oxidation displayed extremely high affinity for both NH4+ and oxygen. The positive linear correlations between NH4+ oxidation rates and in situ NH4+ concentrations and ammonia monooxygenase subunit A (amoA) gene abundances in the upper oxycline indicate that the natural assemblage of ammonia oxidizers responds to in situNH4+ concentrations or supply by adjusting their population size, which determines the NH4+ oxidation potential. The depth distribution of archaeal and bacterial amoA gene abundances and N2O concentration, along with independently reported simultaneous direct N2O production rate measurements, suggests that AOA were predominantly responsible for NH4+ oxidation, which was a major source of N2O production at oxygen concentrations > 5 µM.

  18. Nitrification and its oxygen consumption along the turbid Changjiang River plume

    NASA Astrophysics Data System (ADS)

    Hsiao, S. S.-Y.; Hsu, T.-C.; Liu, J.-W.; Xie, X.; Zhang, Y.; Lin, J.; Wang, H.; Yang, J.-Y. T.; Hsu, S.-C.; Dai, M.; Kao, S.-J.

    2013-05-01

    Nitrification rates of bulk water (NRb) and particle free (NRpf, particle > 3 μm eliminated) were determined along the Changjiang River plume in August 2011 by nitrogen isotope tracer technique. Dissolved oxygen (DO), community respiration rate (CR), nutrients, dissolved organic nitrogen, total suspended matter (TSM), particulate organic carbon/nitrogen (POC/PON), acid-leachable iron and manganese on suspended particles and both archaeal and β-proteobacterial amoA abundance on size-fractioned particle (> 3 μm and 0.22-3 μm) were measured. The NRb ranged from undetectable up to 4.6 μmol L-1 d-1 peaking at salinity of ~ 29. NRb values were positively correlated with ammonia concentration suggesting the importance of substrate in nitrification. In river mouth and inner plume, NRb was much higher than NRpf indicating nitrifying bacteria is mainly particle-associated, which was supported by amoA gene abundance and regression analysis of TSM and NRb. The estimated oxygen demand of nitrification accounted for 0.4% to 317% of CR. The nitrification oxygen demand is much higher than Redfield model's estimation (23%) indicating that oxygen might not be the sole oxidant though DO was sufficient (> 58 μmol kg-1). The excess nitrification oxygen demand showed tendency to occur at lower DO samples accompanying with higher acid-leachable Fe/Mn, which implied reactive Fe3+/Mn4+ may play a role as oxidant in nitrification process. Stoichiometric calculation suggested reactive Fe on particles was even 10-fold the oxidant demand for complete ammonia oxidation along all areas of the plume. The involvement of reactive iron and manganese in nitrification process in oxygenated water further complicated the nitrogen cycling in turbid river plume.

  19. 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

  20. 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

  1. Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary.

    PubMed

    Abell, Guy C J; Revill, Andrew T; Smith, Craig; Bissett, Andrew P; Volkman, John K; Robert, Stanley S

    2010-02-01

    Nitrification and denitrification are key steps in nitrogen (N) cycling. The coupling of these processes, which affects the flow of N in ecosystems, requires close interaction of nitrifying and denitrifying microorganisms, both spatially and temporally. The diversity, temporal and spatial variations in the microbial communities affecting these processes was examined, in relation to N cycling, across 12 sites in the Fitzroy river estuary, which is a turbid subtropical estuary in central Queensland. The estuary is a major source of nutrients discharged to the Great Barrier Reef near-shore zone. Measurement of nitrogen fluxes showed an active denitrifying community during all sampling months. Archaeal ammonia monooxygenase (amoA of AOA, functional marker for nitrification) was significantly more abundant than Betaproteobacterial (beta-AOB) amoA. Nitrite reductase genes, functional markers for denitrification, were dominated by nirS and not nirK types at all sites during the year. AOA communities were dominated by the soil/sediment cluster of Crenarchaeota, with sequences found in estuarine sediment, marine and terrestrial environments, whereas nirS sequences were significantly more diverse (where operational taxonomic units were defined at both the threshold of 5% and 15% sequence similarity) and were closely related to sequences originating from estuarine sediments. Terminal-restriction fragment length polymorphism (T-RFLP) analysis revealed that AOA population compositions varied spatially along the estuary, whereas nirS populations changed temporally. Statistical analysis of individual T-RF dominance suggested that salinity and C:N were associated with the community succession of AOA, whereas the nirS-type denitrifier communities were related to salinity and chlorophyll-alpha in the Fitzroy river estuary.

  2. Genetic and biogeochemical investigation of sedimentary nitrogen cycling communities responding to tidal and seasonal dynamics in Cape Fear River Estuary

    NASA Astrophysics Data System (ADS)

    Lisa, Jessica A.; Song, Bongkeun; Tobias, Craig R.; Hines, David E.

    2015-12-01

    Tidal and seasonal fluctuations in the oligohaline reaches of estuaries may alter geochemical features that influence structure and function of microbial communities involved in sedimentary nitrogen (N) cycling. In order to evaluate sediment community responses to short-term (tidal) and long-term (seasonal) changes in different tidal regimes, nitrogen cycling rates and genes were quantified in three sites that span a range of tidal influence in the upper portion of the Cape Fear River Estuary. Environmental parameters were monitored during low and high tides in winter and spring. 15N tracer incubation experiments were conducted to measure nitrification, denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonia (DNRA). Abundances of functional genes including bacterial and archaeal ammonia monooxygenase (amoA), nitrite reductases (nirS and nrfA), nitrous oxide reductase (nosZ), and hydrazine oxidoreductase (hzo) were measured using quantitative PCR assays. Denitrification rates were highest among the measured N cycling processes while bacteria carrying nrfA genes were most abundant. A discernable pattern in the short-term variation of N cycling rates and gene abundance was not apparent under the different tidal regimes. Significant seasonal variation in nitrification, denitrification, and anammox rates as well as bacterial amoA, nirS and nosZ gene abundance was observed, largely explained by increases in substrate availability during winter, with sediment ammonium playing a central role. These results suggest that the coupling of nitrification to N removal pathways is primarily driven by organic carbon mineralization and independent of tidal or salinity changes. Finally, changes in denitrification and nitrification activities were strongly reflected by the abundance of the respective functional genes, supporting a linkage between the structure and function of microbial communities.

  3. Age- and behaviour-related changes in the expression of biogenic amine receptor genes in the antennae of honey bees (Apis mellifera).

    PubMed

    McQuillan, Henry J; Barron, Andrew B; Mercer, Alison R

    2012-10-01

    We recently identified changes in amine-receptor gene expression in the antennae of the honey bee that correlate with shifts in the behavioural responsiveness of worker bees towards queen mandibular pheromone. Here we examine whether variations in expression of amine-receptor genes are related to age and/or to behavioural state. Colonies with a normal age structure were used to collect bees of different ages, as well as pollen foragers of unknown age. Single- and double-cohort colonies were established also to generate nurses and pollen foragers of the same age. Amdop1 was the only gene examined that showed no significant change in expression levels across the age groups tested. However, expression of this gene was significantly higher in 6-day-old nurses than in pollen foragers of the same age. Levels of expression of Amdop2 were very variable, particularly during the first week of adult life, and showed no correlation with nursing or foraging behaviour. Amdop3 and Amtyr1 expression levels changed dramatically with age. Interestingly, Amtyr1 expression was significantly higher in 15-day-old pollen foragers than in same-age nurses, whereas the opposite was true for Amoa1. While Amoa1 expression in the antennae was lower in 6- and 15-day-old pollen foragers than in nurses of the same age, differences in gene expression levels between nurses and pollen foragers could not be detected in 22-day-old bees. Our data show dynamic modulation of gene expression in the antennae of worker bees and suggest a peripheral role for biogenic amines in regulating behavioural plasticity in the honey bee.

  4. Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo).

    PubMed

    Llirós, Marc; Gich, Frederic; Plasencia, Anna; Auguet, Jean-Christophe; Darchambeau, François; Casamayor, Emilio O; Descy, Jean-Pierre; Borrego, Carles

    2010-10-01

    Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4',6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone (∼50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.

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

    PubMed

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

    2014-11-01

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

  6. 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

  7. Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers.

    PubMed

    Lee, Sung-Woo; Im, Jeongdae; Dispirito, Alan A; Bodrossy, Levente; Barcelona, Michael J; Semrau, Jeremy D

    2009-11-01

    Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5% moisture content) along with 15 mg NH (4) (+) (kg soil)(-1) and 0.1 mg phenylacetylene(kg soil)(-1) provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

  8. Quantification of Nitrosomonas oligotropha-Like Ammonia-Oxidizing Bacteria and Nitrospira spp. from Full-Scale Wastewater Treatment Plants by Competitive PCR

    PubMed Central

    Dionisi, Hebe M.; Layton, Alice C.; Harms, Gerda; Gregory, Igrid R.; Robinson, Kevin G.; Sayler, Gary S.

    2002-01-01

    Utilizing the principle of competitive PCR, we developed two assays to enumerate Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and nitrite-oxidizing bacteria belonging to the genus Nitrospira. The specificities of two primer sets, which were designed for two target regions, the amoA gene and Nitrospira 16S ribosomal DNA (rDNA), were verified by DNA sequencing. Both assays were optimized and applied to full-scale, activated sludge wastewater treatment plant (WWTP) samples. If it was assumed that there was an average of 3.6 copies of 16S rDNA per cell in the total population and two copies of the amoA gene per ammonia-oxidizing bacterial cell, the ammonia oxidizers examined represented 0.0033% ± 0.0022% of the total bacterial population in a municipal WWTP. N. oligotropha-like ammonia-oxidizing bacteria were not detected in an industrial WWTP. If it was assumed that there was one copy of the 16S rDNA gene per nitrite-oxidizing bacterial cell, Nitrospira spp. represented 0.39% ± 0.28% of the biosludge population in the municipal WWTP and 0.37% ± 0.23% of the population in the industrial WWTP. The number of Nitrospira sp. cells in the municipal WWTP was more than 62 times greater than the number of N. oligotropha-like cells, based on a competitive PCR analysis. The results of this study extended our knowledge of the comparative compositions of nitrifying bacterial populations in wastewater treatment systems. Importantly, they also demonstrated that we were able to quantify these populations, which ultimately will be required for accurate prediction of process performance and stability for cost-effective design and operation of WWTPs. PMID:11772633

  9. 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.

  10. 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.

  11. 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.

  12. Parent material and vegetation influence soil microbial community structure following 30-years of rock weathering and pedogenesis.

    PubMed

    Yarwood, Stephanie; Wick, Abbey; Williams, Mark; Daniels, W Lee

    2015-02-01

    The process of pedogenesis and the development of biological communities during primary succession begin on recently exposed mineral surfaces. Following 30 years of surface exposure of reclaimed surface mining sites (Appalachian Mountains, USA), it was hypothesized that microbial communities would differ between sandstone and siltstone parent materials and to a lesser extent between vegetation types. Microbial community composition was examined by targeting bacterial and archaeal (16S ribosomal RNA (rRNA)) and fungal (internal transcribed spacer (ITS)) genes and analyzed using Illumina sequencing. Microbial community composition significantly differed between parent materials and between plots established with tall fescue grass or pitch x loblolly pine vegetation types, suggesting that both factors are important in shaping community assembly during early pedogenesis. At the phylum level, Acidobacteria and Proteobacteria differed in relative abundance between sandstone and siltstone. The amount of the heavy fraction carbon (C) was significantly different between sandstone (2.0 mg g(-1)) and siltstone (5.2 mg g(-1)) and correlated with microbial community composition. Soil nitrogen (N) cycling was examined by determining gene copy numbers of ureC, archaeal amoA, and bacterial amoA. Gene quantities tended to be higher in siltstone compared to sandstone but did not differ by vegetation type. This was consistent with differences in extractable ammonium (NH4 (+)) concentrations between sandstone and siltstone (16.4 vs 8.5 μg NH4 (+)-N g(-1) soil), suggesting that nitrification rates may be higher in siltstone. Parent material and early vegetation are important determinants of early microbial community assembly and could be drivers for the trajectory of ecosystem development over longer time scales.

  13. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils.

    PubMed

    Lammel, Daniel R; Feigl, Brigitte J; Cerri, Carlos C; Nüsslein, Klaus

    2015-01-01

    Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world's largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our

  14. Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon

    PubMed Central

    Wang, Baozhan; Zheng, Yan; Huang, Rong; Zhou, Xue; Wang, Dongmei; He, Yuanqiu

    2014-01-01

    All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of Nitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of Nitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that 13CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both 13C-labeled amoA and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptive growth of Nitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated. PMID:24375137

  15. 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.

  16. Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials.

    PubMed

    Taylor, Anne E; Zeglin, Lydia H; Wanzek, Thomas A; Myrold, David D; Bottomley, Peter J

    2012-11-01

    It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH(4)(+)-availability that exist in the field.

  17. Nitrification inhibition by hexavalent chromium Cr(VI)--Microbial ecology, gene expression and off-gas emissions.

    PubMed

    Kim, Young Mo; Park, Hongkeun; Chandran, Kartik

    2016-04-01

    The goal of this study was to investigate the responses in the physiology, microbial ecology and gene expression of nitrifying bacteria to imposition of and recovery from Cr(VI) loading in a lab-scale nitrification bioreactor. Exposure to Cr(VI) in the reactor strongly inhibited nitrification performance resulting in a parallel decrease in nitrate production and ammonia consumption. Cr(VI) exposure also led to an overall decrease in total bacterial concentrations in the reactor. However, the fraction of ammonia oxidizing bacteria (AOB) decreased to a greater extent than the fraction of nitrite oxidizing bacteria (NOB). In terms of functional gene expression, a rapid decrease in the transcript concentrations of amoA gene coding for ammonia oxidation in AOB was observed in response to the Cr(VI) shock. In contrast, transcript concentrations of the nxrA gene coding for nitrite oxidation in NOB were relatively unchanged compared to Cr(VI) pre-exposure levels. Therefore, Cr(VI) exposure selectively and directly inhibited activity of AOB, which indirectly resulted in substrate (nitrite) limitation to NOB. Significantly, trends in amoA expression preceded performance trends both during imposition of and recovery from inhibition. During recovery from the Cr(VI) shock, the high ammonia concentrations in the bioreactor resulted in an irreversible shift towards AOB populations, which are expected to be more competitive in high ammonia environments. An inadvertent impact during recovery was increased emission of nitrous oxide (N2O) and nitric oxide (NO), consistent with recent findings linking AOB activity and the production of these gases. Therefore, Cr(VI) exposure elicited multiple responses on the microbial ecology, gene expression and both aqueous and gaseous nitrogenous conversion in a nitrification process. A complementary interrogation of these multiple responses facilitated an understanding of both direct and indirect inhibitory impacts on nitrification.

  18. 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.

  19. Microbial Community Structure of Relict Niter-Beds Previously Used for Saltpeter Production

    PubMed Central

    Narihiro, Takashi; Tamaki, Hideyuki; Akiba, Aya; Takasaki, Kazuto; Nakano, Koichiro; Kamagata, Yoichi; Hanada, Satoshi; Maji, Taizo

    2014-01-01

    From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3−, Cl−, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB) and “Ca. Nitrososphaera”-type ammonia-oxidizing archaea (AOA), respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems. PMID:25111392

  20. Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea

    PubMed Central

    Bennett, Kristen; Sadler, Natalie C.; Wright, Aaron T.; Yeager, Chris

    2016-01-01

    Nitrosomonas europaea is an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2−) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4+-dependent O2 uptake by N. europaea by 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, and de novo protein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and matrix-assisted laser desorption ionization–tandem time of flight (MALDI-TOF/TOF) analyses also confirmed that the fluorescent 28-kDa polypeptide was AmoA. PMID:26826234

  1. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments.

    PubMed

    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.

  2. [Dynamic changes in functional genes for nitrogen bioremediation of petroleum-contaminated soil cycle during].

    PubMed

    Wu, Bin-Bin; Lu, Dian-Nan; Liu, Zheng

    2012-06-01

    Microorganisms in nitrogen cycle serve as an important part of the ecological function of soil. The aim of this research was to monitor the abundance of nitrogen-fixing, denitrifying and nitrifying bacteria during bioaugmentation of petroleum-contaminated soil using real-time polymerase chain reaction (real-time PCR) of nifH, narG and amoA genes which encode the key enzymes in nitrogen fixation, nitrification and ammoniation respectively. Three different kinds of soils, which are petroleum-contaminated soil, normal soil, and remediated soil, were monitored. It was shown that the amounts of functional microorganisms in petroleum-contaminated soil were far less than those in normal soil, while the amounts in remediated soil and normal soil were comparable. Results of this experiment demonstrate that nitrogen circular functional bacteria are inhibited in petroleum-contaminated soil and can be recovered through bioremediation. Furthermore, copies of the three functional genes as well as total petroleum hydrocarbons (TPH) for soils with six different treatments were monitored. Among all treatments, the one, into which both E. cloacae as an inoculant and wheat straw as an additive were added, obtained the maximum copies of 2.68 x 10(6), 1.71 x 10(6) and 8.54 x 10(4) per gram dry soil for nifH, narG and amoA genes respectively, companying with the highest degradation rate (48% in 40 days) of TPH. The recovery of functional genes and removal of TPH were better in soil inoculated with E cloacae and C echinulata collectively than soil inoculated with E cloacae only. All above results suggest that the nitrogen circular functional genes could be applied to monitor and assess the bioremediation of petroleum-contaminated soil.

  3. Turbid Bottom Waters and Ammonium-Rich Freshwaters as Nitrification Hotspots in a Large Urban Estuary (San Francisco Bay, CA)

    NASA Astrophysics Data System (ADS)

    Damashek, J.; Casciotti, K. L.; Francis, C.

