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Sample records for ammonia-oxidizing bacterium nitrosococcus

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

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    Lisa Y Stein

    2013-09-01

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

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

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

    2013-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-01-01

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

  4. Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant.

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    Tokuyama, Tatsuaki; Mine, Atsusi; Kamiyama, Kaoru; Yabe, Ryuichi; Satoh, Kazuo; Matsumoto, Hirotoshi; Takahashi, Reiji; Itonaga, Koji

    2004-01-01

    An ammonia-oxidizing bacterium (strain YNSRA) was isolated from the rhizoplane of the reed (Phragmites communis) used in an aquaponics plant which is a wastewater treatment plant. Strain YNSRA was identified as Nitrosomonas communis by taxonomic studies. The hydroxylamine-cytochrome c reductase (HCR) of strain YNSRA was found to have a higher activity (25.60 u/mg) than that of Nitrosomonas europaea ATCC25978T (8.94 u/mg). Ribulose-1,5-bisphosphate carboxylase (RubisCO) activity was detected at very low levels in strain YNSRA, whereas strain ATCC25978T had definite activity.

  5. Isolation and characterization of two cryptic plasmids in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11.

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    Yamagata, A; Kato, J; Hirota, R; Kuroda, A; Ikeda, T; Takiguchi, N; Ohtake, H

    1999-06-01

    Two plasmids were discovered in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11, which was isolated from activated sludge. The plasmids, designated pAYS and pAYL, were relatively small, being approximately 1.9 kb long. They were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance or heavy metal resistance markers. The complete nucleotide sequences of pAYS and pAYL were determined, and their physical maps were constructed. There existed two major open reading frames, ORF1 in pAYS and ORF2 in pAYL, each of which was more than 500 bp long. The predicted product of ORF2 was 28% identical to part of the replication protein of a Bacillus plasmid, pBAA1. However, no significant similarity to any known protein sequences was detected with the predicted product of ORF1. pAYS and pAYL had a highly homologous region, designated HHR, of 262 bp. The overall identity was 98% between the two nucleotide sequences. Interestingly, HHR-homologous sequences were also detected in the genomes of ENI-11 and the plasmidless strain Nitrosomonas europaea IFO14298. Deletion analysis of pAYS and pAYL indicated that HHR, together with either ORF1 or ORF2, was essential for plasmid maintenance in ENI-11. To our knowledge, pAYS and pAYL are the first plasmids found in the ammonia-oxidizing autotrophic bacteria.

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

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    C. H. Frame

    2010-09-01

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

  7. Catalyst for Ammonia Oxidation

    DEFF Research Database (Denmark)

    2015-01-01

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

  8. Diversity and abundance of ammonia-oxidizing

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

    2013-01-01

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

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

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

    2012-01-27

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

  10. Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.

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    Martens-Habbena, Willm; Stahl, David A

    2011-01-01

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

  11. Ammonia-oxidizing bacteria: A model for molecular microbial ecology

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

    2001-01-01

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

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

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    J.S. Norman; J.E. Barrett

    2014-01-01

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

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

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

    2015-03-01

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

  14. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

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

    2012-01-01

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

  15. Inhibition of bacterial ammonia oxidation by organohydrazines in soil microcosms

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    Yucheng eWu

    2012-01-01

    Full Text Available Hydroxylamine oxidation by hydroxylamine oxidoreductase (HAO is a key step for energy-yielding in support of the growth of ammonia-oxidizing bacteria (AOB. Organohydrazines have been shown to inactivate HAO from Nitrosomonas europaea, and may serve as selective inhibitors to differentiate bacterial from archaeal ammonia oxidation due to the absence of bacterial HAO gene homologue in known ammonia-oxidizing archaea (AOA. In this study, the effects of three organohydrazines on activity, abundance and composition of AOB and AOA were evaluated in soil microcosms. The results indicate that phenylhydrazine and methylhydrazine at the concentration of 100 mol per gram dry weight soil completely suppressed the activity of soil nitrification. DGGE fingerprinting and sequencing analysis of bacterial ammonia monooxygenase subunit A gene (amoA clearly demonstrated that nitrification activity change is well paralleled with the growth of Nitrosomonas europaea-like AOB in soil microcosms. No significant correlation between AOA community structure and nitrification activity was observed among all treatments during the incubation period, although incomplete inhibition of nitrification activity occurred in 2-hydroxyethylhydrazine-amended soil microcosms. These findings show that the HAO-targeted organohydrazines can effectively inhibit bacterial nitrification in soil, and the mechanism of organohydrazine affecting AOA remains unclear.