    2015-12-01

    Nitrification is the link between reduced and oxidized forms of inorganic nitrogen, and is therefore a crucial step in the estuarine nitrogen cycle. Ammonia-oxidizing microorganisms catalyze the rate-limiting step of ammonia oxidation to nitrite and thus play key roles in the biogeochemical cycling nutrient-rich estuaries. Yet, few studies have measured nitrification rates in tandem with ammonia oxidizer functional gene (amoA) expression, abundance, and diversity in estuary waters. Here, we present a multi-year data set on the microbial ecology and biogeochemistry of nitrification in the San Francisco Bay-Delta, the largest estuary on the North American west coast, collected throughout all regions of the estuary from 2012 to 2014. Data on microbial community distributions use functional gene-based PCR assays to assess the diversity, abundance, and mRNA expression of ammonia oxidizers, while stable isotope tracer experiments were used to measure nitrification rates. Ammonia-oxidizing archaea (AOA) typically outnumbered ammonia-oxidizing bacteria (AOB) throughout the sampled gradient, though the relative abundance of AOB was often greater in brackish regions. mRNA expression of amoA appeared to largely track DNA abundance, but suggested only a fraction of the ammonia-oxidizing community was typically active. AOA were always numerically dominant in the Sacramento River, where average nitrification rates were highest, suggesting the AOA communities in this river are responsible for a relatively constant nitrification hotspot. Additionally, depth profiles of nitrification rates suggested high biogeochemical activity near the sediment-water interface in samples with abnormally high turbidity, indicating similar but transient nitrification hotspots in bottom waters containing resuspended sediments. This work increases our knowledge of the ecology and dynamics of ammonia oxidizers in the San Francisco Bay-Delta, with time series data allowing for the putative

  4. Influence of chemical speciation and biofilm composition on mercury accumulation by freshwater biofilms.

    PubMed

    Dranguet, P; Le Faucheur, S; Cosio, C; Slaveykova, V I

    2017-01-25

    Mercury (Hg) is a pollutant of high concern for aquatic systems due to the biomagnification of its methylated form along the food chain. However, in contrast to other metals, gaining knowledge of its bioavailable forms for aquatic microorganisms remains challenging, making Hg risk assessment difficult. Ubiquitous and sessile freshwater biofilms are well known to accumulate and to transform Hg present in their ambient environment. The present study thus aims to evaluate whether non-extractable (proxy of intracellular) Hg accumulated by biofilms could be a good indicator of Hg bioavailability for microorganisms in freshwater. To that end, the link between Hg concentration and speciation, as well as biofilm composition (percentage of abiotic, biotic, chlorophyll and phycocyanin-fractions and abundance of dsrA, gcs, merA and hgcA bacterial genes) and biofilm Hg accumulation was examined. The studied biofilms were grown on artificial substrata in four reservoirs along the Olt River (Romania), which was contaminated by Hg coming from chlor-alkali plant effluents. The 0.45 μm-filterable Hg concentrations in ambient waters were measured and inorganic IHg speciation was modelled. Biofilms were analyzed for their non-extractable IHg and methylmercury (MeHg) contents as well as for their composition. The non-extractable IHg content was related, but not significantly, to the concentration of total IHg (r(2) = 0.88, p = 0.061) whereas a significant correlation was found with the predicted IHg concentration that is not bound to dissolved organic matter (r(2) = 0.95, p = 0.027), despite its extremely low concentrations (10(-25) M), showing a limitation of the thermodynamic Hg modelling to predict Hg bioavailability. The studied biofilms were different in biomass and composition and a principal component analysis showed that the non-extractable IHg content correlated with the abundance of the merA and hgcA genes, while MeHg accumulation was only linked with the abundance of the r

  5. Russian Meteorological and Geophysical Rockets of New Generation

    NASA Astrophysics Data System (ADS)

    Yushkov, V.; Gvozdev, Yu.; Lykov, A.; Shershakov, V.; Ivanov, V.; Pozin, A.; Afanasenkov, A.; Savenkov, Yu.; Kuznetsov, V.

    2015-09-01

    To study the process in the middle and upper atmosphere, ionosphere and near-Earth space, as well as to monitor the geophysical environment in Russian Federal Service for Hydrology and Environmental Monitoring (ROSHYDROMET) the development of new generation of meteorological and geophysical rockets has been completed. The modern geophysical research rocket system MR-30 was created in Research and Production Association RPA "Typhoon". The basis of the complex MR-30 is a new geophysical sounding rocket MN-300 with solid propellant, Rocket launch takes place at an angle of 70º to 90º from the launcher, which is a farm with a guide rail type required for imparting initial rotation rocket. The Rocket is spin stabilized with a spin rate between 5 and 7 Hz. Launch weight is 1564 kg, and the mass of the payload of 50 to 150 kg. MR-300 is capable of lifting up to 300 km, while the area of dispersion points for booster falling is an ellipse with parameters 37x 60 km. The payload of the rocket MN-300 consists of two sections: a sealed, located below the instrument compartment, and not sealed, under the fairing. Block of scientific equipment is formed on the platform in a modular layout. This makes it possible to solve a wide range of tasks and conduct research and testing technologies using a unique environment of space, as well as to conduct technological experiments testing and research systems and spacecraft equipment. New Russian rocket system MERA (MEteorological Rocket for Atmospheric Research) belongs to so called "dart" technique that provide lifting of small scientific payload up to altitude 100 km and descending with parachute. It was developed at Central Aerological Observatory jointly with State Unitary Enterprise Instrument Design Bureau. The booster provides a very rapid acceleration to about Mach 5. After the burning phase of the buster the dart is separated and continues ballistic flight for about 2 minutes. The dart carries the instrument payload+ parachute

  6. Potentiometric Surface in the Sparta-Memphis Aquifer of the Mississippi Embayment, Spring 2007

    USGS Publications Warehouse

    Schrader, T.P.

    2008-01-01

    The most widely used aquifer for industry and public supply in the Mississippi embayment in Arkansas, Louisiana, Mississippi, and Tennessee is the Sparta-Memphis aquifer. Decades of pumping from the Sparta-Memphis aquifer have affected ground-water levels throughout the Mississippi embayment. Regional assessments of water-level data from the aquifer are important to document regional water-level conditions and to develop a broad view of the effects of ground-water development and management on the sustainability and availability of the region's water supply. This information is useful to identify areas of water-level declines, identify cumulative areal declines that may cross State boundaries, evaluate the effectiveness of ground-water management strategies practiced in different States, and identify areas with substantial data gaps that may preclude effective management of ground-water resources. A ground-water flow model of the northern Mississippi embayment is being developed by the Mississippi Embayment Regional Aquifer Study (MERAS) to aid in answering questions about ground-water availability and sustainability. The MERAS study area covers parts of eight states including Alabama, Arkansas, Illinois, Kentucky, Louisiana, Mississippi, Missouri, and Tennessee and covers approximately 70,000 square miles. The U.S. Geological Survey (USGS) and the Mississippi Department of Environmental Quality Office of Land and Water Resources measured water levels in wells completed in the Sparta-Memphis aquifer in the spring of 2007 to assist in the MERAS model calibration and to document regional water-level conditions. Measurements by the USGS and the Mississippi Department of Environmental Quality Office of Land and Water Resources were done in cooperation with the Arkansas Natural Resources Commission; the Arkansas Geological Survey; Memphis Light, Gas and Water; Shelby County, Tennessee; and the city of Germantown, Tennessee. In 2005, total water use from the Sparta

  7. Proteomics Analysis Revealed that Crosstalk between Helicobacter pylori and Streptococcus mitis May Enhance Bacterial Survival and Reduces Carcinogenesis

    PubMed Central

    Khosravi, Yalda; Loke, Mun Fai; Goh, Khean Lee; Vadivelu, Jamuna

    2016-01-01

    Helicobacter pylori is the dominant species of the human gastric microbiota and is present in the stomach of more than half of the human population worldwide. Colonization by H. pylori causes persistent inflammatory response and H. pylori-induced gastritis is the strongest singular risk factor for the development of gastric adenocarcinoma. However, only a small proportion of infected individuals develop malignancy. Besides H. pylori, other microbial species have also been shown to be related to gastritis. We previously reported that interspecies microbial interaction between H. pylori and S. mitis resulted in alteration of their metabolite profiles. In this study, we followed up by analyzing the changing protein profiles of H. pylori and S. mitis by LC/Q-TOF mass spectrometry to understand the different response of the two bacterial species in a multi-species micro-environment. Differentially-expressed proteins in mono- and co-cultures could be mapped into 18 biological pathways. The number of proteins involve in RNA degradation, nucleotide excision repair, mismatch repair, and lipopolysaccharide (LPS) biosynthesis were increased in co-cultured H. pylori. On the other hand, fewer proteins involve in citrate cycle, glycolysis/ gluconeogenesis, aminoacyl-tRNA biosynthesis, translation, metabolism, and cell signaling were detected in co-cultured H. pylori. This is consistent with our previous observation that in the presence of S. mitis, H. pylori was transformed to coccoid. Interestingly, phosphoglycerate kinase (PGK), a major enzyme used in glycolysis, was found in abundance in co-cultured S. mitis and this may have enhanced the survival of S. mitis in the multi-species microenvironment. On the other hand, thioredoxin (TrxA) and other redox-regulating enzymes of H. pylori were less abundant in co-culture possibly suggesting reduced oxidative stress. Oxidative stress plays an important role in tissue damage and carcinogenesis. Using the in vitro co-culture model

  8. Rifampin Resistance rpoB Alleles or Multicopy Thioredoxin/Thioredoxin Reductase Suppresses the Lethality of Disruption of the Global Stress Regulator spx in Staphylococcus aureus

    PubMed Central

    Villanueva, Maite; Jousselin, Ambre; Baek, Kristoffer T.; Prados, Julien; Andrey, Diego O.; Renzoni, Adriana; Ingmer, Hanne; Frees, Dorte

    2016-01-01

    ABSTRACT Staphylococcus aureus is capable of causing a remarkable spectrum of disease, ranging from mild skin eruptions to life-threatening infections. The survival and pathogenic potential of S. aureus depend partly on its ability to sense and respond to changes in its environment. Spx is a thiol/oxidative stress sensor that interacts with the C-terminal domain of the RNA polymerase RpoA subunit, leading to changes in gene expression that help sustain viability under various conditions. Using genetic and deep-sequencing methods, we show that spx is essential in S. aureus and that a previously reported Δspx strain harbored suppressor mutations that allowed it to grow without spx. One of these mutations is a single missense mutation in rpoB (a P-to-L change at position 519 encoded by rpoB [rpoB-P519L]) that conferred high-level resistance to rifampin. This mutation alone was found to be sufficient to bypass the requirement for spx. The generation of rifampin resistance libraries led to the discovery of an additional rpoB mutation, R484H, which supported strains with the spx disruption. Other rifampin resistance mutations either failed to support the Δspx mutant or were recovered at unexpectedly low frequencies in genetic transduction experiments. The amino acid residues encoded by rpoB-P519L and -R484H map in close spatial proximity and comprise a highly conserved region of RpoB. We also discovered that multicopy expression of either trxA (encoding thioredoxin) or trxB (encoding thioredoxin reductase) supports strains with the deletion of spx. Our results reveal intriguing properties, especially of RNA polymerase, that compensate for the loss of an essential gene that is a key mediator of diverse processes in S. aureus, including redox and thiol homeostasis, antibiotic resistance, growth, and metabolism. IMPORTANCE The survival and pathogenicity of S. aureus depend on complex genetic programs. An objective for combating this insidious organism entails dissecting

  9. KSC-03PD-1591

    NASA Technical Reports Server (NTRS)

    2003-01-01

    KENNEDY SPACE CENTER, FLA. On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is raised off the transporter. When vertical, it will be lifted up the launch tower and mated to the Delta rocket (in the background) to launch Mars Exploration Rover 2. NASAs twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans cant yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  10. MARIE: Current Status and Results from 20 Months of Observations at Mars

    NASA Technical Reports Server (NTRS)

    Zeitlin, C.; Andersen, V.; Atwell, W.; Cleghorn, T. F.; Cucinotta, F. A.; Lee, K. T.; Pinsky, L.; Saganti, P.

    2004-01-01

    The MARIE instrument aboard the 2001 Mars Odyssey spacecraft detects energetic charged particles in the Galactic Cosmic Radiation (GCR) and during solar particle events (SPE) [1]. As of this writing (January 2004), MARIE has been turned off, after losing communication with the spacecraft during the large SPE of October 28, 2003. However, during the prior 20 months, MARIE collected data almost continuously, observing several solar events and the nearly-constant GCR. There is still a possibility the instrument can be recovered, and troubleshooting efforts are scheduled to begin in May 2004, following the completion of the primary missions of MER-A (Spirit) and MER-B (Opportunity). At present, Odyssey is acting as a telecommunications relay for the rovers and only routine science operations are permitted in this mode.

  11. IncA/C Plasmid Carrying bla(NDM-1), bla(CMY-16), and fosA3 in a Salmonella enterica Serovar Corvallis Strain Isolated from a Migratory Wild Bird in Germany.

    PubMed

    Villa, L; Guerra, B; Schmoger, S; Fischer, J; Helmuth, R; Zong, Z; García-Fernández, A; Carattoli, A

    2015-10-01

    A Salmonella enterica serovar Corvallis strain was isolated from a wild bird in Germany. This strain carried the IncA/C2 pRH-1238 plasmid. Complete sequencing of the plasmid was performed, identifying the blaNDM-1, blaCMY-16, fosA3, sul1, sul2, strA, strB, aac(6')-Ib, aadA5, aphA6, tetA(A), mphA, floR, dfrA7, and merA genes, which confer clinically relevant resistance to most of the antimicrobial classes, including β-lactams with carbapenems, fosfomycin, aminoglycosides, co-trimoxazole, tetracyclines, and macrolides. The strain likely originated from the Asiatic region and was transferred to Germany through the Milvus migrans migratory route.

  12. Long-term Hg pollution-induced structural shifts of bacterial community in the terrestrial isopod (Porcellio scaber) gut.

    PubMed

    Lapanje, Ales; Zrimec, Alexis; Drobne, Damjana; Rupnik, Maja

    2010-10-01

    In previous studies we detected lower species richness and lower Hg sensitivity of the bacteria present in egested guts of Porcellio scaber (Crustacea, Isopoda) from chronically Hg polluted than from unpolluted environment. Basis for such results were further investigated by sequencing of 16S rRNA genes of mercury-resistant (Hgr) isolates and clone libraries. We observed up to 385 times higher numbers of Hgr bacteria in guts of animals from polluted than from unpolluted environment. The majority of Hgr strains contained merA genes. Sequencing of 16S rRNA clones from egested guts of animals from Hg-polluted environments showed elevated number of bacteria from Pseudomonas, Listeria and Bacteroidetes relatives groups. In animals from pristine environment number of bacteria from Achromobacter relatives, Alcaligenes, Paracoccus, Ochrobactrum relatives, Rhizobium/Agrobacterium, Bacillus and Microbacterium groups were elevated. Such bacterial community shifts in guts of animals from Hg-polluted environment could significantly contribute to P. scaber Hg tolerance.

  13. Five-week use of a monopivot centrifugal blood pump as a right ventricular assist device in severe dilated cardiomyopathy.

    PubMed

    Inoue, Takamichi; Kitamura, Tadashi; Torii, Shinzo; Hanayama, Naoji; Oka, Norihiko; Itatani, Keiichi; Tomoyasu, Takahiro; Irisawa, Yusuke; Shibata, Miyuki; Hayashi, Hidenori; Ono, Minoru; Miyaji, Kagami

    2014-03-01

    Right heart failure is a critical complication in patients requiring mechanical ventricular support. However, it is often difficult to provide adequate right ventricular support in the acute phase. A 41-year-old woman diagnosed with dilated cardiomyopathy with severe right heart failure underwent implantation of a paracorporeal pulsatile left ventricular assist device (LVAD, Nipro Corporation, Tokyo, Japan) and a MERA monopivot centrifugal pump (Senko Medical Instrument Manufacturing Co., Ltd., Tokyo, Japan) as a right ventricular assist device (RVAD). The patient developed ischemic enteritis 3 weeks after surgery, necessitating fasting and reversal of anticoagulation therapy. A target international normalized ratio of 1.5 was selected, and aspirin administration was discontinued. Following recovery without thromboembolic events, the patient failed the RVAD discontinuation test. Five weeks after surgery, the monopivot centrifugal pump was exchanged for a pulsatile pump. No thrombus was evident on the centrifugal pump. The patient was undergoing cardiac rehabilitation at the time of this writing and awaiting heart transplantation.

  14. KSC-03PD-1593

    NASA Technical Reports Server (NTRS)

    2003-01-01

    KENNEDY SPACE CENTER, FLA. While one solid rocket booster (SRB) is suspended in the launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station, another is raised from its transporter for a similar lift. They are two of nine SRBs that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASAs twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans cant yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  15. Chemistry of Martian Soils from the Mars Exploration Rover APXS Instruments

    NASA Technical Reports Server (NTRS)

    Mittlefehldt, D. W.; Gellert, R.; Yen, A.

    2007-01-01

    The martian surface is covered with debris formed by several mechanisms and mobilized by various processes. Volcanism, impact, physical weathering and chemical alteration combine to produce particles of sizes from dust to boulders composed of primary mineral and rock fragments, partially altered primary materials, alteration minerals and shock-modified materials from all of these. Impacts and volcanism produce localized deposits. Winds transport roughly sand-sized material over intermediate distances, while periodic dust storms deposit a global dust layer of the finest fraction. The compositions of clastic sediments can be used to evaluate regional differences in crustal composition and/or weathering processes. Here we examine the growing body of chemical data on soils in Gusev crater and Meridiani Planum returned by the Alpha Particle X-ray Spectrometer (APXS) instruments on the rovers Spirit (MERA) and Opportunity (MERB), following on earlier results based on smaller data sets [1-4].

  16. KSC-03PD-1589

    NASA Technical Reports Server (NTRS)

    2003-01-01

    KENNEDY SPACE CENTER, FLA. On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is prepared to raise it to vertical and lift up the launch tower. It is one of nine that will be mated to the Delta rocket (in the background) to launch Mars Exploration Rover 2. NASAs twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans cant yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  17. KSC-03PD-1587

    NASA Technical Reports Server (NTRS)

    2003-01-01

    KENNEDY SPACE CENTER, FLA. A solid rocket booster arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASAs twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans cant yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  18. Beam-path gas analyzer based on a tunable CO/sub 2/ laser with frequency doubling

    SciTech Connect

    Andreev, Yu.M.; Voevodin, V.G.; Gribenyukov, A.I.; Davydov, V.N.; Zhuravlev, V.I.; Kapitanov, V.A.; Lezina, T.D.; Struchebrov, G.A.; Khmel'nitskii, G.S.