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

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

    2016-08-01

    Ammonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in the in situ quantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (δ(15)NNO2- and δ(18)ONO2-, respectively) are geochemical tracers for evaluating the sources and the in situ rate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilic Thaumarchaeota populations composed almost entirely of "Candidatus Nitrosocaldus." The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The δ(18)O value of nitrite produced from ammonia oxidation varied with the δ(18)O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH ≥6.6, the rate of ammonia oxidation by thermophilic Thaumarchaeota could be estimated using δ(18)ONO2- in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments. Because ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying the regulation of

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

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

    2014-05-01

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

  18. Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.

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

    2018-04-11

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

  19. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

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    Vidya eDe Gannes

    2012-07-01

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

  20. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

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    C. R. Löscher

    2012-07-01

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

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

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

    Science.gov (United States)

    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

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

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    Mariusz Cycoń

    2015-01-01

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

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

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

    2012-05-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    2015-01-01

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

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

    Science.gov (United States)

    Dong, Yuwei; Zhang, Yanqiu; Tu, Baojun

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

  7. Ammonia oxidation at high pressure and intermediate temperatures

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2010-08-01

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

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

    Digital Repository Service at National Institute of Oceanography (India)

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

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

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

    Science.gov (United States)

    Monteiro, Maria; Séneca, Joana; Magalhães, Catarina

    2014-07-01

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

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

    OpenAIRE

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

    2017-01-01

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

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

    OpenAIRE

    Nakagawa, Tatsunori; Stahl, David A.

    2013-01-01

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

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

    Science.gov (United States)

    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 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments.

    Science.gov (United States)

    Zhao, Dayong; He, Xiaowei; Huang, Rui; Yan, Wenming; Yu, Zhongbo

    2017-07-01

    Ammonia oxidation is a crucial process in global nitrogen cycling, which is catalyzed by the ammonia oxidizers. Emergent plants play important roles in the freshwater ecosystem. Therefore, it is meaningful to investigate the effects of emergent macrophytes on the abundance and community composition of ammonia oxidizers. In the present study, two commonly found emergent macrophytes (Zizania caduciflora and Phragmitas communis) were obtained from freshwater lakes and the abundance and community composition of the ammonia-oxidizing prokaryotes in the rhizosphere sediments of these emergent macrophytes were investigated. The abundance of the bacterial amoA gene was higher in the rhizosphere sediments of the emergent macrophytes than those of bulk sediments. Significant positive correlation was found between the potential nitrification rates (PNRs) and the abundance of bacterial amoA gene, suggesting that ammonia-oxidizing bacteria (AOB) might play an important role in the nitrification process of the rhizosphere sediments of emergent macrophytes. The Nitrosotalea cluster is the dominant ammonia-oxidizing archaea (AOA) group in all the sediment samples. Analysis of AOB group showed that the N. europaeal cluster dominated the rhizosphere sediments of Z. caduciflora and the bulk sediments, whereas the Nitrosospira cluster was the dominant AOB group in the rhizosphere sediments of P. communis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

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

    2017-12-01

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

  17. Degradation of halogenated aliphatic compounds by the ammonia- oxidizing bacterium Nitrosomonas europaea.

    Science.gov (United States)

    Vannelli, T; Logan, M; Arciero, D M; Hooper, A B

    1990-01-01

    Suspensions of Nitrosomonas europaea catalyzed the ammonia-stimulated aerobic transformation of the halogenated aliphatic compounds dichloromethane, dibromomethane, trichloromethane (chloroform), bromoethane, 1,2-dibromoethane (ethylene dibromide), 1,1,2-trichloroethane, 1,1,1-trichloroethane, monochloroethylene (vinyl chloride), gem-dichloroethylene, cis- and trans-dichloroethylene, cis-dibromoethylene, trichloroethylene, and 1,2,3-trichloropropane, Tetrachloromethane (carbon tetrachloride), tetrachloroethylene (perchloroethylene), and trans-dibromoethylene were not degraded. PMID:2339874