    1988-01-01

    In an attempt to bring the high power and versatility of carbon dioxide lasers to bear on atmospheric measurements for pollutants such as carbon monoxide, nitrogen oxides, and sulfur dioxide, the authors propose parametric frequency converters for carbon dioxide laser radiation in the spectral range required. Field measurements are discussed of the densities of a number of atmospheric gas components, including CO, and of the transparency of the atmosphere to beam paths using a beam-path gas analyzer containing a frequency doubler for a carbon dioxide laser based on the zinc phosphide-germanium phosphide monocrystal. The KAMAK MERA-60 computer system 23 does programmed tuning of the carbon dioxide laser radiation wavelength by rotation of a diffraction grating.

  19. Phytoremediation of Ionic and Methyl Mercury Pollution

    SciTech Connect

    Meagher, Richard B.

    2004-12-01

    Phytoremediation is defined as the use of plants to extract, resist, detoxify, and/or sequester toxic environmental pollutants. The long-term goal of the proposed research is to develop and test highly productive, field-adapted plant species that have been engineered for the phytoremediation of mercury. A variety of different genes, which should enable plants to clean mercury polluted sites are being tested as tools for mercury phytoremediation, first in model laboratory plants and then in potential field species. Several of these genes have already been shown to enhance mercury phytoremediation. Mercury pollution is a serious, world-wide problem affecting the health of human and wildlife populations. Environmentally, the most serious mercury threat is the production of methylmercury (CH3Hg+) by native bacteria at mercury contaminated wetland sites. Methylmercury is inherently more toxic than metallic (Hg(0)) or ionic (Hg(II)) mercury, and because methylmercury is prolifically biomagnified up the food chain, it poses the most immediate danger to animal populations. We have successfully engineered two model plants, Arabidopsis and tobacco, to use the bacterial merB gene to convert methylmercury to less toxic ionic mercury and to use the bacterial merA gene to further detoxify ionic mercury to the least toxic form of mercury, metallic mercury. Plants expressing both MerA and MerB proteins detoxify methylmercury in two steps to the metallic form. These plants germinate, grow, and set seed at normal growth rates on levels of methylmercury or ionic mercury that are lethal to normal plants. Our newest efforts involve engineering plants with several additional bacterial and plant genes that allow for higher levels of mercury resistance and mercury hyperaccumulation. The potential for these plants to hyperaccumulate mercury was further advanced by developing constitutive, aboveground, and root-specific gene expression systems.

  20. Mercury (II) removal by resistant bacterial isolates and mercuric (II) reductase activity in a new strain of Pseudomonas sp. B50A.

    PubMed

    Giovanella, Patricia; Cabral, Lucélia; Bento, Fátima Menezes; Gianello, Clesio; Camargo, Flávio Anastácio Oliveira

    2016-01-25

    This study aimed to isolate mercury resistant bacteria, determine the minimum inhibitory concentration for Hg, estimate mercury removal by selected isolates, explore the mer genes, and detect and characterize the activity of the enzyme mercuric (II) reductase produced by a new strain of Pseudomonas sp. B50A. The Hg removal capacity of the isolates was determined by incubating the isolates in Luria Bertani broth and the remaining mercury quantified by atomic absorption spectrophotometry. A PCR reaction was carried out to detect the merA gene and the mercury (II) reductase activity was determined in a spectrophotometer at 340 nm. Eight Gram-negative bacterial isolates were resistant to high mercury concentrations and capable of removing mercury, and of these, five were positive for the gene merA. The isolate Pseudomonas sp. B50A removed 86% of the mercury present in the culture medium and was chosen for further analysis of its enzyme activity. Mercuric (II) reductase activity was detected in the crude extract of this strain. This enzyme showed optimal activity at pH 8 and at temperatures between 37 °C and 45 °C. The ions NH4(+), Ba(2+), Sn(2+), Ni(2+) and Cd(2+) neither inhibited nor stimulated the enzyme activity but it decreased in the presence of the ions Ca(2+), Cu(+) and K(+). The isolate and the enzyme detected were effective in reducing Hg(II) to Hg(0), showing the potential to develop bioremediation technologies and processes to clean-up the environment and waste contaminated with mercury.

  1. Seasonal and Elevational Variations of Black Carbon and Dust in Snow and Ice in the Solu-Khumbu, Nepal and Estimated Radiative Forcings

    NASA Astrophysics Data System (ADS)

    Kaspari, S.; Painter, T. H.; Gysel, M.; Skiles, M.; Schwikowski, M.

    2014-12-01

    Black carbon (BC) and dust deposited on snow and glacier surfaces can reduce the surface albedo, accelerate melt, and trigger albedo feedback. Assessing BC and dust concentrations in snow and ice in the Himalaya is of interest because this region borders large BC and dust sources, and seasonal snow and glacier ice in this region are an important source of water resources. Snow and ice samples were collected from crevasse profiles and snowpits at elevations between 5400 and 6400 m asl from Mera glacier located in the Solu-Khumbu region of Nepal. The samples were measured for Fe concentrations (used as a dust proxy) via ICP-MS, total impurity content gravimetrically, and BC concentrations using a Single Particle Soot Photometer (SP2). BC and Fe concentrations are substantially higher at elevations < 6000 m due to post-depositional processes including melt and sublimation and greater loading in the lower troposphere. Because the largest areal extent of snow and ice resides at elevations < 6000 m, the higher BC and dust concentrations at these elevations can reduce the snow and glacier albedo over large areas, accelerating melt, affecting glacier mass-balance and water resources, and contributing to a positive climate forcing. Radiative transfer modeling constrained by measurements at 5400 m at Mera La indicates that BC concentrations in the winter-spring snow/ice horizons are sufficient to reduce albedo by 6-10% relative to clean snow, corresponding to localized instantaneous radiative forcings of 75-120 W m-2. The other bulk impurity concentrations, when treated separately as dust, reduce albedo by 40-42% relative to clean snow and give localized instantaneous radiative forcings of 488 to 525 W m-2. Adding the BC absorption to the other impurities results in additional radiative forcings of 3 W m-2. While these results suggest that the snow albedo and radiative forcing effect of dust is considerably greater than BC, there are several sources of uncertainty.

  2. Phytoremediation of Ionic and Methyl Mercury Pollution

    SciTech Connect

    Meagher, Richard B.

    2005-06-01

    Phytoremediation is defined as the use of plants to extract, resist, detoxify, and/or sequester toxic environmental pollutants. The long-term goal of the proposed research is to develop and test highly productive, field-adapted plant species that have been engineered for the phytoremediation of mercury. A variety of different genes, which should enable plants to clean mercury polluted sites are being tested as tools for mercury phytoremediation, first in model laboratory plants and then in potential field species. Several of these genes have already been shown to enhance mercury phytoremediation. Mercury pollution is a serious, world-wide problem affecting the health of human and wildlife populations. Environmentally, the most serious mercury threat is the production of methylmercury (CH3Hg+) by native bacteria at mercury contaminated wetland sites. Methylmercury is inherently more toxic than metallic (Hg(0)) or ionic (Hg(II)) mercury, and because methylmercury is prolifically biomagnified up the food chain, it poses the most immediate danger to animal populations. We have successfully engineered two model plants, Arabidopsis and tobacco, to use the bacterial merB gene to convert methylmercury to less toxic ionic mercury and to use the bacterial merA gene to further detoxify ionic mercury to the least toxic form of mercury, metallic mercury. Plants expressing both MerA and MerB proteins detoxify methylmercury in two steps to the metallic form. These plants germinate, grow, and set seed at normal growth rates on levels of methylmercury or ionic mercury that are lethal to normal plants. Our newest efforts involve engineering plants with several additional bacterial and plant genes that allow for higher levels of mercury resistance and mercury hyperaccumulation. The potential for these plants to hyperaccumulate mercury was further advanced by developing constitutive, aboveground, and root-specific gene expression systems. Our current strategy is to engineer plants to

  3. Renormalization group constructions of topological quantum liquids and beyond

    NASA Astrophysics Data System (ADS)

    Swingle, Brian; McGreevy, John

    2016-01-01

    We give a detailed physical argument for the area law for entanglement entropy in gapped phases of matter arising from local Hamiltonians. Our approach is based on renormalization group (RG) ideas and takes a resource oriented perspective. We report four main results. First, we argue for the "weak area law": any gapped phase with a unique ground state on every closed manifold obeys the area law. Second, we introduce an RG based classification scheme and give a detailed argument that all phases within the classification scheme obey the area law. Third, we define a special subclass of gapped phases, topological quantum liquids, which captures all examples of current physical relevance, and we rigorously show that topological quantum liquids obey an area law. Fourth, we show that all topological quantum liquids have MERA representations which achieve unit overlap with the ground state in the thermodynamic limit and which have a bond dimension scaling with system size L as ec logd(1+δ )(L ) for all δ >0 . For example, we show that chiral phases in d =2 dimensions have an approximate MERA with bond dimension ec log2(1+δ )(L ). We discuss extensively a number of subsidiary ideas and results necessary to make the main arguments, including field theory constructions. While our argument for the general area law rests on physically motivated assumptions (which we make explicit) and is therefore not rigorous, we may conclude that "conventional" gapped phases obey the area law and that any gapped phase which violates the area law must be a dragon.

  4. Chlor-alkali plant contamination of Aussa River sediments induced a large Hg-resistant bacterial community

    NASA Astrophysics Data System (ADS)

    Baldi, Franco; Marchetto, Davide; Gallo, Michele; Fani, Renato; Maida, Isabel; Covelli, Stefano; Fajon, Vesna; Zizek, Suzana; Hines, Mark; Horvat, Milena

    2012-11-01

    A closed chlor-alkali plant (CAP) discharged Hg for decades into the Aussa River, which flows into Marano Lagoon, resulting in the large-scale pollution of the lagoon. In order to get information on the role of bacteria as mercury detoxifying agents, analyses of anions in the superficial part (0-1 cm) of sediments were conducted at four stations in the Aussa River. In addition, measurements of biopolymeric carbon (BPC) as a sum of the carbon equivalent of proteins (PRT), lipids (LIP), and carbohydrates (CHO) were performed to correlate with bacterial biomass such as the number of aerobic heterotrophic cultivable bacteria and their percentage of Hg-resistant bacteria. All these parameters were used to assess the bioavailable Hg fraction in sediments and the potential detoxification activity of bacteria. In addition, fifteen isolates were characterized by a combination of molecular techniques, which permitted their assignment into six different genera. Four out of fifteen were Gram negative with two strains of Stenotrophomonas maltophilia, one Enterobacter sp., and one strain of Brevibacterium frigoritolerans. The remaining strains (11) were Gram positive belonging to the genera Bacillus and Staphylococcus. We found merA genes in only a few isolates. Mercury volatilization from added HgCl2 and the presence of plasmids with the merA gene were also used to confirm Hg reductase activity. We found the highest number of aerobic heterotrophic Hg-resistant bacteria (one order magnitude higher) and the highest number of Hg-resistant species (11 species out of 15) at the confluence of the River Aussa and Banduzzi's channel, which transport Hg from the CAP, suggesting that Hg is strongly detoxified [reduced to Hg(0)] at this location.

  5. Competition for Ammonia Structures the Composition of a Hydrothermal Microbial Community

    NASA Astrophysics Data System (ADS)

    Hamilton, T. L.; Peters, J.; Boyd, E. S.

    2012-12-01

    All life requires fixed nitrogen (N), and its bioavailability is what often limits ecosystem productivity. Biological nitrogen fixation, or the reduction of dinitrogen (N2) to ammonia (NH3), is a keystone process in N limited ecosystems, providing bioavailable forms of fixed nitrogen for members of the community. N2 fixing organisms likely represent a 'bottom up control' on the structure of communities that develop in N limited environments. N2 fixation is catalyzed by a limited number of metabolically diverse bacteria and some of the methanogenic Archaea and occurs in a variety of physically and geochemically diverse environments. Nitrification, or the sequential oxidation of NH4+ to nitrite (NO2-) and ultimately nitrate (NO3-), is catalyzed by several lineages of Proteobacteria at temperatures of < 62°C and by members of the Thaumarcheota at temperatures up to 90°C. Nitrification can thus be considered a top down control on the structure of communities that develop in N limited environments. Our preliminary assessment of 16S rRNA genes and their transcripts at the source of Perpetual Spouter, Yellowstone National Park, Wyoming (pH = 7.2, Temp. = 84°C) reveals the presence of diazotrophs and archaeal nitrifiers. Likewise, chemical analyses of source water revealed low concentrations of NH4+ but relatively high concentrations of NO2- and NO3-. Together, these data suggest that the oxidation of NH4+ by archaeal nitrifiers may be maintaining the low concentration of the NH4+ despite the production of NH4+ by diazotrophs. In an effort to better define the interaction between archaeal nitrifiers and diazotrophs, we undertook coupled transcriptional and activity-based assays in the presence and absence of allylthiourea (ATU), an inhibitor of nitrification, as well as ammonia, which suppresses N2 fixation. In addition, sequence based analyses of nifH (encode a protein required for N2 fixation) and amoA transcripts (encode a protein required for archaeal nitrification

  6. The N cycle in Earth subsurface. Reactivity of functional genes to anthropogenic CO2 injections.

    NASA Astrophysics Data System (ADS)

    Trias, Rosalia; Gérard, Emmanuelle; Le Campion, Paul; Gíslason, Sigurður R.; Aradóttir, Edda S.; Alfreðsson, Helgui A.; Mesfin, Kiflom G.; Snæbjörnsdóttir, Sandra Ó.; Ménez, Bénédicte

    2014-05-01

    The Nitrogen cycle has been widely studied in surface ecosystems, due to the importance of this nutrient for the organisms' development, and to the impact in the environment of most of the N forms, many of them being considered pollutants. However, little is known about the importance of the N-related metabolisms in subsurface systems now recognized to host diverse and active microbial life. In this study, we have periodically sampled the subsurface aquifers of the Icelandic pilot site for CO2 storage associated with the geothermal plant of Hellisheidi (operated by Reykjavik Energy; http://www.or.is/en/projects/carbfix). With the aim of understanding the dynamics of N-cycle in the subsurface, and its reactivity to CO2 injections, we quantified through qPCR the functional genes amoA (archaea), amoA (bacteria), nirK, nirS, nosZ, nifH, and the 16SrRNA genes of the anammox, total archaea and total bacteria. The 16SrRNA gene quantification provided values of around 107 gene copies/l at non injection periods. CO2 injection caused first a slight decrease probably due to pH decrease or toxicity by oxygen contamination during the injections. Two months after injection, the copy numbers increased up to 109 gene copies/l, and slowly returned to pre-injection values. The archaeal 16S rDNA copy numbers showed a similar reaction, with higher toxicity effects, and a lower increase afterwards. Due to the high reactivity of the microbial populations to CO2 injections, all the N cycle quantifications were related to the total 16S rDNA copies for normalization. Nitrifying genes (amoA) were mainly represented by the ammonia oxidizing archaea, and were apparently not affected by CO2 injections. Anammox bacteria were present in a very low percentage, and the obtained copy numbers tended to decrease after the injection. These results were surprising due to the autotrophic character of ammonia oxidizers, but could be explained by a competitive exclusion. On the contrary, N-fixation (nif

  7. Subsurface Nitrogen-Cycling Microbial Communities at Uranium Contaminated Sites in the Colorado River Basin

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Bargar, J.; Williams, K. H.; Dam, W. L.; Francis, C.

    2015-12-01

    Throughout the Colorado River Basin (CRB), uranium (U) persists as a relic contaminant of former ore processing activities. Elevated solid-phase U levels exist in fine-grained, naturally-reduced zone (NRZ) sediments intermittently found within the subsurface floodplain alluvium of the following Department of Energy-Legacy Management sites: Rifle, CO; Naturita, CO; and Grand Junction, CO. Coupled with groundwater fluctuations that alter the subsurface redox conditions, previous evidence from Rifle, CO suggests this resupply of U may be controlled by microbially-produced nitrite and nitrate. Nitrification, the two-step process of archaeal and bacterial ammonia-oxidation followed by bacterial nitrite oxidation, generates nitrate under oxic conditions. Our hypothesis is that when elevated groundwater levels recede and the subsurface system becomes anoxic, the nitrate diffuses into the reduced interiors of the NRZ and stimulates denitrification, the stepwise anaerobic reduction of nitrate/nitrite to dinitrogen gas. Denitrification may then be coupled to the oxidation of sediment-bound U(IV) forming mobile U(VI), allowing it to resupply U into local groundwater supplies. A key step in substantiating this hypothesis is to demonstrate the presence of nitrogen-cycling organisms in U-contaminated, NRZ sediments from the upper CRB. Here we investigate how the diversity and abundances of nitrifying and denitrifying microbial populations change throughout the NRZs of the subsurface by using functional gene markers for ammonia-oxidation (amoA, encoding the α-subunit of ammonia monooxygenase) and denitrification (nirK, nirS, encoding nitrite reductase). Microbial diversity has been assessed via clone libraries, while abundances have been determined through quantitative polymerase chain reaction (qPCR), elucidating how relative numbers of nitrifiers (amoA) and denitrifiers (nirK, nirS) vary with depth, vary with location, and relate to uranium release within NRZs in sediment

  8. 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

  9. Pyrosequencing reveals the influence of elevated atmospheric CO2 on the composition of archaeal communities in the rhizosphere of C3 and C4 crops

    NASA Astrophysics Data System (ADS)

    Nelson, D. M.; Cann, I. K.; Mackie, R. I.