  18. Degradation of halogenated aliphatic compounds by the ammonia- oxidizing bacterium Nitrosomonas europaea.

    OpenAIRE

    Vannelli, T; Logan, M; Arciero, D M; Hooper, A B

    1990-01-01

    Suspensions of Nitrosomonas europaea catalyzed the ammonia-stimulated aerobic transformation of the halogenated aliphatic compounds dichloromethane, dibromomethane, trichloromethane (chloroform), bromoethane, 1,2-dibromoethane (ethylene dibromide), 1,1,2-trichloroethane, 1,1,1-trichloroethane, monochloroethylene (vinyl chloride), gem-dichloroethylene, cis- and trans-dichloroethylene, cis-dibromoethylene, trichloroethylene, and 1,2,3-trichloropropane, Tetrachloromethane (carbon tetrachloride),...

  19. Nitrification and the ammonia-oxidizing communities in the central Baltic Sea water column

    Science.gov (United States)

    Jäntti, Helena; Ward, Bess B.; Dippner, Joachim W.; Hietanen, Susanna

    2018-03-01

    The redoxclines that form between the oxic and anoxic water layers in the central Baltic Sea are sites of intensive nitrogen cycling. To gain better understanding of nitrification, we measured the biogeochemical properties along with potential nitrification rates and analyzed the assemblages of ammonia-oxidizing bacteria and archaea using functional gene microarrays. To estimate nitrification in the entire water column, we constructed a regression model for the nitrification rates and applied it to the conditions prevailing in the area in 2008-2012. The highest ammonia oxidation rates were found in a thin layer at the top of the redoxcline and the rates quickly decreased below detection limit when oxygen was exhausted. This is probably because extensive suboxic layers, which are known to harbor pelagic nitrification, are formed only for short periods after inflows in the Baltic Sea. The nitrification rates were some of the highest measured in the water columns, but the thickness of the layer where conditions were favorable for nitrification, was very small and it remained fairly stable between years. However, the depth of the nitrification layer varied substantially between years, particularly in the eastern Gotland Basin (EGB) due to turbulence in the water column. The ammonia oxidizer communities clustered differently between the eastern and western Gotland Basin (WGB) and the composition of ammonia-oxidizing assemblages correlated with the environmental variables. The ammonia oxidizer community composition was more even in the EGB, which may be related to physical instability of the redoxcline that does not allow predominance of a single archetype, whereas in the WGB, where the position of the redoxcline is more constant, the ammonia-oxidizing community was less even. Overall the ammonia-oxidizing communities in the Baltic Sea redoxclines were very evenly distributed compared to other marine environments where microarrays have been applied previously.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    Stahl, David A.

    2013-01-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Science.gov (United States)

    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.

  5. Benthic Ammonia Oxidizers Differ in Community Structure and Biogeochemical Potential Across a Riverine Delta

    Directory of Open Access Journals (Sweden)

    Julian eDamashek

    2015-01-01

    Full Text Available Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California’s Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the massive discharge of ammonium into the Sacramento River has altered this ecosystem by increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (encoding the α-subunit of ammonia monooxygenase. There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB outnumbering ammonia-oxidizing archaea (AOA only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The community structure and biogeochemical function of benthic ammonia oxidizers appears related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.

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

    Science.gov (United States)

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

    2011-08-01

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

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

    NARCIS (Netherlands)

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

    2011-01-01

    Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain

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

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

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

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

    NARCIS (Netherlands)

    Bollmann, A.; Laanbroek, H.J.

    2001-01-01

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

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

    NARCIS (Netherlands)

    Bollmann, A.; Laanbroek, H.J.

    2001-01-01

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

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

    NARCIS (Netherlands)

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

    2002-01-01

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

  12. Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient

    Science.gov (United States)

    S. Pierre; I. Hewson; J. P. Sparks; C. M. Litton; C. Giardina; P. M. Groffman; T. J. Fahey

    2017-01-01

    Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of...

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

    KAUST Repository

    Bagchi, Samik

    2014-12-05

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

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

    KAUST Repository

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

    2014-01-01

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

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

    Science.gov (United States)

    Ke, Xiubin; Lu, Yahai

    2012-04-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  18. Bacteria dominate ammonia oxidation in soils used for outdoor cattle overwintering

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

  20. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

    OpenAIRE

    Abby, Sophie S.; Melcher, Michael; Kerou, Melina; Krupovic, Mart; Stieglmeier, Michaela; Rossel, Claudia; Pfeifer, Kevin; Schleper, Christa

    2018-01-01

    Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally ...