    2008-12-01

    The projected increase in atmospheric CO2 concentrations throughout the 21st century is likely to increase aboveground and belowground plant productivity and cause changes in the quantity and quality of plant root exudates, although plants using C4 photosynthesis are likely to be only affected during times of drought (Leakey et al., 2006, Plant Physiology, 140, 779). Evidence is emerging from molecular tools that these changes may influence the abundance and composition of soil microbial communities that regulate key soil processes, such as nitrogen cycling (Lesaulnier et al., 2008, Environmental Microbiology, 10, 926). However, most molecular tools are not well-suited for comparing multiple samples at great sequencing depth, which is critical when considering soil microbial communities of high diversity. To overcome these limitations we used pyrosequencing and quantitative PCR (qPCR) of two genes (the V3 region of 16S rDNA and the amoA gene) to examine intra- and inter-treatment variability in the abundance and composition of microbial communities in the rhizosphere of soybean (C3) and maize (C4) grown in field conditions under ambient (~380 ppm) and elevated (~550 ppm) CO2 using FACE (free-air concentration enrichment) technology during the 2006 growing season in central Illinois. We specifically focused on archaeal communities because of their key role in nitrification (Leininger et al., 2006, Nature, 442, 806). The majority (>97%) of recovered sequences were from members of the phylum Crenarchaeota. Principle component analysis of sequence results from the V3 and amoA genes indicated significant (p<0.05) differences in the composition of rhizosphere archaeal communities between ambient and elevated CO2 beneath soybean, but not maize. qPCR suggested no significant difference in the abundance of archaea between treatments for soybean and maize. The lack of response of archaeal community composition beneath maize to elevated CO2 is consistent with relatively high

  10. Enhancing Nitrification at Low Temperature with Zeolite in a Mining Operations Retention Pond

    PubMed Central

    Miazga-Rodriguez, Misha; Han, Sukkyun; Yakiwchuk, Brian; Wei, Kai; English, Colleen; Bourn, Steven; Bohnert, Seth; Stein, Lisa Y.

    2012-01-01

    Ammonium nitrate explosives are used in mining operations at Diavik Diamond Mines Inc. in the Northwest Territories, Canada. Residual nitrogen is washed into the mine pit and piped to a nearby retention pond where its removal is accomplished by microbial activity prior to a final water treatment step and release into the sub-Arctic lake, Lac de Gras. Microbial removal of ammonium in the retention pond is rapid during the brief ice-free summer, but often slows under ice cover that persists up to 9 months of the year. The aluminosilicate mineral zeolite was tested as an additive to retention pond water to increase rates of ammonium removal at 4°C. Water samples were collected across the length of the retention pond monthly over a year. The structure of the microbial community (bacteria, archaea, and eukarya), as determined by denaturing gradient gel electrophoresis of PCR-amplified small subunit ribosomal RNA genes, was more stable during cold months than during July–September, when there was a marked phytoplankton bloom. Of the ammonia-oxidizing community, only bacterial amoA genes were consistently detected. Zeolite (10 g) was added to retention pond water (100 mL) amended with 5 mM ammonium and incubated at 12°C to encourage development of a nitrifying biofilm. The biofilm community was composed of different amoA phylotypes from those identified in gene clone libraries of native water samples. Zeolite biofilm was added to fresh water samples collected at different times of the year, resulting in a significant increase in laboratory measurements of potential nitrification activity at 4°C. A significant positive correlation between the amount of zeolite biofilm and potential nitrification activity was observed; rates were unaffected in incubations containing 1–20 mM ammonium. Addition of zeolite to retention ponds in cold environments could effectively increase nitrification rates year-round by concentrating active nitrifying biomass. PMID:22866052

  11. Wastewater and Saltwater: Studying the Biogeochemistry and Microbial Activity Associated with Wastewater Inputs to San Francisco Bay

    NASA Astrophysics Data System (ADS)

    Challenor, T.; Menendez, A. D.; Damashek, J.; Francis, C. A.; Casciotti, K. L.

    2014-12-01

    Nitrification is the process of converting ammonium (NH­­4+) into nitrate (NO3-), and is a crucial step in removing nitrogen (N) from aquatic ecosystems. This process is governed by ammonia-oxidizing bacteria (AOB) and archaea (AOA) that utilize the ammonia monooxygenase gene (amoA). Studying the rates of nitrification and the abundances of ammonia-oxidizing microorganisms in south San Francisco Bay's Artesian Slough, which receives treated effluent from the massive San Jose-Santa Clara Regional Wastewater Facility, are important for understanding the cycling of nutrients in this small but complex estuary. Wastewater inputs can have negative environmental impacts, such as the release of nitrous oxide, a byproduct of nitrification and a powerful greenhouse gas. Nutrient inputs can also increase productivity and sometimes lead to oxygen depletion. Assessing the relative abundance and diversity of AOA and AOB, along with measuring nitrification rates gives vital information about the biology and biogeochemistry of this important N-cycling process. To calculate nitrification rates, water samples were spiked with 15N-labeled ammonium and incubated in triplicate for 24 hours. Four time-points were extracted across the incubation and the "denitrifier" method was used to measure the isotopic ratio of nitrate in the samples over time. In order to determine relative ratios of AOB to AOA, DNA was extracted from water samples and used in clade-specific amoA PCR assays. Nitrification rates were detectable in all locations sampled and were higher than in other regions of the bay, as were concentrations of nitrate and ammonium. Rates were highest in the regions of Artesian Slough most directly affected by wastewater effluent. AOB vastly outnumbered AOA, which is consistent with other studies showing that AOB prefer high nutrient environments. AOB diversity includes clades of Nitrosospira and Nitrosomonas prevalent in estuarine settings. Many of the sequenced genes are related

  12. Nitrification and its oxygen consumption along the turbid Chang Jiang River plume

    NASA Astrophysics Data System (ADS)

    Hsiao, S. S.-Y.; Hsu, T.-C.; Liu, J.-w.; Xie, X.; Zhang, Y.; Lin, J.; Wang, H.; Yang, J.-Y. T.; Hsu, S.-C.; Dai, M.; Kao, S.-J.

    2014-04-01

    Nitrification is a series of processes that oxidizes ammonia to nitrate, which contributes to hypoxia development in coastal oceans, especially in eutrophicated regions. The nitrification rate of bulk water (NRb) and particle free water (NRpf, particle > 3 μm eliminated) were determined along the Chang Jiang River plume in August 2011 by nitrogen isotope tracer technique. Measurements of dissolved oxygen (DO), community respiration rate (CR), nutrients, dissolved organic nitrogen (DON), total suspended matter (TSM), particulate organic carbon/nitrogen (POC / PON), acid-leachable iron and manganese on suspended particles and both archaeal and β-proteobacterial ammonia monooxygenase subunit A gene (amoA) abundance on size-fractioned particles (> 3 μm and 0.22-3 μm) were conducted. The NRb ranged from undetectable up to 4.6 μmol L-1 day-1, peaking at a salinity of ~ 29. NRb values were positively correlated with ammonium concentration, suggesting the importance of substrate in nitrification. In the river mouth and the inner plume, NRb was much higher than NRpf, indicating that the nitrifying microorganism is mainly particle associated, which was supported by its significant correlation with amoA gene abundance and TSM concentration. The estimated oxygen demands of nitrification accounted for 0.32 to 318% of CR, in which 50% samples demanded more oxygen than that predicted by by the Redfield model (23%), indicating that oxygen might not be the sole oxidant though DO was sufficient (> 58 μmol kg-1) throughout the observation period. The excess nitrification-associated oxygen demand (NOD) showed a tendency to occur at lower DO samples accompanied by higher acid-leachable Fe / Mn, which implied reactive Fe3+ / Mn4+ may play a role as oxidant in the nitrification process. Stoichiometric calculation suggested that reactive Fe on particles was 10 times the oxidant demand required to complete ammonia oxidation in the entire plume. The potential involvement of reactive

  13. 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

  14. Unraveling the active microbial populations involved in nitrogen utilization in a vertical subsurface flow constructed wetland treating urban wastewater.

    PubMed

    Pelissari, Catiane; Guivernau, Miriam; Viñas, Marc; de Souza, Samara Silva; García, Joan; Sezerino, Pablo Heleno; Ávila, Cristina

    2017-04-15

    The dynamics of the active microbial populations involved in nitrogen transformation in a vertical subsurface flow constructed wetland (VF) treating urban wastewater was assessed. The wetland (1.5m(2)) operated under average loads of 130gCODm(-2)d(-1) and 17gTNm(-2)d(-1) in Period I, and 80gCODm(-2)d(-1) and 19gTNm(-2)d(-1) in Period II. The hydraulic loading rate (HLR) was 375mmd(-1) and C/N ratio was 2 in both periods. Samples for microbial characterization were collected from the filter medium (top and bottom layers) of the wetland, water influent and effluent at the end of Periods I (Jun-Oct) and II (Nov-Jan). The combination of qPCR and high-throughput sequencing (NGS, MiSeq) assessment at DNA and RNA level of 16S rRNA genes and nitrogen-based functional genes (amoA and nosZ-clade I) revealed that nitrification was associated both with ammonia-oxidizing bacteria (AOB) (Nitrosospira) and ammonia-oxidizing archaea (AOA) (Nitrososphaeraceae), and nitrite-oxidizing bacteria (NOB) such as Nitrobacter. Considering the active abundance (based in amoA transcripts), the AOA population revealed to be more stable than AOB in both periods and depths of the wetland, being less affected by the organic loading rate (OLR). Although denitrifying bacteria (nosZ copies and transcripts) were actively detected in all depths, the denitrification process was low (removal of 2gTNm(-2)d(-1) for both periods) concomitant with NOx-N accumulation in the effluent. Overall, AOA, AOB and denitrifying bacteria (nosZ) were observed to be more active in bottom than in top layer at lower OLR (Period II). A proper design of OLR and HLR seems to be crucial to control the activity of microbial biofilms in VF wetlands on the basis of oxygen, organic-carbon and NOx-N forms, to improve their capacity for total nitrogen removal.

  15. Nitrification and Nitrifying Bacteria in the Lower Seine River and Estuary (France)

    PubMed Central

    Cébron, Aurélie; Berthe, Thierry; Garnier, Josette

    2003-01-01

    The Achères wastewater treatment plant, located just downstream of Paris, discharges its effluents into the lower Seine River. The effluents contain large numbers of heterotrophic bacteria, organic matter, and ammonium and are a source of nitrifying bacteria. As a result, degradation of organic matter by heterotrophic bacteria and subsequent oxygen depletion occur immediately downstream of the effluent outlet, whereas nitrifying bacteria apparently need to build up a significant biomass before ammonium oxidation significantly depletes the oxygen. We quantified the potential total nitrifying activity and the potential activities of the ammonia- and nitrite-oxidizing communities along the Seine River. In the summer, the maximum nitrifying activity occurs in the upper freshwater estuary, ∼200 km downstream of Achères. The quantities of nitrifying bacteria, based on amoA gene copy numbers, and of Nitrobacter organisms, based on 16S rRNA gene copy numbers, were correlated with the potential nitrifying activities. The species composition of ammonia-oxidizing bacteria was investigated at two sites: the Triel station just downstream from Achères (km 84) and the Seine freshwater estuary at the Duclair station (km 278). By means of PCR primers targeting the amoA gene, a gene library was created. Phylogenetic analysis revealed that the majority of the analyzed clones at both sites were affiliated with the genus Nitrosomonas. The Nitrosomonas oligotropha- and Nitrosomonas urea-related clones represented nearly 81% of the community of ammonia-oxidizing bacteria at Triel and 60% at Duclair. Two other ammonia-oxidizing clusters of the β subclass of the Proteobacteria, i.e., Nitrosomonas europaea- and Nitrosospira-like bacteria, were found in smaller numbers. The major change in the ammonia-oxidizing community between the two stations along the Seine River-upper estuary continuum was the replacement of the N. oligotropha- and N. urea-related bacteria by the Nitrosospira

  16. Potential for Nitrogen Fixation and Nitrification in the Granite-Hosted Subsurface at Henderson Mine, CO

    PubMed Central

    Swanner, Elizabeth D.; Templeton, Alexis S.

    2011-01-01

    The existence of life in the deep terrestrial subsurface is established, yet few studies have investigated the origin of nitrogen that supports deep life. Previously, 16S rRNA gene surveys cataloged a diverse microbial community in subsurface fluids draining from boreholes 3000 feet deep at Henderson Mine, CO, USA (Sahl et al., 2008). The prior characterization of the fluid chemistry and microbial community forms the basis for the further investigation here of the source of NH4+. The reported fluid chemistry included N2, NH4+ (5–112 μM), NO2− (27–48 μM), and NO3− (17–72 μM). In this study, the correlation between low NH4+ concentrations in dominantly meteoric fluids and higher NH4+ in rock-reacted fluids is used to hypothesize that NH4+ is sourced from NH4+-bearing biotite. However, biotite samples from the host rocks and ore-body minerals were analyzed by Fourier transform infrared (FTIR) microscopy and none-contained NH4+. However, the nitrogenase-encoding gene nifH was successfully amplified from DNA of the fluid sample with high NH4+, suggesting that subsurface microbes have the capability to fix N2. If so, unregulated nitrogen fixation may account for the relatively high NH4+ concentrations in the fluids. Additionally, the amoA and nxrB genes for archaeal ammonium monooxygenase and nitrite oxidoreductase, respectively, were amplified from the high NH4+ fluid DNA, while bacterial amoA genes were not. Putative nitrifying organisms are closely related to ammonium-oxidizing Crenarchaeota and nitrite-oxidizing Nitrospira detected in other subsurface sites based upon 16S rRNA sequence analysis. Thermodynamic calculations underscore the importance of NH4+ as an energy source in a subsurface nitrification pathway. These results suggest that the subsurface microbial community at Henderson is adapted to the low nutrient and energy environment by their capability of fixing nitrogen, and that fixed nitrogen may support subsurface biomass via

  17. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils

    PubMed Central

    Lammel, Daniel R.; Feigl, Brigitte J.; Cerri, Carlos C.; Nüsslein, Klaus

    2015-01-01

    Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve

  18. 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

  19. Evaluating the effects of land use and cover change on the decrease of surface wind speed over China in recent 30 years using a statistical downscaling method

    NASA Astrophysics Data System (ADS)

    Wu, Jian; Zha, Jinlin; Zhao, Deming

    2017-01-01

    The long-term decrease of surface wind speed (SWS) has been revealed by previous studies in China in recent decades, but the reasons for the SWS decrease remain uncertain. In this paper, we evaluated the effects of land use and cover change (LUCC) on the SWS decrease during 1980-2011 over the Eastern China Plain (ECP) region using a combined method of statistical downscaling and observation minus reanalysis data, which was used to improve the climate prediction of general circulation models and to evaluate the influence of LUCC on climate change. To exclude the potential influence of LUCC on SWS observation, a statistical downscaling model (SDM) was established during 1980-1992 because a lower extent of LUCC occurred during this period than in later periods. The skill of the SDM was checked by comparing the results of different predictor combinations. Then, SDM was used to improve the wind speed data at 10 m above the surface in the ERA-Interim reanalysis data (V10m-ERA) during 1993-2011, which decreased the error in the reanalysis wind speed as far as possible. Then, the difference between the station observed SWS (V10m-OBV) and the downscaled SWS (V10m-SDM) during 1993-2011 (SWSD) was considered the quantitative estimation of the influence of the LUCC on SWS in this period. The V10m-SDM can capture both the large-scale and local characteristics in the observation, and their patterns are very similar. V10m-SDM has better performance in the spatial-temporal changes than does V10m-ERA with respect to V10m-OBV. The impact of LUCC on the SWS was pronounced, the SWSD was -0.24 m s-1 in 1993, and the SWSD reached -0.56 m s-1 in 2011. LUCC could induce a 0.17 m s-1 wind speed decrease per 10 year in the ECP region during 1993-2011. Furthermore, each 10 % rise of the urbanization rate could cause an approximately 0.12 m s-1 decrease in wind speed. Additionally, pressure-gradient force was eliminated as the primary cause of the observed long-term decrease of SWS in ECP by

  20. Manila clams from Hg polluted sediments of Marano and Grado lagoons (Italy) harbor detoxifying Hg resistant bacteria in soft tissues

    SciTech Connect

    Baldi, Franco; Gallo, Michele; Marchetto, Davide; Faleri, Claudia; Maida, Isabel; Fani, Renato

    2013-08-15

    A mechanism of mercury detoxification has been suggested by a previous study on Hg bioaccumulation in Manila clams (Ruditapes philippinarum) in the polluted Marano and Grado lagoons and in this study we demonstrate that this event could be partly related to the detoxifying activities of Hg-resistant bacteria (MRB) harbored in clam soft tissues. Therefore, natural clams were collected in six stations during two different periods (winter and spring) from Marano and Grado Lagoons. Siphons, gills and hepatopancreas from acclimatized clams were sterile dissected to isolate MRB. These anatomical parts were glass homogenized or used for whole, and they were lying on a solid medium containing 5 mg l{sup −1} HgCl{sub 2} and incubated at 30 °C. A total of fourteen bacterial strains were isolated and were identified by 16S rDNA sequencing and analysis, revealing that strains were representative of eight bacterial genera, four of which were Gram-positive (Enterococcus, Bacillus, Jeotgalicoccus and Staphylococcus) and other four were Gram-negative (Stenotrophomonas, Vibrio, Raoultella and Enterobacter). Plasmids and merA genes were found and their sequences determined. Fluorescence in situ hybridization (FISH) technique shows the presence of Firmicutes, Actinobacteria and Gammaproteobacteria by using different molecular probes in siphon and gills. Bacterial clumps inside clam flesh were observed and even a Gram-negative endosymbiont was disclosed by transmission electronic microscope inside clam cells. Bacteria harbored in cavities of soft tissue have mercury detoxifying activity. This feature was confirmed by the determination of mercuric reductase in glass-homogenized siphons and gills. -- Highlights: ► We isolated Gram-positive and Gram-negative Hg resistant strains from soft tissues of Ruditapes philippinarum. ► We identify 14 mercury resistant strains by 16S rRNA gene sequences. ► Bacteria in siphon and gill tissues of clams were observed by TEM and identified

  1. Executive functions in anorexia nervosa.

    PubMed

    Jáuregui-Lobera, Ignacio

    2014-03-01

    Introducción: Los mecanismos fisiopatológicos que explican el desarrollo y la persistencia de la anorexia nerviosa (AN) siguen sin estar claros. Con respecto al funcionamiento neuropsicológico, se han señalado alteraciones en las funciones ejecutivas, especialmente en la flexibilidad cognitiva y en los procesos de toma de decisiones. Objetivos: El objetivo de este trabajo fue revisar el estado actual de los estudios neuropsicológicos sobre anorexia nerviosa, especialmente los centrados en las funciones ejecutivas. Métodos: Se realizó un proceso de búsqueda con tres relevantes bases de datos electrónicas, así como una búsqueda adicional con las referencias incluidas en los documentos analizados. Finalmente hay que mencionar otras revisiones ya publicadas y una búsqueda manual de otras fuentes. Resultados y discusión: Los datos de comparación de pacientes y controles sanos siguen siendo controvertidos, así como la comparación entre los diferentes trastornos de la alimentación con respecto a la disfunción neuropsicológica. El papel de variables como depresión, ansiedad y obsesividad necesita ser aclarado. Parece que hay alguna base para afirmar que existen algunos puntos en común entre los llamados trastornos de peso extremo (anorexia, obesidad). El vínculo entre la disfunción neuropsicológica en AN y biomarcadores aún no está claro. El papel de los déficits neuropsicológicos en la AN, como factores iniciales o simplemente como meras consecuencias, tampoco está aclarado. La relación entre los trastornos de imagen corporal y la disfunción neuropsicológica debe asimismo aclararse. Los datos sobre las similitudes, en cuanto a la disfunción neuropsicológica, entre AN y otros trastornos mentales pueden ser considerados, hasta la fecha, como una mera aproximación. Lo mismo ocurre con la relación entre el rendimiento neuropsicológico de los pacientes con AN y la personalidad o el género.