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

    OpenAIRE

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

  3. Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile.

    Science.gov (United States)

    Höfferle, Špela; Nicol, Graeme W; Pal, Levin; Hacin, Janez; Prosser, James I; Mandić-Mulec, Ines

    2010-11-01

    Oxidation of ammonia, the first step in nitrification, is carried out in soil by bacterial and archaeal ammonia oxidizers and recent studies suggest possible selection for the latter in low-ammonium environments. In this study, we investigated the selection of ammonia-oxidizing archaea and bacteria in wetland soil vertical profiles at two sites differing in terms of the ammonium supply rate, but not significantly in terms of the groundwater level. One site received ammonium through decomposition of organic matter, while the second, polluted site received a greater supply, through constant leakage of an underground septic tank. Soil nitrification potential was significantly greater at the polluted site. Quantification of amoA genes demonstrated greater abundance of bacterial than archaeal amoA genes throughout the soil profile at the polluted site, whereas bacterial amoA genes at the unpolluted site were below the detection limit. At both sites, archaeal, but not the bacterial community structure was clearly stratified with depth, with regard to the soil redox potential imposed by groundwater level. However, depth-related changes in the archaeal community structure may also be associated with physiological functions other than ammonia oxidation. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-07-01

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

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

    Science.gov (United States)

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

    2015-04-01

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

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

    Science.gov (United States)

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

    2014-02-01

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

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

    Science.gov (United States)

    Dong, Lianhua; Meng, Ying; Wang, Jing

    2014-03-04

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Hongmei Jing

    2017-06-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2012-03-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

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

    Science.gov (United States)

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

    2012-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Ziye eHu

    2014-07-01

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

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

    Science.gov (United States)

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

    2018-02-01

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

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

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    Wenge Hu

    2016-03-01

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

  17. Ammonia oxidizing bacteria community dynamics in a pilot-scale wastewater treatment plant.

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    Xiaohui Wang

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

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

    Science.gov (United States)

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

    2012-12-01

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

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

    Science.gov (United States)

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

    1999-01-01

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

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

    Science.gov (United States)

    Francis, Somilez Asya

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2007-01-01

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

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

    NARCIS (Netherlands)

    Bollmann, A.; Laanbroek, H.J.

    2002-01-01

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

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

    Science.gov (United States)

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

    2011-10-01

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

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

    NARCIS (Netherlands)

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

    2002-01-01

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

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

    NARCIS (Netherlands)

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

    2002-01-01

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

  6. Substrate availability drives spatial patterns in richness of ammonia-oxidizing bacteria and archaea in temperate forest soils

    Science.gov (United States)

    J.S. Norman; J.E. Barrett

    2016-01-01

    We sought to investigate the drivers of richness of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in temperate forest soils. We sampled soils across four experimental watersheds in the Coweeta Hydrologic Laboratory, North Carolina USA. These watersheds are geographically close, but vary in soil chemistry due to differences in land use history. While we...

  7. Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils

    NARCIS (Netherlands)

    Bruns, M.A.; Stephen, J.R.; Kowalchuk, G.A.; Prosser, J.I.; Paul, E.A.

    1999-01-01

    Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO

  8. Potato cultivar type affects the structure of ammonia oxidizer communities in field soil under potato beyond the rhizosphere

    NARCIS (Netherlands)

    Cavalcante Franco Dias, A.; Hoogwout, E.F.; de Cassia Pereira e Silva, M.; Falcão Salles, J.; van Overbeek, L.S.; van Elsas, J.D.

    The effects of plants on the microbiota involved in the oxidation of ammonia in soils have been controversial. Here, we investigated the dynamics in the abundances and community structures of the bacterial and archaeal ammonia oxidizers (AOB and AOA, respectively) in two fields that were cropped

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

    Science.gov (United States)

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

    2017-05-01

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

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

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    Diallo, MD.

    2015-01-01

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

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

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2006-01-01

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

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

    Science.gov (United States)

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

    2014-04-01

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

  13. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

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    Sophie S. Abby

    2018-01-01

    Full Text Available Ammonia oxidizing archaea (AOA of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

  14. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome.