  2. Mercury resistance transposons in Bacilli strains from different geographical regions.

    PubMed

    Matsui, Kazuaki; Yoshinami, Satoshi; Narita, Masaru; Chien, Mei-Fang; Phung, Le T; Silver, Simon; Endo, Ginro

    2016-03-01

    A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of TnMERI1-like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn5084, Tn5085, Tn(d)MER3 (a newly identified deleted transposon-like fragment) and Tn6294 (a newly identified transposon). Tn(d)MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn6294 is an 8.5-kb sequence that is possibly derived from Tn(d)MER3 by integration of a TnMERI1-type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn5084 of B. cereus strain RC607. Strains with Tn6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn(d)MER3 and Tn6294 are shorter prototypes for TnMERI1-like transposons. Identification of Tn6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of TnMERI1-like transposons across bacterial species and geographical barriers.

  3. Seasonal changes of mercury reduction and methylation in Gulf of Trieste (north Adriatic Sea)

    NASA Astrophysics Data System (ADS)

    Horvat, M.; Bratkic, A.; Koron, N.; Faganeli, J.; Ribeiro Guevara, S.; Tinta, T.

    2014-12-01

    We have successfully improved and applied the 197Hg radiotracer method during the sampling campaign from March until November 2011, collecting and incubating sediments and waters with low 197Hg2+ additions without significantly increasing natural levels. The evolution of Me197Hg and DGM197 was followed. In addition, we have performed Hg speciation of the water column and sediment, determined diversity of microbial community and investigated microbial resistance to Hg through presence of merA and merB genes. Our results showed repeatedly that methylation does not occur in the water column of the GoT, and confirmed that sediments are the principal methylation site, as well as the source of MeHg to the water column. Its formation seems to be closely linked to nutrient cycling at the sediment-water interface, where degradation of organic matter with accompanying oxygen consumption significantly stimulates MeHg production (range 0.85 pM - 3.39 pM). The water column showed a pronounced capability for 197Hg2+ reduction (up to 25% d-1), confirming that the GoT is a source of Hg to the atmosphere. Whether reduction was directly linked to genetic resistance; was a consequence of non-specific redox reactions or of other microbial mechanisms could not be demonstrated. Neither merA nor merB genes were detected, but the microbial community structure was changing in the water column seasonally, as did the reduction rates in the experiments. Most importantly, it was shown that 197Hg methodology is sensitive enough to follow Hg biogeochemical transformations at environmental levels. The advantage is that the minimal additions of 197Hg do not disturb the natural processes occurring in the environment and that very small changes can be detected. Hg stress in the Gulf can directly manifest itself in biota and consequently result in a threat to environmental and public health and therefore needs to be seen in the light of changing global climate and marine environment.

  4. Geometry and lithofacies of coarse-grained injectites and extrudites in a late Pliocene trench-slope basin on the southern Boso Peninsula, Japan

    NASA Astrophysics Data System (ADS)

    Ito, Makoto; Ishimoto, Sakumi; Ito, Kento; Kotake, Nobuhiro

    2016-10-01

    This study investigates the geometry and internal structures of coarse- to very coarse-grained volcanic sandstones and volcanic breccias with many siltstone clasts (interpreted to be sill-like injectites and extrudites) occurring in an upper Pliocene trench-slope basin succession on the southern Boso Peninsula, Japan. The injectites occur in the uppermost Shiramazu Formation, and pinch out laterally into siltstone-dominated deposits of the Mera Formation. Their thicknesses vary from a few centimeters to 2 m. The basal and upper contacts of the injectites with host muddy deposits are sharp and/or erosional, and are locally discordant with the bedding of the host deposits. Siltstone clasts, which were ripped up or ripped down from the host muddy deposits, are commonly incorporated into the injectites, although some siltstone clasts have geological ages older than those of the host deposits. Seven lithofacies have been identified in the injectites based on the internal structures. The combinations of internal structures are different from those of high-density turbidity current deposits and debrites, and suggest that injection was promoted by a combination of turbulent and laminar flow conditions. The extrudites show an overall convex-up geometry and possess lithological features similar to those of the injectites. They have been identified in the Rendaiji Conglomerate Member, which is encased in the Mera Formation, and which rests on the uppermost Shiramazu Formation. The extrudites are characterized by gently undulating waveforms that show upstream migration and climbing stacking patterns similar to the cross-sectional geometry of cyclic steps or upstream-migrating antidunes. The active eruption of solid-liquid mixtures onto the seafloor and sedimentary piles may have subsequently collapsed to produce supercritical high-density gravity currents down the flanks of a neptunian volcano. The injectites and extrudites locally contain Calyptogena shells and shell

  5. The physical basis of enhanced temperature index ice melt parameterizations in the Nepal Himalaya.

    NASA Astrophysics Data System (ADS)

    Litt, Maxime; Shea, Joseph; Koch, Inka; Wagnon, Patrick

    2016-04-01

    Glacier melt is an important component of seasonal water flows in the Himalayas. Due to scarce data availability and computational convenience, most glaciological projections in the Himalayan region derive ice melt from temperature index (TI) or enhanced temperature index (ETI) parameterizations, which require only temperature and solar radiation as inputs. Still, the processes linking these variables to melt remain poorly documented under high-altitude climates, where the air is cold, and the main input is shortwave radiation. In this study, we question the physical basis of enhanced temperature index (ETI) melt parameterizations in the Nepal Himalayas. Using atmospheric weather station (AWS) installed on Yala glacier at 5090 m a.s.l and Mera glaciers at 6350 m a.s.l., we study the surface energy balance (SEB) during one melt season, i.e, the monsoon and surrounding weeks, in 2014. The SEB estimates provide insights into the atmospheric controls on the glaciers. We study the variability of correlation coefficients linking daily means of temperature, SEB and SEB components. On Yala at 5090 m a.s.l, energy inputs are high during the pre-monsoon due to low surface albedo and strong incoming solar radiation near the solstice, and melt is strong. The temperature correlates moderately with the SEB (R = 0.58) mainly through sublimation and net longwave radiation. During the monsoon snow deposition reduces the magnitude of net shortwave radiation, thus dampening the melt rates. Strong longwave emission from clouds compensates for the surface emission, and the correlation of temperature with the SEB, mainly explained through net shortwave radiation, decreases (R = 0.49). During the post-monsoon, high albedo, heat losses through sublimation and clear-skies favoring longwave losses at the surface lead to a near zero SEB, and reduced melt. Temperature correlates well with the SEB (R = 0.88) through net longwave radiation. On Mera at 6300 m a.s.l, high surface albedo and

  6. Influence of altitude on ozone levels and variability in the lower troposphere: a ground-based study for western Europe over the period 2001-2004

    NASA Astrophysics Data System (ADS)

    Chevalier, A.; Gheusi, F.; Delmas, R.; Ordó\\ Nez, C.; Sarrat, C.; Zbinden, R.; Thouret, V.; Athier, G.; Cousin, J.-M.

    2007-01-01

    The PAES (French acronym for synoptic scale atmospheric pollution) network focuses on the chemical composition (ozone, CO, NOx/y and aerosols) of the lower troposphere (0-3000 m). Its high-altitude surface stations located in different mountainous areas in France complete the low-altitude rural MERA stations (the French contribution to the european program EMEP, European Monitoring and Evaluation Program). They are representative of pollution at the scale of the French territory because they are away from any major source of pollution. This study deals with ozone observations between 2001 and 2004 at 11 stations from PAES and MERA, in addition to 16 elevated stations located in mountainous areas of Switzerland, Germany, Austria, Italy and Spain. The set of stations covers a range of altitudes between 115 and 3550 m. The comparison between recent ozone mixing ratios with those of the last decade found in the literature for two high-elevation sites (Pic du Midi, 2877 m and Jungfraujoch, 3580 m) leads to a trend that has slowed down compared to old trends but remains positive. This could be attribuable to the reduction of ozone precursors at European scale, that however do not compensate an ozone increase at the global scale. Averaged levels of ozone increase with elevation in good agreement with data provided by the airborne observation system MOZAIC (Measurement of OZone and water vapour by Airbus In-service airCraft), showing a highly stratified ozone field in the lower troposphere, with a transition at about 1000 m asl between a sharp gradient (30 ppb/km) below but a gentler gradient (3 ppb/km) above. Ozone variability also reveals a clear transition between boundary-layer and free-tropospheric regimes at the same altitude. Below, diurnal photochemistry accounts for about the third of the variability in summer, but less than 20% above - and at all levels in winter - where ozone variability is mostly due to day-to-day changes (linked to weather conditions or

  7. Influence of Edaphic, Climatic, and Agronomic Factors on the Composition and Abundance of Nitrifying Microorganisms in the Rhizosphere of Commercial Olive Crops

    PubMed Central

    Caliz, Joan; Montes-Borrego, Miguel; Triadó-Margarit, Xavier; Metsis, Madis; Landa, Blanca B.; Casamayor, Emilio O.

    2015-01-01

    The microbial ecology of the nitrogen cycle in agricultural soils is an issue of major interest. We hypothesized a major effect by farm management systems (mineral versus organic fertilizers) and a minor influence of soil texture and plant variety on the composition and abundance of microbial nitrifiers. We explored changes in composition (16S rRNA gene) of ammonia-oxidizing archaea (AOA), bacteria (AOB), and nitrite-oxidizing bacteria (NOB), and in abundance of AOA and AOB (qPCR of amoA genes) in the rhizosphere of 96 olive orchards differing in climatic conditions, agricultural practices, soil properties, and olive variety. Majority of archaea were 1.1b thaumarchaeota (soil crenarchaeotic group, SCG) closely related to the AOA genus Nitrososphaera. Most AOB (97%) were identical to Nitrosospira tenuis and most NOB (76%) were closely related to Nitrospira sp. Common factors shaping nitrifiers assemblage composition were pH, soil texture, and olive variety. AOB abundance was positively correlated with altitude, pH, and clay content, whereas AOA abundances showed significant relationships with organic nitrogen content and exchangeable K. The abundances of AOA differed significantly among soil textures and olive varieties, and those of AOB among soil management systems and olive varieties. Overall, we observed minor effects by orchard management system, soil cover crop practices, plantation age, or soil organic matter content, and major influence of soil texture, pH, and olive tree variety. PMID:25950678

  8. Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico.

    PubMed

    Gillies, Lauren E; Thrash, J Cameron; deRada, Sergio; Rabalais, Nancy N; Mason, Olivia U

    2015-10-01

    Areas of low oxygen have spread exponentially over the past 40 years, and are cited as a key stressor on coastal ecosystems. The world's second largest coastal hypoxic (≤ 2 mg of O2 l(-1)) zone occurs annually in the northern Gulf of Mexico. The net effect of hypoxia is the diversion of energy flow away from higher trophic levels to microorganisms. This energy shunt is consequential to the overall productivity of hypoxic water masses and the ecosystem as a whole. In this study, water column samples were collected at 39 sites in the nGOM, 21 of which were hypoxic. Analysis of the microbial community along a hypoxic to oxic dissolved oxygen gradient revealed that the relative abundance (iTag) of Thaumarchaeota species 16S rRNA genes (> 40% of the microbial community in some hypoxic samples), the absolute abundance (quantitative polymerase chain reaction; qPCR) of Thaumarchaeota 16S rRNA genes and archaeal ammonia-monooxygenase gene copy number (qPCR) were significantly higher in hypoxic samples. Spatial interpolation of the microbial and chemical data revealed a continuous, shelfwide band of low dissolved oxygen waters that were dominated by Thaumarchaeota (and Euryarchaeota), amoA genes and high concentrations of phosphate in the nGOM, thus implicating physicochemical forcing on microbial abundance.

  9. Ancient landscapes and the relationship with microbial nitrification

    NASA Astrophysics Data System (ADS)

    Jenkins, Sasha N.; Murphy, Daniel V.; Waite, Ian S.; Rushton, Steven P.; O’Donnell, Anthony G.

    2016-08-01

    Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive nitrification and their population dynamics impact directly on the global nitrogen cycle. AOA predominate in the majority of soils but an increasing number of studies have found that nitrification is largely attributed to AOB. The reasons for this remain poorly understood. Here, amoA gene abundance was used to study the distribution of AOA and AOB in agricultural soils on different parent materials and in contrasting geologic landscapes across Australia (n = 135 sites). AOA and AOB abundances separated according to the geologic age of the parent rock with AOB higher in the more weathered, semi-arid soils of Western Australia. AOA dominated the younger, higher pH soils of Eastern Australia, independent of any effect of land management and fertilization. This differentiation reflects the age of the underlying parent material and has implications for our understanding of global patterns of nitrification and soil microbial diversity. Western Australian soils are derived from weathered archaean laterite and are acidic and copper deficient. Copper is a co-factor in the oxidation of ammonia by AOA but not AOB. Thus, copper deficiency could explain the unexpectedly low populations of AOA in Western Australian soils.

  10. Ancient landscapes and the relationship with microbial nitrification.

    PubMed

    Jenkins, Sasha N; Murphy, Daniel V; Waite, Ian S; Rushton, Steven P; O'Donnell, Anthony G

    2016-08-02

    Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive nitrification and their population dynamics impact directly on the global nitrogen cycle. AOA predominate in the majority of soils but an increasing number of studies have found that nitrification is largely attributed to AOB. The reasons for this remain poorly understood. Here, amoA gene abundance was used to study the distribution of AOA and AOB in agricultural soils on different parent materials and in contrasting geologic landscapes across Australia (n = 135 sites). AOA and AOB abundances separated according to the geologic age of the parent rock with AOB higher in the more weathered, semi-arid soils of Western Australia. AOA dominated the younger, higher pH soils of Eastern Australia, independent of any effect of land management and fertilization. This differentiation reflects the age of the underlying parent material and has implications for our understanding of global patterns of nitrification and soil microbial diversity. Western Australian soils are derived from weathered archaean laterite and are acidic and copper deficient. Copper is a co-factor in the oxidation of ammonia by AOA but not AOB. Thus, copper deficiency could explain the unexpectedly low populations of AOA in Western Australian soils.

  11. Ancient landscapes and the relationship with microbial nitrification

    PubMed Central

    Jenkins, Sasha N.; Murphy, Daniel V.; Waite, Ian S.; Rushton, Steven P.; O’Donnell, Anthony G.

    2016-01-01

    Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive nitrification and their population dynamics impact directly on the global nitrogen cycle. AOA predominate in the majority of soils but an increasing number of studies have found that nitrification is largely attributed to AOB. The reasons for this remain poorly understood. Here, amoA gene abundance was used to study the distribution of AOA and AOB in agricultural soils on different parent materials and in contrasting geologic landscapes across Australia (n = 135 sites). AOA and AOB abundances separated according to the geologic age of the parent rock with AOB higher in the more weathered, semi-arid soils of Western Australia. AOA dominated the younger, higher pH soils of Eastern Australia, independent of any effect of land management and fertilization. This differentiation reflects the age of the underlying parent material and has implications for our understanding of global patterns of nitrification and soil microbial diversity. Western Australian soils are derived from weathered archaean laterite and are acidic and copper deficient. Copper is a co-factor in the oxidation of ammonia by AOA but not AOB. Thus, copper deficiency could explain the unexpectedly low populations of AOA in Western Australian soils. PMID:27480661

  12. Radiation sensitivity of hyperthermal composting microorganisms

    NASA Astrophysics Data System (ADS)

    Choi, Jong-Il; Yoon, Min-Chul; Kim, Jae-Hun; Yamashita, Masamichi; Kim, Geun Joong; Lee, Ju-Woon

    In the space station and vehicles designed for long human mission, high-temperature compost is a promising technology for decomposing organic waste and producing the fertilizers. In space, the microorganisms could have the changed biological activities or even be mutated by ionizing irradiation. Therefore, in this study, the effect of gamma irradiation on the sensitivity of bacteria in hyperthermal composting was investigated. The sequence analysis of the amplified 16s rDNA genes and amoA gene were used for the identification of composting microorganisms. Viability of microorganisms in compost soil after gamma irradiation was directly visualized with LIVE/DEAD Baclight viability kit. The dominant bacterial genera are Weissella cibaria and Leuconostoc sp. and fungus genera are Metschnikowia bicuspidate and Pichia guilliermondii, respectively. By the gamma irradiation up to the dose of 1 kGy, the microbial population was not changed. Also, the enzyme activities of amylase and cellulose were sustained by the gamma irradiation. These results show that these hyperthermia microorganisms might have the high resistance to gamma radiation and could be used for agriculture in the Space Station.

  13. Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

    PubMed Central

    Lehtovirta-Morley, Laura E.; Ross, Jenna; Hink, Linda; Weber, Eva B.; Gubry-Rangin, Cécile; Thion, Cécile; Prosser, James I.; Nicol, Graeme W.