    Science.gov (United States)

    Abby, Sophie S; Melcher, Michael; Kerou, Melina; Krupovic, Mart; Stieglmeier, Michaela; Rossel, Claudia; Pfeifer, Kevin; Schleper, Christa

    2018-01-01

    Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amo AXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

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

    Science.gov (United States)

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

    2015-10-01

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

  16. 3,4-Dimethylpyrazole phosphate (DMPP) reduces activity of ammonia oxidizers without adverse effects on non-target soil microorganisms and functions

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Wenjie Yang

    2017-11-01

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

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

    Science.gov (United States)

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

    2014-12-01

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

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

    Science.gov (United States)

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

    2013-12-01

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

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

    Science.gov (United States)

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

    2007-01-01

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

  1. Evaluating four mathematical models for nitrous oxide production by autotrophic ammonia-oxidizing bacteria.

    Science.gov (United States)

    Ni, Bing-Jie; Yuan, Zhiguo; Chandran, Kartik; Vanrolleghem, Peter A; Murthy, Sudhir

    2013-01-01

    There is increasing evidence showing that ammonia-oxidizing bacteria (AOB) are major contributors to N(2)O emissions from wastewater treatment plants (WWTPs). Although the fundamental metabolic pathways for N(2)O production by AOB are now coming to light, the mechanisms responsible for N(2)O production by AOB in WWTP are not fully understood. Mathematical modeling provides a means for testing hypotheses related to mechanisms and triggers for N(2)O emissions in WWTP, and can then also become a tool to support the development of mitigation strategies. This study examined the ability of four mathematical model structures to describe two distinct mechanisms of N(2)O production by AOB. The production mechanisms evaluated are (1) N(2)O as the final product of nitrifier denitrification with NO(2)- as the terminal electron acceptor and (2) N(2)O as a byproduct of incomplete oxidation of hydroxylamine (NH(2)OH) to NO(2)-. The four models were compared based on their ability to predict N(2)O dynamics observed in three mixed culture studies. Short-term batch experimental data were employed to examine model assumptions related to the effects of (1) NH4+ concentration variations, (2) dissolved oxygen (DO) variations, (3) NO(2)- accumulations and (4) NH(2OH as an externally provided substrate. The modeling results demonstrate that all these models can generally describe the NH4+, NO(2)-, and NO(3)- data. However, none of these models were able to reproduce all measured N(2)O data. The results suggest that both the denitrification and NH(2)OH pathways may be involved in N(2)O production and could be kinetically linked by a competition for intracellular reducing equivalents. A unified model capturing both mechanisms and their potential interactions needs to be developed with consideration of physiological complexity. Copyright © 2012 Wiley Periodicals, Inc.

  2. Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.

    Science.gov (United States)

    Laloo, Andrew E; Wei, Justin; Wang, Dongbo; Narayanasamy, Shaman; Vanwonterghem, Inka; Waite, David; Steen, Jason; Kaysen, Anne; Heintz-Buschart, Anna; Wang, Qilin; Schulz, Benjamin; Nouwens, Amanda; Wilmes, Paul; Hugenholtz, Philip; Yuan, Zhiguo; Bond, Philip L

    2018-05-01

    Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA.

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

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    Oliver Müller

    2018-01-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Anne Daebeler

    2018-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Shaolan eYu

    2016-02-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2011-11-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  11. Quantitative evaluation of inhibitory effect of various substances on anaerobic ammonia oxidation (anammox).

    Science.gov (United States)

    Nakamura, Tomotaka; Harigaya, Yuhki; Kimura, Yuya; Kuroiwa, Megumi; Kurata, Yuhri; Isaka, Kazuichi; Suwa, Yuichi