    2016-01-01

    Studies of the distribution of ammonia oxidising archaea (AOA) and bacteria (AOB) suggest distinct ecological niches characterised by ammonia concentration and pH, arising through differences in substrate affinity and ammonia tolerance. AOA form five distinct phylogenetic clades, one of which, the ‘Nitrososphaera sister cluster’, has no cultivated isolate. A representative of this cluster, named ‘Candidatus Nitrosocosmicus franklandus’, was isolated from a pH 7.5 arable soil and we propose a new cluster name: ‘Nitrosocosmicus’. While phylogenetic analysis of amoA genes indicates its association with the Nitrososphaera sister cluster, analysis of 16S rRNA genes provided no support for a relative branching that is consistent with a ‘sister cluster’, indicating placement within a lineage of the order Nitrososphaerales. ‘Ca. N. franklandus’ is capable of ureolytic growth and its tolerances to nitrite and ammonia are higher than in other AOA and similar to those of typical soil AOB. Similarity of other growth characteristics of ‘Ca. N. franklandus’ with those of typical soil AOB isolates reduces support for niche differentiation between soil AOA and AOB and suggests that AOA have a wider physiological diversity than previously suspected. In particular, the high ammonia tolerance of ‘Ca. N. franklandus’ suggests potential contributions to nitrification in fertilised soils. PMID:26976843

  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. A soluble form of ammonia monooxygenase in Nitrosomonas europaea.

    PubMed

    Gilch, Stefan; Meyer, Ortwin; Schmidt, Ingo

    2009-09-01

    Ammonia monooxygenase (AMO) of Nitrosomonas europaea is a metalloenzyme that catalyzes the oxidation of ammonia to hydroxylamine. This study shows that AMO resides in the cytoplasm of the bacteria in addition to its location in the membrane and is distributed approximately equally in both subcellular fractions. AMO in both fractions catalyzes the oxidation of ammonia and binds [(14)C]acetylene, a mechanism-based inhibitor which specifically interacts with catalytically active AMO. Soluble AMO was purified 12-fold to electrophoretic homogeneity with a yield of 8%. AMO has a molecular mass of approximately 283 kDa with subunits of ca. 27 kDa (alpha-subunit, AmoA), ca. 42 kDa (beta-subunit, AmoB), and ca. 24 kDa (gamma-subunit, cytochrome c(1)) in an alpha(3)beta(3)gamma(3) sub-unit structure. Different from the beta-subunit of membrane-bound AMO, AmoB of soluble AMO possesses an N-terminal signal sequence. AMO contains Cu (9.4+/-0.6 mol per mol AMO), Fe (3.9+/-0.3 mol per mol AMO), and Zn (0.5 to 2.6 mol per mol AMO). Upon reduction the visible absorption spectrum of AMO reveals absorption bands characteristic of cytochrome c. Electron para-magnetic resonance spectroscopy of air-oxidized AMO at 50 K shows a paramagnetic signal originating from Cu(2+) and at 10 K a paramagnetic signal characteristic of heme-Fe.

  16. 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

  17. 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

  18. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

    PubMed Central

    Simonin, Marie; Richaume, Agnès; Guyonnet, Julien P.; Dubost, Audrey; Martins, Jean M. F.; Pommier, Thomas

    2016-01-01

    Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg−1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function. PMID:27659196

  19. Microbial community biofabrics in a geothermal mine adit.

    PubMed

    Spear, John R; Barton, Hazel A; Robertson, Charles E; Francis, Christopher A; Pace, Norman R

    2007-10-01

    Speleothems such as stalactites and stalagmites are usually considered to be mineralogical in composition and origin; however, microorganisms have been implicated in the development of some speleothems. We have identified and characterized the biological and mineralogical composition of mat-like biofabrics in two novel kinds of speleothems from a 50 degrees C geothermal mine adit near Glenwood Springs, CO. One type of structure consists of 2- to 3-cm-long, 3- to 4-mm-wide, leather-like, hollow, soda straw stalactites. Light and electron microscopy indicated that the stalactites are composed of a mineralized biofabric with several cell morphotypes in a laminated form, with gypsum and sulfur as the dominant mineral components. A small-subunit rRNA gene phylogenetic community analysis along the stalactite length yielded a diverse gradient of organisms, with a relatively simple suite of main constituents: Thermus spp., crenarchaeotes, Chloroflexi, and Gammaproteobacteria. PCR analysis also detected putative crenarchaeal ammonia monooxygenase subunit A (amoA) genes in this community, the majority related to sequences from other geothermal systems. The second type of speleothem, dumpling-like rafts floating on a 50 degrees C pool on the floor of the adit, showed a mat-like fabric of evidently living organisms on the outside of the dumpling, with a multimineral, amorphous, gypsum-based internal composition. These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments.

  20. Nitrogen removal pathway of anaerobic ammonium oxidation in on-site aged refuse bioreactor.

    PubMed

    Wang, Chao; Zhao, Youcai; Xie, Bing; Peng, Qing; Hassan, Muhammad; Wang, Xiaoyuan

    2014-05-01

    The nitrogen removal pathways and nitrogen-related functional genes in on-site three-stage aged refuse bioreactor (ARB) treating landfill leachate were investigated. It was found that on average 90.0% of CODCr, 97.6% of BOD5, 99.3% of NH4(+)-N, and 81.0% of TN were removed with initial CODCr, BOD5, NH4(+)-N, and TN concentrations ranging from 2323 to 2754, 277 to 362, 1237 to 1506, and 1251 to 1580 mg/L, respectively. Meanwhile, the functional genes amoA, nirS and anammox 16S rRNA gene were found to coexist in every bioreactor, and their relative proportions in each bioreactor were closely related to the pollutant removal performance of the corresponding bioreactor, which indicated the coexistence of multiple nitrogen removal pathways in the ARB. Detection of anammox expression proved the presence of the anammox nitrogen removal pathway during the process of recirculating mature leachate to the on-site ARB, which provides important information for nitrogen management in landfills.

  1. Molecular microbial diversity of a soil sample and detection of ammonia oxidizers from Cape Evans, Mcmurdo Dry Valley, Antarctica.

    PubMed

    Shravage, Bhupendra V; Dayananda, Kannayakanahalli M; Patole, Milind S; Shouche, Yogesh S

    2007-01-01

    The aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, Cape Evans, McMurdo, Antarctica by an SSU rDNA gene library approach. Our study by sequencing of clones from SSU rDNA gene library approach revealed high diversity in the soil sample from Antarctica. More than 50% of clones showed homology to Cytophaga-Flavobacterium-Bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, Thermus-Deinococcus and high GC gram-positive group; Phylogenetic analysis of the SSU rDNA clones showed the presence of species belonging to Cytophaga spp., Vitellibacter vladivostokensis, Aequorivita lipolytica, Aequorivita crocea, Flavobacterium spp., Flexibacter sp., Subsaxibacter broadyi, Bacteroidetes, Roseobacter sp., Sphingomonas baekryungensis, Nitrosospira sp., Nitrosomonas cryotolerans, Psychrobacter spp., Chromohalobacter sp., Psychrobacter okhotskensis, Psychrobacter fozii, Psychrobacter urativorans, Rubrobacter radiotolerans, Marinobacter sp., Rubrobacteridae, Desulfotomaculum aeronauticum and Deinococcus sp. The presence of ammonia oxidizing bacteria in Antarctica soil was confirmed by the presence of the amoA gene. Phylogenetic analysis revealed grouping of clones with their respective groups.

  2. The nitrogen cycle in cryoconites: naturally occurring nitrification-denitrification granules on a glacier.

    PubMed

    Segawa, Takahiro; Ishii, Satoshi; Ohte, Nobuhito; Akiyoshi, Ayumi; Yamada, Akinori; Maruyama, Fumito; Li, Zhongqin; Hongoh, Yuichi; Takeuchi, Nozomu

    2014-10-01

    Cryoconites are microbial aggregates commonly found on glacier surfaces where they tend to take spherical, granular forms. While it has been postulated that the microbes in cryoconite granules play an important role in glacier ecosystems, information on their community structure is still limited, and their functions remain unclear. Here, we present evidence for the occurrence of nitrogen cycling in cryoconite granules on a glacier in Central Asia. We detected marker genes for nitrogen fixation, nitrification and denitrification in cryoconite granules by digital polymerase chain reaction (PCR), while digital reverse transcription PCR analysis revealed that only marker genes for nitrification and denitrification were abundantly transcribed. Analysis of isotope ratios also indicated the occurrence of nitrification; nitrate in the meltwater on the glacier surface was of biological origin, while nitrate in the snow was of atmospheric origin. The predominant nitrifiers on this glacier belonged to the order Nitrosomonadales, as suggested by amoA sequences and 16S ribosomal RNA pyrosequencing analysis. Our results suggest that the intense carbon and nitrogen cycles by nitrifiers, denitrifiers and cyanobacteria support abundant and active microbes on the Asian glacier.

  3. Archaeal communities associated with roots of the common reed (Phragmites australis) in Beijing Cuihu Wetland.

    PubMed

    Liu, Yin; Li, Hong; Liu, Qun Fang; Li, Yan Hong

    2015-05-01

    The richness, phylogeny and composition of archaeal community associated with the roots of common reed (Phragmites australis) growing in the Beijing Cuihu Wetland, China was investigated using a 16S rDNA library. In total, 235 individual sequences were collected, and a phylogenetic analysis revealed that 69.4 and 11.5 % of clones were affiliated with the Euryarchaeota and the Crenarchaeota, respectively. In Euryarchaeota, the archaeal community was dominated by species in following genera: Methanobacterium in the order Methanobacteriales (60.7 %); Methanoregula and Methanospirillum in the order Methanomicrobiales (20.2 %), and Methanomethylovorans, Methanosarcina and Methanosaeta in the order Methanosarcinales (17.2 %). Of 27 sequences assigned to uncultured Crenarchaeota, 22 were grouped into Group 1.3, and five grouped into Group 1.1b. Hence, the archaeal communities associated with reed roots are largely involved in methane production, and, to a lesser extent, in ammonia oxidization. Quantification of the archaeal amoA gene indicated that ammonia oxidizing archaea were more numerous in the rhizosphere soil than in the root tissue or surrounding water. A total of 19.1 % of the sequences were unclassified, suggesting that many unidentified archaea are probably involved in the reed wetland ecosystem.

  4. 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.

  5. Effects of oxygen and carbon content on nitrogen removal capacities in landfill bioreactors and response of microbial dynamics.

    PubMed

    Xu, Weiqing; Wu, Dong; Wang, Jie; Huang, Xinghua; Xie, Bing

    2016-07-01

    In this study, landfill bioreactors were tested to treat the recalcitrant leachate-nitrogen and the impacts of relevant operational parameters on its conversion were comprehensively investigated. We found that the highly diverse microbial community in landfill bioreactors could be substantially affected by increasing biodegradable carbon and oxygen content, which led to the whole system's intrinsic nitrogen removal capacity increasing from 50 to 70 %, and meanwhile, the contribution of anammox was detected less than 20 %. The sequencing and q-PCR results showed that microbial community in bioreactor was dominated by Proteobacteria (∼35 %) and Acidobacteria (~20 %) during the whole experiment. The abundance of anammox functioning bacteria (Amx) kept at a stable level (-2.5 to -2.2 log (copies/16S rRNA)) and was not statistically correlated to the abundance of anammox bacteria. However, significant linear correlation (p < 0.05) was determined between the abundance of nirS and Proteobacteria; amoA and AOB. Redundancy analysis (RDA) suggested that although oxygen and biodegradable carbon can both impose effects on microbial community structure, only biodegradable carbon content is the determinant in the total nitrogen removal.

  6. 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

  7. Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

    PubMed

    Singh, Sunil; Gupta, Rashi; Kumari, Madhu; Sharma, Shilpi

    2015-08-01

    Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments.

  8. Growing media constituents determine the microbial nitrogen conversions in organic growing media for horticulture.

    PubMed

    Grunert, Oliver; Reheul, Dirk; Van Labeke, Marie-Christine; Perneel, Maaike; Hernandez-Sanabria, Emma; Vlaeminck, Siegfried E; Boon, Nico

    2016-05-01

    Vegetables and fruits are an important part of a healthy food diet, however, the eco-sustainability of the production of these can still be significantly improved. European farmers and consumers spend an estimated €15.5 billion per year on inorganic fertilizers and the production of N-fertilizers results in a high carbon footprint. We investigated if fertilizer type and medium constituents determine microbial nitrogen conversions in organic growing media and can be used as a next step towards a more sustainable horticulture. We demonstrated that growing media constituents showed differences in urea hydrolysis, ammonia and nitrite oxidation and in carbon dioxide respiration rate. Interestingly, mixing of the growing media constituents resulted in a stimulation of the function of the microorganisms. The use of organic fertilizer resulted in an increase in amoA gene copy number by factor 100 compared to inorganic fertilizers. Our results support our hypothesis that the activity of the functional microbial community with respect to nitrogen turnover in an organic growing medium can be improved by selecting and mixing the appropriate growing media components with each other. These findings contribute to the understanding of the functional microbial community in growing media and its potential role towards a more responsible horticulture.

  9. Assessment of nitrification in groundwater filters for drinking water production by qPCR and activity measurement.

    PubMed

    de Vet, W W J M; Kleerebezem, R; van der Wielen, P W J J; Rietveld, L C; van Loosdrecht, M C M

    2011-07-01

    In groundwater treatment for drinking water production, the causes of nitrification problems and the effectiveness of process optimization in rapid sand filters are often not clear. To assess both issues, the performance of a full-scale groundwater filter with nitrification problems and another filter with complete nitrification and pretreatment by subsurface aeration was monitored over nine months. Quantitative real-time polymerase chain reaction (qPCR) targeting the amoA gene of bacteria and archaea and activity measurements of ammonia oxidation were used to regularly evaluate water and filter sand samples. Results demonstrated that subsurface aeration stimulated the growth of ammonia-oxidizing prokaryotes (AOP) in the aquifer. Cell balances, using qPCR counts of AOP for each filter, showed that the inoculated AOP numbers from the aquifer were marginal compared with AOP numbers detected in the filter. Excessive washout of AOP was not observed and did not cause the nitrification problems. Ammonia-oxidizing archaea grew in both filters, but only in low numbers compared to bacteria. The cell-specific nitrification rate in the sand and backwash water samples was high for the subsurface aerated filter, but systematically much lower for the filter with nitrification problems. From this, we conclude that incomplete nitrification was caused by nutrient limitation.

  10. Effect of gamma irradiation on hyperthermal composting microorganisms for feasible application in space

    NASA Astrophysics Data System (ADS)

    Yoon, Minchul; Choi, Jong-il; Yamashita, Masamichi

    2013-05-01

    The composting system is the most efficient method for processing organic waste in space; however, the composting activity of microorganisms can be altered by cosmic rays. In this study, the effect of ionizing irradiation on composting bacteria was investigated. Sequence analyses of amplified 16S rRNA, 18S rRNA, and amoA genes were used to identify hyperthermal composting microorganisms. The viability of microorganisms in compost soil after gamma irradiation was directly determined using LIVE/DEAD BacLight viability kit. The dominant bacterial genera were Weissella cibaria and Leuconostoc sp., and the fungal genera were Metschnikowia bicuspidata and Pichia guilliermondii. Gamma irradiation up to a dose of 10 kGy did not significantly alter the microbial population. Furthermore, amylase and cellulase activities were maintained after high-dose gamma irradiation. Our results show that hyperthermal microorganisms can be used to recycle agricultural and fermented material in space stations and other human-inhabiting facilities on the Moon, Mars, and other planets.

  11. Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin.

    PubMed

    Roussel, Erwan G; Sauvadet, Anne-Laure; Chaduteau, Carine; Fouquet, Yves; Charlou, Jean-Luc; Prieur, Daniel; Cambon Bonavita, Marie-Anne

    2009-09-01

    The distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average approximately 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities.

  12. 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.

  13. 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

  14. 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.

  15. Archaea on Human Skin

    PubMed Central

    Probst, Alexander J.; Auerbach, Anna K.; Moissl-Eichinger, Christine

    2013-01-01

    The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin. PMID:23776475

  16. Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil.

    PubMed

    Banning, Natasha C; Maccarone, Linda D; Fisk, Louise M; Murphy, Daniel V

    2015-06-08

    Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0-10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10-90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.

  17. Impact of oxygen on the coexistence of nitrification, denitrification, and sulfate reduction in oxygen-based membrane aerated biofilm.

    PubMed

    Liu, Hong; Tan, Shuying; Sheng, Zhiya; Yu, Tong; Liu, Yang

    2015-03-01

    Membrane aerated biofilms (MABs) are subject to "counter diffusion" of oxygen and substrates. In a membrane aerated biofilm reactor, gases (e.g., oxygen) diffuse through the membrane into the MAB, and liquid substrates pass from the bulk liquid into the MAB. This behavior can result in a unique biofilm structure in terms of microbial composition, distribution, and community activity in the MAB. Previous studies have shown simultaneous aerobic oxidation, nitrification, and denitrification within a single MAB. Using molecular techniques, we investigated the growth of sulfate-reducing bacteria (SRB) in the oxygen-based MAB attached to a flat sheet membrane. Denaturing gradient gel electrophoresis of the amplified 16S rRNA gene fragments and functional gene fragments specific for ammonia-oxidizing bacteria (amoA), denitrifying bacteria (nirK), and SRB (dsrB) demonstrated the coexistence of nitrifiers, denitrifiers, and SRB communities within a single MAB. The functional diversities of SRB and denitrifiers decreased with an increase in the oxygen concentration in the bulk water of the reactor.