    2017-09-01

    The inhibitory effect of 20 substances of various chemical species on the anaerobic ammonia oxidation (anammox) activity of an enrichment culture, predominated by Candidatus Brocadia, was determined systematically by using a 15 N tracer technique. The initial anammox rate was determined during first 25 min with a small-scale anaerobic batch incubation supplemented with possible inhibitors. Although Cu 2+ and Mn 2+ did not inhibit anammox, the remaining 18 substances [Ni 2+ , Zn 2+ , Co 2+ , [Formula: see text] , Fe 2+ , 4 amines, ethylenediaminetetraacetic acid (EDTA), ethylenediamine-N,N'-bis (2-hydroxyphenylacetic acid) (EDDHA), citric acid, nitrilotriacetic acid (NTA), N,N-dimethylacetamide (DMA), 1,4-dioxane, dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF) and tetrahydrofuran (THF)] were inhibitory. Inhibitory effect of NTA, EDDHA, THF, DMF, DMA and amines on anammox was first determined in this study. Inhibitory effects of metals were re-evaluated because chelators, which may interfere inhibitory effect, have been used to dissolve metal salts into assay solution. The relative anammox activities as a function of concentration of each substance were described successfully (R 2  > 0.91) either with a linear inhibition model or with a Michaelis-Menten-based inhibition model. IC 50 values were estimated based on either model, and were compared. The IC 50 values of the 4 chelators (0.06-2.7 mM) and 5 metal ions (0.02-1.09 mM) were significantly lower than those of the 4 amines (10.6-29.1 mM) and 5 organic solvents (3.5-82 mM). Although it did not show any inhibition within 25 min, 0.1 mM Cu 2+ completely inhibited anammox activity in 240 min, suggesting that the inhibitory effect caused by Cu 2+ is time-dependent. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Puntipar Sonthiphand

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

  13. Microbial activities in boreal soils: Biodegradation of organic contaminants at low temperature and ammonia oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Kurola, J. (University of Helsinki, Faculty of Biosciences, Department of Ecological and Environmental Sciences, Lahti (FI))

    2006-07-01

    This thesis deals with the response of biodegradation of selected anthropogenic organic contaminants and natural autochthonous organic matter to low temperature in boreal surface soils. Furthermore, the thesis describes activity, diversity and population size of autotrophic ammonia-oxidizing bacteria (AOB) in a boreal soil used for landfarming of oil-refinery wastes, and presents a new approach, in which the particular AOB were enriched and cultivated in situ from the landfarming soil onto cation exchange membranes. This thesis demonstrates that rhizosphere fraction of natural forest humus soil and agricultural clay loam soil from Helsinki Metropolitan area were capable of degrading of low to moderate concentrations (0.2 - 50 mug cm-3) of PCP, phenanthrene and 2,4,5-TCP at temperatures realistic to boreal climate (-2.5 to +15 deg C). At the low temperatures, the biodegradation of PCP, phenanthrene and 2,4,5-TCP was more effective (Q10-values from 1.6 to 7.6) in the rhizosphere fraction of the forest soil than in the agricultural soil. Q10-values of endogenous soil respiration (carbon dioxide evolution) and selected hydrolytic enzyme activities (acetate-esterase, butyrate-esterase and beta-glucosidase) in acid coniferous forest soil were 1.6 to 2.8 at temperatures from -3 to +30 deg C. The results indicated that the temperature dependence of decomposition of natural autochthonous soil organic matter in the studied coniferous forest was only moderate. The numbers of AOB in the landfarming (sandy clay loam) soil were determined with quantitative polymerase chain reaction (real-time PCR) and with Most Probable Number (MPN) methods, and potential ammonium oxidation activity was measured with the chlorate inhibition technique. The results indicated presence of large and active AOB populations in the heavily oil-contaminated and urea-fertilised landfarming soil. Assessment of the populations of AOB with denaturing gradient gel electrophoresis (DGGE) profiling and sequence

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

    Science.gov (United States)

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

    1990-02-01

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

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

    OpenAIRE

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

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Science.gov (United States)

    de la Torre, J. R.

    2010-12-01

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

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

    Science.gov (United States)

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

    2011-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Xu Sun

    2014-03-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

    Daebeler, Anne; Abell, Guy C. J.; Bodelier, Paul L. E.; Bodrossy, Levente; Frampton, Dion M. F.; Hefting, Mariet M.; Laanbroek, Hendrikus J.

    2012-01-01

    The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization. PMID:23060870

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

    Directory of Open Access Journals (Sweden)

    Anne eDaebeler

    2012-10-01

    Full Text Available The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of the associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilisation site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative PCR suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while the measured soil physico-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.

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

    Science.gov (United States)

    Daebeler, Anne; Abell, Guy C J; Bodelier, Paul L E; Bodrossy, Levente; Frampton, Dion M F; Hefting, Mariet M; Laanbroek, Hendrikus J

    2012-01-01

    The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.