  18. Isolation of 'Candidatus Nitrosocosmicus franklandus', a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration.

    PubMed

    Lehtovirta-Morley, Laura E; Ross, Jenna; Hink, Linda; Weber, Eva B; Gubry-Rangin, Cécile; Thion, Cécile; Prosser, James I; Nicol, Graeme W

    2016-05-01

    Studies of the distribution of ammonia oxidising archaea (AOA) and bacteria (AOB) suggest distinct ecological niches characterised by ammonia concentration and pH, arising through differences in substrate affinity and ammonia tolerance. AOA form five distinct phylogenetic clades, one of which, the 'Nitrososphaera sister cluster', has no cultivated isolate. A representative of this cluster, named 'Candidatus Nitrosocosmicus franklandus', was isolated from a pH 7.5 arable soil and we propose a new cluster name:'Nitrosocosmicus' While phylogenetic analysis of amoA genes indicates its association with the Nitrososphaera sister cluster, analysis of 16S rRNA genes provided no support for a relative branching that is consistent with a 'sister cluster', indicating placement within a lineage of the order Nitrososphaerales 'Ca.N. franklandus' is capable of ureolytic growth and its tolerances to nitrite and ammonia are higher than in other AOA and similar to those of typical soil AOB. Similarity of other growth characteristics of 'Ca.N. franklandus' with those of typical soil AOB isolates reduces support for niche differentiation between soil AOA and AOB and suggests that AOA have a wider physiological diversity than previously suspected. In particular, the high ammonia tolerance of 'Ca.N. franklandus' suggests potential contributions to nitrification in fertilised soils.

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

    PubMed

    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 (r(2) = 0.32, p<0.1), whereas AOA abundance was inversely correlated with lake elevation (r(2) = 0.43, p<0.05). We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.

  20. Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu).

    PubMed

    Hou, Jie; Song, Chunlei; Cao, Xiuyun; Zhou, Yiyong

    2013-05-01

    Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic ecosystems. Recent findings have expanded the known ammonia-oxidizing prokaryotes from Bacteria to Archaea. However, the relative importance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in nitrification is still debated. Here we showed that, in two large eutrophic lakes in China (Lake Taihu and Lake Chaohu), the abundance of AOA and AOB varied in opposite patterns according to the trophic state, although both AOA and AOB were abundant. In detail, from mesotrophic to eutrophic sites, the AOA abundance decreased, while the AOB increased in abundance and outnumbered the AOA at hypertrophic sites. In parallel, the nitrification rate increased along these trophic gradients and was significantly correlated with both the AOB abundance and the numerical ratio of AOB to AOA. Phylogenetic analysis of bacterial amoA sequences showed that Nitrosomonas oligotropha- and Nitrosospira-affiliated AOB dominated in both lakes, while Nitrosomonas communis-related AOB were only detected at the eutrophic sites. The diversity of AOB increased from mesotrophic to eutrophic sites and was positively correlated with the nitrification rate. Overall, this study enhances our understanding of the ecology of ammonia-oxidizing prokaryotes by elucidating conditions that AOB may numerically predominated over AOA, and indicated that AOA may play a less important role than AOB in the nitrification process of eutrophic lakes.

  1. Impact of food to microorganism (F/M) ratio and colloidal chemical oxygen demand on nitrification performance of a full-scale membrane bioreactor treating thin film transistor liquid crystal display wastewater.

    PubMed

    Wu, Yi-Ju; Whang, Liang-Ming; Chang, Ming-Yu; Fukushima, Toshikazu; Lee, Ya-Chin; Cheng, Sheng-Shung; Hsu, Shu-Fu; Chang, Cheng-Huey; Shen, Wason; Yang, Charn-Yi; Fu, Ryan; Tsai, Tsair-Yuan

    2013-08-01

    This study investigated impact of food to microorganism (F/M) ratio and colloidal chemical oxygen demand (COD) on nitrification performance in one full-scale membrane bioreactor (MBR) treating monoethanolamine (MEA)/dimethyl sulfoxide (DMSO)-containing thin film transistor liquid crystal display (TFT-LCD) wastewater. Poor nitrification was observed under high organic loading and high colloidal COD conditions, suggesting that high F/M ratio and colloidal COD situations should be avoided to minimize their negative impacts on nitrification. According to the nonmetric multidimensional scaling (NMS) statistical analyses on terminal restriction fragment length polymorphism (T-RFLP) results of ammonia monooxygenase (amoA) gene, the occurrence of Nitrosomonas oligotropha-like ammonia oxidizing bacteria (AOB) was positively related to successful nitrification in the MBR systems, while Nitrosomonas europaea-like AOB was positively linked to nitrification rate, which can be attributed to the high influent total nitrogen condition. Furthermore, Nitrobacter- and Nitrospira-like nitrite oxidizing bacteria (NOB) were both abundant in the MBR systems, but the continuously low nitrite environment is likely to promote the growth of Nitrospira-like NOB.

  2. Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria.

    PubMed

    Medeiros, J D; Araújo, L X; da Silva, V L; Diniz, C G; Cesar, D E; Del'Duca, A; Coelho, C M

    2014-08-01

    This study aimed to investigate microbes involved in the nitrogen cycle and potentially pathogenic bacteria from urban and rural sites of the São Pedro stream. Water samples were collected from two sites. A seasonal survey of bacterial abundance was conducted. The dissolved nutrient content was analysed. PCR and FISH analysis were performed to identify and quantify microbes involved in the nitrogen cycle and potentially pathogenic bacteria. The seasonal survey revealed that the bacterial abundance was similar along the year on the rural area but varied on the urban site. Higher concentration of dissolved nutrients in the urban area indicated a eutrophic system. Considering the nitrifying microbes, the genus Nitrobacter was found, especially in the urban area, and may act as the principal bacteria in converting nitrite into nitrate at this site. The molecular markers napA, amoA, and nfrA were more accumulated at the urban site, justifying the higher content of nutrients metabolised by these enzymes. Finally, high intensity of amplicons from Enterococcus, Streptococcus, Bacteroides/Prevotella/Porphyromonas, Salmonella, S. aureus, P. aeruginosa and the diarrheagenic lineages of E. coli were observed at the urban site. These results indicate a change in the structure of the microbial community imposed by anthrophic actions. The incidence of pathogenic bacteria in aquatic environments is of particular importance to public health, emphasising the need for sewage treatment to minimise the environmental impacts associated with urbanisation.

  3. Assessment of N2O emission from a photobioreactor treating ammonia-rich swine wastewater digestate.

    PubMed

    Mezzari, Melissa P; da Silva, Márcio L B; Nicoloso, Rodrigo S; Ibelli, Adriana M G; Bortoli, Marcelo; Viancelli, Aline; Soares, Hugo M

    2013-12-01

    This study investigated the interactions between naturally occurring bacteria and the microalgae Chlorella vulgaris within a lab scale photobioreactor treating ammonia-rich swine wastewater digestate effluent. Nitrification and denitrification were assessed by targeting ammonia monoxygenases (amoA), nitrate (narG), nitrite (nirS), nitric oxide (norB) and nitrous oxide (nosZ) reductases genes. Oxygen produced from microalgae photosynthesis stimulated nitrification. Under limiting carbon availability (i.e., <1.44 for mg TOC/mg NO2-N and 1.72 for mg TOC/mg NO3-N), incomplete denitrification led to accumulation of NO2 and NO3. Significant N2O emission (up to 118 μg N2O-N) was linked to NO2 metabolism in Chlorella. The addition of acetate as external carbon source recovered heterotrophic denitrification activity suppressing N2O emission. Effluent methane concentrations trapped within photobioreactor was removed concomitantly with ammonia. Overall, closed photobioreactors can be built to effectively remove nitrogen and mitigate simultaneously greenhouse gases emissions that would occur otherwise in open microalgae-based wastewater treatment systems.

  4. Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil

    NASA Astrophysics Data System (ADS)

    Banning, Natasha C.; Maccarone, Linda D.; Fisk, Louise M.; Murphy, Daniel V.

    2015-06-01

    Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0-10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10-90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.

  5. Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms

    PubMed Central

    Bowen, Jennifer L.; Babbin, Andrew R.; Kearns, Patrick J.; Ward, Bess B.

    2014-01-01

    Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which genetic signals vary and how they relate to key functions. We used quantitative PCR of DNA and cDNA, along with biogeochemical modeling to assess how the abundance and expression of microbes responsible for two steps in the nitrogen cycle changed over time in estuarine sediment mesocosms. Sediments and water were collected from coastal Massachusetts and maintained in replicated 20 L mesocosms for 45 days. Concentrations of all major inorganic nitrogen species were measured daily and used to derive rates of nitrification and denitrification from a Monte Carlo-based non-negative least-squares analysis of finite difference equations. The mesocosms followed a classic regeneration sequence in which ammonium released from the decomposition of organic matter was subsequently oxidized to nitrite and then further to nitrate, some portion of which was ultimately denitrified. Normalized abundances of ammonia oxidizing archaeal ammonia monoxoygenase (amoA) transcripts closely tracked rates of ammonia oxidation throughout the experiment. No such relationship, however, was evident between denitrification rates and the normalized abundance of nitrite reductase (nirS and nirK) transcripts. These findings underscore the complexity of directly linking the structure of the microbial community to rates of biogeochemical processes. PMID:25191309

  6. Dissimilatory Nitrite Reductase Genes from Autotrophic Ammonia-Oxidizing Bacteria

    PubMed Central

    Casciotti, Karen L.; Ward, Bess B.

    2001-01-01

    The presence of a copper-containing dissimilatory nitrite reductase gene (nirK) was discovered in several isolates of β-subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were designed based on published nirK sequences from denitrifying bacteria and used to amplify a 540-bp fragment of the nirK gene from Nitrosomonas marina and five additional isolates of ammonia-oxidizing bacteria. Amplification products of the expected size were cloned and sequenced. Alignment of the nucleic acid and deduced amino acid (AA) sequences shows significant similarity (62 to 75% DNA, 58 to 76% AA) between nitrite reductases present in these nitrifiers and the copper-containing nitrite reductase found in classic heterotrophic denitrifiers. While the presence of a nitrite reductase in Nitrosomonas europaea is known from early biochemical work, preliminary sequence data from its genome indicate a rather low similarity to the denitrifier nirKs. Phylogenetic analysis of the partial nitrifier nirK sequences indicates that the topology of the nirK tree corresponds to the 16S rRNA and amoA trees. While the role of nitrite reduction in the metabolism of nitrifying bacteria is still uncertain, these data show that the nirK gene is present in closely related nitrifying isolates from many oceanographic regions and suggest that nirK sequences retrieved from the environment may include sequences from ammonia-oxidizing bacteria. PMID:11319103

  7. Characterization of Microbial Communities and Composition in Constructed Dairy Wetland Wastewater Effluent

    PubMed Central

    Ibekwe, A. Mark; Grieve, Catherine M.; Lyon, Stephen R.

    2003-01-01

    Constructed wetlands have been recognized as a removal treatment option for high concentrations of contaminants in agricultural waste before land application. The goal of this study was to characterize microbial composition in two constructed wetlands designed to remove contaminants from dairy washwater. Water samples were collected weekly for 11 months from two wetlands to determine the efficiency of the treatment system in removal of chemical contaminants and total and fecal coliforms. The reduction by the treatment was greatest for biological oxygen demand, suspended solids, chemical oxygen demand, nitrate, and coliforms. There was only moderate removal of total nitrogen and phosphorus. Changes in the total bacterial community and ammonia-oxidizing bacterial composition were examined by using denaturing gradient gel electrophoresis (DGGE) and sequencing of PCR-amplified fragments of the gene carrying the α subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and DGGE bands. DGGE analysis of wetlands and manure samples revealed that the total bacterial community composition was dominated by bacteria from phylogenetic clusters related to Bacillus, Clostridium, Mycoplasma, Eubacterium, and Proteobacteria originally retrieved from the gastrointestinal tracts of mammals. The population of ammonia-oxidizing bacteria showed a higher percentage of Nitrosospira-like sequences from the wetland samples, while a higher percentage of Nitrosomonas-like sequences from manure, feces, raw washwater, and facultative pond was found. These results show that the wetland system is a natural process dependent upon the development of healthy microbial communities for optimal wastewater treatment. PMID:12957887

  8. Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples.

    PubMed

    La Cono, Violetta; Smedile, Francesco; La Spada, Gina; Arcadi, Erika; Genovese, Maria; Ruggeri, Gioacchino; Genovese, Lucrezia; Giuliano, Laura; Yakimov, Michail M

    2015-06-01

    Dark ocean microbial communities are actively involved in chemoautotrophic and anaplerotic fixation of bicarbonate. Thus, aphotic pelagic realm of the ocean might represent a significant sink of CO2 and source of primary production. However, the estimated metabolic activities in the dark ocean are fraught with uncertainties. Typically, deep-sea samples are recovered to the sea surface for downstream processing on deck. Shifts in ambient settings, associated with such treatments, can likely change the metabolic activity and community structure of deep-sea adapted autochthonous microbial populations. To estimate influence of recovery and short-term handling of deep-sea samples, we monitored the succession of bathypelagic microbial community during its 3 days long on deck incubation. We demonstrated that at the end of exposition, the deep-sea archaeal population decreased threefold, whereas the bacterial fraction doubled in size. As revealed by phylogenetic analyses of amoA gene transcripts, dominance of the active ammonium-oxidizing bathypelagic Thaumarchaeota groups shifted over time very fast. These findings demonstrated the simultaneous existence of various 'deep-sea ecotypes', differentially reacting to the sampling and downstream handling. Our study supports the hypothesis that metabolically active members of meso- and bathypelagic Thaumarchaeota possess the habitat-specific distribution, metabolic complexity and genetic divergence at subpopulation level.

  9. Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

    PubMed Central

    Kutvonen, Heini; Rajala, Pauliina; Carpén, Leena; Bomberg, Malin

    2015-01-01

    We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using 15N-based stable isotope probing (SIP) and enrichment with 14∕15N-ammonium or 14∕15N-nitrate complemented with methane. Twenty-eight days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG) gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG) from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium, and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. 15N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used 15N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system. PMID:26528251

  10. Nitrogen removal and nitrifying and denitrifying bacteria quantification in a stormwater bioretention system.

    PubMed

    Chen, Xiaolu; Peltier, Edward; Sturm, Belinda S M; Young, C Bryan

    2013-03-15

    In this study, we examine the biological processes involved in ammonia and nitrate removal in a bioretention system characterized by low infiltration rates and long drainage times. The system removed 33% of influent nitrate and 56% of influent total nitrogen. While influent ammonia concentrations were low (<0.3 mg/L), the bioretention cell also removed ammonia produced within the treatment system. Soil cores collected from the bioretention cell were analyzed for total 16S rDNA and both nitrification and denitrification genes (amoA, nirS, nirK, norB, and nosZ) using quantitative PCR. Total bacterial 16S rDNA levels in the surface layer were similar to those in very sandy soils. Gene counts for both nitrification and denitrification genes decreased as a function of depth in the media, and corresponded to similar changes in total 16S rDNA. The abundance of denitrification genes was also positively correlated with the average inundation time at each sampling location, as determined by modeling of stormwater data from a three-year period. These results suggest that both nitrification and denitrification can occur in bioretention media. Time of saturation, filter medium, and organic carbon content can all affect the extent of denitrification in bioretention systems.

  11. 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

  12. Diversity and seasonal dynamics of airborne archaea

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Ruzene Nespoli, C.; Pickersgill, D. A.; Galand, P. E.; Müller-Germann, I.; Nunes, T.; Gomes Cardoso, J.; Almeida, S. M.; Pio, C.; Andreae, M. O.; Conrad, R.; Pöschl, U.; Després, V. R.

    2014-11-01

    Archaea are widespread and abundant in many terrestrial and aquatic environments, and are thus outside extreme environments, accounting for up to ~10% of the prokaryotes. Compared to bacteria and other microorganisms, however, very little is known about the abundance, diversity, and dispersal of archaea in the atmosphere. By means of DNA analysis and Sanger sequencing targeting the 16S rRNA (435 sequences) and amoA genes in samples of air particulate matter collected over 1 year at a continental sampling site in Germany, we obtained first insights into the seasonal dynamics of airborne archaea. The detected archaea were identified as Thaumarchaeota or Euryarchaeota, with soil Thaumarchaeota (group I.1b) being present in all samples. The normalized species richness of Thaumarchaeota correlated positively with relative humidity and negatively with temperature. This together with an increase in bare agricultural soil surfaces may explain the diversity peaks observed in fall and winter. The detected Euryarchaeota were mainly predicted methanogens with a low relative frequency of occurrence. A slight increase in their frequency during spring may be linked to fertilization processes in the surrounding agricultural fields. Comparison with samples from the Cape Verde islands (72 sequences) and from other coastal and continental sites indicates that the proportions of Euryarchaeota are enhanced in coastal air, which is consistent with their suggested abundance in marine surface waters. We conclude that air transport may play an important role in the dispersal of archaea, including assumed ammonia-oxidizing Thaumarchaeota and methanogens.

  13. Nitrospira-dominated biofilm within a thermal artesian spring: a case for nitrification-driven primary production in a geothermal setting.

    PubMed

    Marks, C R; Stevenson, B S; Rudd, S; Lawson, P A

    2012-09-01

    Water chemistry, energetic modeling, and molecular analyses were combined to investigate the microbial ecology of a biofilm growing in a thermal artesian spring within Hot Springs National Park, AR. This unique fresh water spring has a low dissolved chemical load and is isolated from both light and direct terrestrial carbon input - resulting in an oligotrophic ecosystem limited for fixed carbon and electron donors. Evaluation of energy yields of lithotrophic reactions putatively linked to autotrophy identified the aerobic oxidation of methane, hydrogen, sulfide, ammonia, and nitrite as the most exergonic. Small subunit (SSU) rRNA gene libraries from biofilm revealed a low-diversity microbial assemblage populated by bacteria and archaea at a gene copy ratio of 45:1. Members of the bacterial family 'Nitrospiraceae', known for their autotrophic nitrite oxidation, dominated the bacterial SSU rRNA gene library (approximately 45%). Members of the Thaumarchaeota ThAOA/HWCGIII (>96%) and Thaumarchaeota Group I.1b (2.5%), which both contain confirmed autotrophic ammonia oxidizers, dominated the archaeal SSU rRNA library. Archaea appear to dominate among the ammonia oxidizers, as only ammonia monooxygenase subunit A (amoA) genes belonging to members of the Thaumarchaeota were detected. The geochemical, phylogenetic, and genetic data support a model that describes a novel thermophilic biofilm built largely by an autotrophic nitrifying microbial assemblage. This is also the first observation of 'Nitrospiraceae' as the dominant organisms within a geothermal environment.

  14. Evidence for biological nitrification inhibition in Brachiaria pastures.

    PubMed

    Subbarao, G V; Nakahara, K; Hurtado, M P; Ono, H; Moreta, D E; Salcedo, A F; Yoshihashi, A T; Ishikawa, T; Ishitani, M; Ohnishi-Kameyama, M; Yoshida, M; Rondon, M; Rao, I M; Lascano, C E; Berry, W L; Ito, O

    2009-10-13

    Nitrification, a key process in the global nitrogen cycle that generates nitrate through microbial activity, may enhance losses of fertilizer nitrogen by leaching and denitrification. Certain plants can suppress soil-nitrification by releasing inhibitors from roots, a phenomenon termed biological nitrification inhibition (BNI). Here, we report the discovery of an effective nitrification inhibitor in the root-exudates of the tropical forage grass Brachiaria humidicola (Rendle) Schweick. Named "brachialactone," this inhibitor is a recently discovered cyclic diterpene with a unique 5-8-5-membered ring system and a gamma-lactone ring. It contributed 60-90% of the inhibitory activity released from the roots of this tropical grass. Unlike nitrapyrin (a synthetic nitrification inhibitor), which affects only the ammonia monooxygenase (AMO) pathway, brachialactone appears to block both AMO and hydroxylamine oxidoreductase enzymatic pathways in Nitrosomonas. Release of this inhibitor is a regulated plant function, triggered and sustained by the availability of ammonium (NH(4)(+)) in the root environment. Brachialactone release is restricted to those roots that are directly exposed to NH(4)(+). Within 3 years of establishment, Brachiaria pastures have suppressed soil nitrifier populations (determined as amoA genes; ammonia-oxidizing bacteria and ammonia-oxidizing archaea), along with nitrification and nitrous oxide emissions. These findings provide direct evidence for the existence and active regulation of a nitrification inhibitor (or inhibitors) release from tropical pasture root systems. Exploiting the BNI function could become a powerful strategy toward the development of low-nitrifying agronomic systems, benefiting both agriculture and the environment.

  15. Microbial Community Biofabrics in a Geothermal Mine Adit▿ †

    PubMed Central

    Spear, John R.; Barton, Hazel A.; Robertson, Charles E.; Francis, Christopher A.; Pace, Norman R.

    2007-01-01

    Speleothems such as stalactites and stalagmites are usually considered to be mineralogical in composition and origin; however, microorganisms have been implicated in the development of some speleothems. We have identified and characterized the biological and mineralogical composition of mat-like biofabrics in two novel kinds of speleothems from a 50°C geothermal mine adit near Glenwood Springs, CO. One type of structure consists of 2- to 3-cm-long, 3- to 4-mm-wide, leather-like, hollow, soda straw stalactites. Light and electron microscopy indicated that the stalactites are composed of a mineralized biofabric with several cell morphotypes in a laminated form, with gypsum and sulfur as the dominant mineral components. A small-subunit rRNA gene phylogenetic community analysis along the stalactite length yielded a diverse gradient of organisms, with a relatively simple suite of main constituents: Thermus spp., crenarchaeotes, Chloroflexi, and Gammaproteobacteria. PCR analysis also detected putative crenarchaeal ammonia monooxygenase subunit A (amoA) genes in this community, the majority related to sequences from other geothermal systems. The second type of speleothem, dumpling-like rafts floating on a 50°C pool on the floor of the adit, showed a mat-like fabric of evidently living organisms on the outside of the dumpling, with a multimineral, amorphous, gypsum-based internal composition. These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments. PMID:17693567

  16. Archaea on human skin.

    PubMed

    Probst, Alexander J; Auerbach, Anna K; Moissl-Eichinger, Christine

    2013-01-01

    The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin.

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

    PubMed

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

    2015-05-01

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

  18. Different behaviour of methanogenic archaea and Thaumarchaeota in rice field microcosms.

    PubMed

    Ke, Xiubin; Lu, Yahai; Conrad, Ralf

    2014-01-01

    Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of archaeal genes (mcrA, amoA, 16S rRNA gene). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota proliferated only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome.

  19. 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.

  20. Nitrogen removal and ammonia-oxidising bacteria in a vertical flow constructed wetland treating inorganic wastewater.

    PubMed

    Domingos, Sergio S; Dallas, Stewart; Skillman, Lucy; Felstead, Stephanie; Ho, Goen

    2011-01-01

    Nitrogen removal performance and the ammonia-oxidising bacterial (AOB) community were assessed in the batch loaded 1.3 ha saturated surface vertical flow wetland at CSBP Ltd, a fertiliser and chemical manufacturer located in Kwinana, Western Australia. From September 2008 to October 2009 water quality was monitored and sediment samples collected for bacterial analyses. During the period of study the wetland received an average inflow of 1,109 m3/day with NH3-N = 40 mg/L and NO3-N = 23 mg/L. Effluent NH3-N and NO3-N were on average 31 and 25 mg/L, respectively. The overall NH3-N removal rate for the period was 1.2 g/m2/day indicating the nitrifying capacity of the wetland. The structure of the AOB community was analysed using group specific primers for the ammonia monooxygenase gene (amoA) by terminal restriction fragment length polymorphism and by clone libraries to identify key members. The majority of sequences obtained were most similar to Nitrosomonas sp. while Nitrosospira sp. was less frequent. Another two vertical flow wetlands, 0.8 ha each, were commissioned at CSBP in July 2009, since then the wetland in this study has received nitrified effluent from these two new cells.

  1. Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea.

    PubMed

    Dang, Hongyue; Zhang, Xiaoxia; Sun, Jin; Li, Tiegang; Zhang, Zhinan; Yang, Guanpin

    2008-07-01

    Ammonia-oxidizing archaea (AOA) have recently been found to be potentially important in nitrogen cycling in a variety of environments, such as terrestrial soils, wastewater treatment reactors, marine waters and sediments, and especially in estuaries, where high input of anthropogenic nitrogen is often experienced. The sedimentary AOA diversity, community structure and spatial distribution in the Changjiang Estuary and the adjacent East China Sea were studied. Multivariate statistical analysis indicated that the archaeal amoA genotype communities could be clustered according to sampling transects, and the station located in an estuarine mixing zone harboured a distinct AOA community. The distribution of AOA communities correlated significantly with the gradients of surface-water salinity and sediment sorting coefficient. The spatial distribution of putative soil-related AOA in certain sampling stations indicated a strong impact of the Changjiang freshwater discharge on the marine benthic microbial ecosystem. Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path.

  2. Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables.

    PubMed

    Herfort, Lydie; Schouten, Stefan; Abbas, Ben; Veldhuis, Marcel J W; Coolen, Marco J L; Wuchter, Cornelia; Boon, Jan P; Herndl, Gerhard J; Sinninghe Damsté, Jaap S

    2007-12-01

    The spatial and temporal distribution of pelagic Archaea was studied in the southern North Sea by rRNA hybridization, sequencing and quantification of 16S rRNA gene and membrane lipid analyses and related to physical, chemical and biological parameters to determine the factors influencing archaeal biogeography. A clear temporal variability was observed, with marine Crenarchaeota (Group I.1a) being relatively more abundant in winter and Euryarchaeota dominating the archaeal assemblage in spring and summer. Spatial differences in the lateral distribution of Crenarchaeota were also evident. In fact, their abundance was positively correlated with the copy number of the gene encoding the alpha subunit of crenarchaeotal ammonia monooxygenase (amoA) and with concentrations of ammonia, nitrate, nitrite and phosphorus. This suggests that most Crenarchaeota in the North Sea are nitrifiers and that their distribution is determined by nutrient concentrations. However, Crenarchaeota were not abundant when larger phytoplankton (>3 microm) dominated the algal population. It is hypothesized that together with nutrient concentration, phytoplankton biomass and community structure can predict crenarchaeotal abundance in the southern North Sea. Euryarchaeotal abundance was positively correlated with chlorophyll a concentrations, but not with phytoplankton community structure. Whether this is related to the potential of Euryarchaeota to perform aerobic anoxygenic phototrophy remains to be shown, but the conspicuous seasonal distribution pattern of Crenarchaeota and Euryarchaeota suggests that they occupy a different ecological niche.

  3. Changes in Bacterial And Archaeal Community Structure And Functional Diversity Along a Geochemically Variable Soil Profile

    SciTech Connect

    Hansel, C.M.; Fendorf, S.; Jardine, P.M.; Francis, C.A.

    2009-05-18

    Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.

  4. 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

  5. Octopamine modulates activity of neural networks in the honey bee antennal lobe.

    PubMed

    Rein, Julia; Mustard, Julie A; Strauch, Martin; Smith, Brian H; Galizia, C Giovanni

    2013-11-01

    Neuronal plasticity allows an animal to respond to environmental changes by modulating its response to stimuli. In the honey bee (Apis mellifera), the biogenic amine octopamine plays a crucial role in appetitive odor learning, but little is known about how octopamine affects the brain. We investigated its effect in the antennal lobe, the first olfactory center in the brain, using calcium imaging to record background activity and odor responses before and after octopamine application. We show that octopamine increases background activity in olfactory output neurons, while reducing average calcium levels. Odor responses were modulated both upwards and downwards, with more odor response increases in glomeruli with negative or weak odor responses. Importantly, the octopamine effect was variable across glomeruli, odorants, odorant concentrations and animals, suggesting that the octopaminergic network is shaped by plasticity depending on an individual animal's history and possibly other factors. Using RNA interference, we show that the octopamine receptor AmOA1 (homolog of the Drosophila OAMB receptor) is involved in the octopamine effect. We propose a network model in which octopamine receptors are plastic in their density and located on a subpopulation of inhibitory neurons in a disinhibitory pathway. This would improve odor-coding of behaviorally relevant, previously experienced odors.

  6. 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

  7. Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea.

    PubMed

    Hou, Manhua; Xiong, Jinbo; Wang, Kai; Ye, Xiansen; Ye, Ran; Wang, Qiong; Hu, Changju; Zhang, Demin

    2014-09-15

    Anthropogenic nitrogen (N) discharges has caused eutrophication in coastal zones. Ammonia-oxidizing bacteria (AOB) convert ammonia to nitrite and play important roles in N transformation. Here, we used pyrosequencing based on the amoA gene to investigate the response of the sediment AOB community to an N pollution gradient in the East China Sea. The results showed that AOB assemblages were primarily affiliated with Nitrosospira-like lineages, and only 0.4% of those belonged to Nitrosomonas-like lineage. The Nitrosospira-like lineage was separated into four clusters that were most similar to the sediment AOB communities detected in adjacent marine regions. Additionally, one clade was out grouped from the AOB lineages, which shared the high similarities with pmoA gene. The AOB community structures substantially changed along the pollution gradient, which were primarily shaped by NH4(+)-N, NO3(-)-N, SO4(2)(-)-S, TP and Eh. These results demonstrated that coastal pollution could dramatically influence AOB communities, which, in turn, may change ecosystem function.

  8. Diversity and seasonal dynamics of airborne Archaea

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Ruzene Nespoli, C.; Pickersgill, D. A.; Galand, P. E.; Müller-Germann, I.; Nunes, T.; Gomes Cardoso, J.; Marta Almeida, S.; Pio, C.; Andreae, M. O.; Conrad, R.; Pöschl, U.; Després, V. R.

    2014-05-01

    Archaea are widespread and abundant in many terrestrial and aquatic environments, accounting for up to ∼10% of the prokaryotes. Compared to Bacteria and other microorganisms, however, very little is known about the abundance, diversity, and dispersal of Archaea in the atmosphere. By DNA analysis targeting the 16S rRNA and amoA genes in samples of air particulate matter collected over one year at a continental sampling site in Germany, we obtained first insights into the seasonal dynamics of airborne Archaea. The detected Archaea were identified as Thaumarchaeota or Euryarchaeota, with soil Thaumarchaeota (group I.1b) being present in all samples. The normalized species richness of Thaumarchaeota correlated positively with relative humidity and negatively with temperature. This together with an increase of bare agricultural soil surfaces may explain the diversity peaks observed in fall and winter. The detected Euryarchaeota were mainly methanogens with a low relative frequency of occurrence. A slight increase in their frequency during spring may be linked to fertilization processes in the surrounding agricultural fields. Comparison with samples from the Cape Verde islands and from other coastal and continental sites indicates that the proportions of Euryarchaeota are enhanced in coastal air, which is consistent with their suggested abundance in marine surface waters. We conclude that air transport may play an important role for the dispersal of Archaea, including ammonia-oxidizing Thaumarchaeota and methanogens. Also, anthropogenic activities might influence the atmospheric abundance and diversity of Archaea.

  9. Sulfur-oxidizing chemolithotrophic proteobacteria dominate the microbiota in high arctic thermal springs on Svalbard.

    PubMed

    Reigstad, Laila Johanne; Jorgensen, Steffen Leth; Lauritzen, Stein-Erik; Schleper, Christa; Urich, Tim

    2011-09-01

    The thermal springs Trollosen and Fisosen, located on the High Arctic archipelago Svalbard, discharge saline groundwaters rich in hydrogen sulfide and ammonium through a thick layer of permafrost. Large amounts of biomass that consist of filamentous microorganisms containing sulfur granules, as analyzed with energy dispersive X-ray analysis, were found in the outflow. Prokaryotic 16S rRNA gene libraries and quantitative polymerase chain reaction (qPCR) analyses reported bacteria of the γ- and ɛ-proteobacterial classes as the dominant organisms in the filaments and the planktonic fractions, closely related to known chemolithoautotrophic sulfur oxidizers (Thiotrix and Sulfurovum). Archaea comprised ∼1% of the microbial community, with the majority of sequences affiliated with the Thaumarchaeota. Archaeal and bacterial genes coding for a subunit of the enzyme ammonia monooxygenase (amoA) were detected, as well as 16S rRNA genes of Nitrospira, all of which is indicative of potential complete nitrification in both springs. 16S rRNA sequences related to methanogens and methanotrophs were detected as well. This study provides evidence that the microbial communities in Trollosen and Fisosen are sustained by chemolithotrophy, mainly through the oxidation of reduced sulfur compounds, and that ammonium and methane might be minor, additional sources of energy and carbon.

  10. 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.

  11. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands.

    PubMed

    Yue, Haowei; Wang, Mengmeng; Wang, Shiping; Gilbert, Jack A; Sun, Xin; Wu, Linwei; Lin, Qiaoyan; Hu, Yigang; Li, Xiangzhen; He, Zhili; Zhou, Jizhong; Yang, Yunfeng

    2015-09-01

    Warming has been shown to cause soil carbon (C) loss in northern grasslands owing to accelerated microbial decomposition that offsets increased grass productivity. Yet, a multi-decadal survey indicated that the surface soil C stock in Tibetan alpine grasslands remained relatively stable. To investigate this inconsistency, we analyzed the feedback responses of soil microbial communities to simulated warming by soil transplant in Tibetan grasslands. Whereas microbial functional diversity decreased in response to warming, microbial community structure did not correlate with changes in temperature. The relative abundance of catabolic genes associated with nitrogen (N) and C cycling decreased with warming, most notably in genes encoding enzymes associated with more recalcitrant C substrates. By contrast, genes associated with C fixation increased in relative abundance. The relative abundance of genes associated with urease, glutamate dehydrogenase and ammonia monoxygenase (ureC, gdh and amoA) were significantly correlated with N2O efflux. These results suggest that unlike arid/semiarid grasslands, Tibetan grasslands maintain negative feedback mechanisms that preserve terrestrial C and N pools. To examine whether these trends were applicable to the whole plateau, we included these measurements in a model and verified that topsoil C stocks remained relatively stable. Thus, by establishing linkages between microbial metabolic potential and soil biogeochemical processes, we conclude that long-term C loss in Tibetan grasslands is ameliorated by a reduction in microbial decomposition of recalcitrant C substrates.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

  13. 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.

  14. The influence of ecological and conventional plant production systems on soil microbial quality under hops (Humulus lupulus).

    PubMed

    Oszust, Karolina; Frąc, Magdalena; Gryta, Agata; Bilińska, Nina

    2014-06-03

    The knowledge about microorganisms-activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a) ecological based on the use of probiotic preparations and organic fertilization (b) conventional-with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA) was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP) of PCR ammonia monooxygenase α-subunit (amoA) gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application.

  15. The ammonia oxidizing and denitrifying prokaryotes associated with sponges from different sea areas.

    PubMed

    Han, Minqi; Li, Zhiyong; Zhang, Fengli

    2013-08-01

    Marine sponges have been suggested to play an important role in the marine nitrogen cycling. However, the role of sponge microbes in the nitrogen transformation remains limited, especially on the bacterial ammonia oxidization and denitrification. Hence, in the present study, using functional genes (amoA, nirS, nirK, and nxrA) involved in ammonia oxidization and denitrification and 16S rRNA genes for specific bacterial groups as markers, phylogenetically diverse prokaryotes including bacteria and archaea, which may be involved in the ammonia oxidization and denitrification processes in sponges, were revealed in seven sponge species. Ammonia oxidizers were found in all species, whereas three sponges (Placospongia sp., Acanthella sp., and Pericharax heteroraphis) harbor only ammonia-oxidizing bacteria (AOB), two sponges (Spirastrellidae diplastrella and Mycale fibrexilis) host only ammonia-oxidizing archaea (AOA), while the remaining two sponges (Haliclona sp. and Lamellomorpha sp.) harbor both AOB and AOA. S. diplastrella and Lamellomorpha sp. also harbor denitrifying bacteria. Nitrite reductase gene nirK was detected only in Lamellomorpha sp. with higher phylogenetic diversity than nirS gene observed only in S. diplastrella. The detected functional genes related to the ammonia oxidization and nitrite reduction in deep-sea and shallow-water sponges highlighted the potential ecological roles of prokaryotes in sponge-related nitrogen transformation.

  16. Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities--A Comparison between Chemical Fertilizers and Bioinoculants.

    PubMed

    Gupta, Rashi; Bisaria, V S; Sharma, Shilpi

    2015-01-01

    Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However, effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. The ability of bioinoculants to reduce the application of chemicals for obtaining optimum yield of legume appears to be of great ecological and economic importance. In the present study, we compared the influence of seed inoculation of Cajanus cajan with a microbial consortium, comprising B