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

    Science.gov (United States)

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

    2010-12-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Elena V Lebedeva

    Full Text Available The discovery of ammonia-oxidizing archaea (AOA of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

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

    Science.gov (United States)

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

    2013-01-01

    The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

  8. Tide as steering factor in structuring archaeal and bacterial ammonia-oxidizing communities in mangrove forest soils dominated by Avicennia germinans and Rhizophora mangle

    NARCIS (Netherlands)

    Marcos, Magali S.; Barboza, A.D.H.; Keijzer, R.M.; Laanbroek, H.J.

    2018-01-01

    Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations

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

    Science.gov (United States)

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

    2017-07-01

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  11. Dynamics of nitrification and denitrification in root- oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Libochant, J.A.; Blom, C.W.P.M.; Laanbroek, H.J.

    1996-01-01

    Oxygen-releasing plants may provide aerobic niches in anoxic sediments and soils for ammonia-oxidizing bacteria, The oxygen- releasing, aerenchymatous emergent macrophyte Glycerin maxima had a strong positive effect on numbers and activities of the nitrifying bacteria in its root zone in spring and

  12. Dynamics of nitrification and denitrification in root- oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Libochant, J.A.; Blom, C.W.P.M.; Laanbroek, H.J.

    1996-01-01

    Oxygen-releasing plants may provide aerobic niches in anoxic sediments and soils for ammonia-oxidizing bacteria. The oxygen-releasing, aerenchymatous emergent macrophyte Glyceria maxima had a strong positive effect on numbers and activities of the nitrifying bacteria in its root zone in spring and

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

    Directory of Open Access Journals (Sweden)

    Barbara eStempfhuber

    2016-01-01

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

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

    Science.gov (United States)

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

    2017-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Juan Ling

    2018-01-01

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

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

    Science.gov (United States)

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

    2015-02-01

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

  17. The response of ammonia-oxidizing microorganisms to trace metals and urine in two grassland soils in New Zealand.

    Science.gov (United States)

    Wang, Pengcheng; Di, Hong J; Cameron, Keith C; Tan, Qiling; Podolyan, Andriy; Zhao, Xiaohu; McLaren, Ron G; Hu, Chengxiao

    2017-01-01

    An incubation experiment was conducted to investigate the response of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the nitrification rate to the contamination of Cu, Zn, and Cd in two New Zealand grassland soils. The soils spiked with different concentrations of Cu (20 and 50 mg kg -1 ), Zn (20 and 50 mg kg -1 ), and Cd (2 and 10 mg kg -1 ) were incubated for 14 days and then treated with 500 mg kg -1 urine-N before continuing incubation for a total of 115 days. Soils were sampled at intervals throughout the incubation. The nitrification rate in soils at each sampling period was determined, and the abundance of AOB and AOA was measured by real-time quantification polymerase chain reaction (qPCR) assay of the amoA gene copy numbers. The results revealed that moderate trace metal stress did not significantly affect the abundance of AOB and AOA in the two soils, probably due to the high organic matter content of the soils which would have reduced the toxic effect of the metals. Nitrification rates were much greater and the observable nitrification period was much shorter in the dairy farm (DF) soil, in which the AOB and AOA abundances were greater than those of the mixed cropping farm (MF) soil. AOB were shown to grow under high nitrogen conditions, whereas AOA were shown to grow under low N environments, with different metal concentrations. Therefore, nitrogen status rather than metal applications was the main determining factor for AOB and AOA growth in the two soils studied.

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

    Science.gov (United States)

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

    2012-01-01

    The spatial distribution and diversity of archaeal and bacterial ammonia oxidizers (AOA and AOB) were evaluated targeting amoA genes in the gradient of a littoral buffer zone which has been identified as a hot spot for N cycling. Here we found high spatial heterogeneity in the nitrification rate and abundance of ammonia oxidizers in the five sampling sites. The bacterial amoA gene was numerically dominant in most of the surface soil but decreased dramatically in deep layers. Higher nitrification potentials were detected in two sites near the land/water interface at 4.4-6.1 microg NO(2-)-N/(g dry weight soil x hr), while only 1.0-1.7 microg NO(2-)-N/(g dry weight soil x hr) was measured at other sites. The potential nitrification rates were proportional to the amoA gene abundance for AOB, but with no significant correlation with AOA. The NH4+ concentration was the most determinative parameter for the abundance of AOB and potential nitrification rates in this study. Higher richness in the surface layer was found in the analysis of biodiversity. Phylogenetic analysis revealed that most of the bacterial amoA sequences in surface soil were affiliated with the genus of Nitrosopira while the archaeal sequences were almost equally affiliated with Candidatus 'Nitrososphaera gargensis' and Candidatus 'Nitrosocaldus yellowstonii'. The spatial distribution of AOA and AOB indicated that bacteria may play a more important role in nitrification in the littoral buffer zone of a N-rich lake.

  19. Physical map location of the multicopy genes coding for ammonia monooxygenase and hydroxylamine oxidoreductase in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11.

    Science.gov (United States)

    Hirota, R; Yamagata, A; Kato, J; Kuroda, A; Ikeda, T; Takiguchi, N; Ohtake, H

    2000-02-01

    Pulsed-field gel electrophoresis of PmeI digests of the Nitrosomonas sp. strain ENI-11 chromosome produced four bands ranging from 1,200 to 480 kb in size. Southern hybridizations suggested that a 487-kb PmeI fragment contained two copies of the amoCAB genes, coding for ammonia monooxygenase (designated amoCAB(1) and amoCAB(2)), and three copies of the hao gene, coding for hydroxylamine oxidoreductase (hao(1), hao(2), and hao(3)). In this DNA fragment, amoCAB(1) and amoCAB(2) were about 390 kb apart, while hao(1), hao(2), and hao(3) were separated by at least about 100 kb from each other. Interestingly, hao(1) and hao(2) were located relatively close to amoCAB(1) and amoCAB(2), respectively. DNA sequence analysis revealed that hao(1) and hao(2) shared 160 identical nucleotides immediately upstream of each translation initiation codon. However, hao(3) showed only 30% nucleotide identity in the 160-bp corresponding region.

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

    Science.gov (United States)

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

    2014-01-01

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

  1. The transformation from anammox granules to deammonification granules in micro-aerobic system by facilitating indigenous ammonia oxidizing bacteria.

    Science.gov (United States)

    Wang, Xiaolong; Gao, Dawen

    2018-02-01

    Granular deammonification process is a good way to retain aerobic and anaerobic ammonia oxidizing bacteria (AOB and anammox bacteria) and exhaust flocculent nitrite oxidizing bacteria (NOB). In this study, to facilitate indigenous AOB growth on anammox granules, by stepwise reducing influent nitrite, anammox granules were effectively transformed into deammonification granules in a micro-aerobic EGSB in 100 days. Total nitrogen removal efficiency of 90% and nitrogen removal rate of 2.3 g N/L/d were reached at stable deammonification stage. High influent FA and limited oxygen supply contributed suppression for Nitrospira-like NOB. In transition stages, Proteobacteria and Chloroflexi were always dominated. Anammox abundance decreased, while AOB abundance grew fast. Anammox bacteria and AOB were dominated by Brocadia fulgida and Nitrosomonas europaea, respectively. Denitrification activity and bacteria existed although without influent organic. The final AOB abundance was about 4.55-13.8 times more than anammox bacteria abundance, with almost equal potential activities. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2013-09-01

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

  3. The Experiment Study of Anaerobic Ammonia Oxidation Start-up by Using the Upflow Double Layer Anaerobic Filter

    Directory of Open Access Journals (Sweden)

    YAO Li

    2018-02-01

    Full Text Available Anammox is an efficient nitrogen removal process, but it is difficult to start-up and operate, and ananammox reactor is the efficient way to resolve this problem. The start-up of anammox reactor by upflow anaerobic filter was studied. Denitrifying sludge, anaerobic sludge, and mixed sludge was inoculated on the packing materials, respectively and an autotrophic denitrification condition was provided by the simulated wastewater influent. Along with the gradual increase of matrix concentration and hydraulic load, the microflora was converted to the anaerobic ammonium oxidation(anammoxreaction. The results showed that the anammox reaction could be started by all the three sludge, and the time of start-up of denitrifying sludge, anaerobic sludge, mixed sludge was 42, 54 days and 45 days, respectively. The best result was that inoculated with denitrifying sludge with 82.2% of the total nitrogen removal rate, which started-up quickly and nitrogen was removed efficiently. Double packing effectively improved the stability of anammox process in the reactor, in which the suitable influent concentration loading for the anammox bacteria was 270 mg·L-1 and 360 mg·L-1 for ammonia nitrogen and nitrite nitrogen, respectively, and the COD concentration could not be more than 150 mg· L-1. Furthermore, there was a coexist-effect for anaerobic ammonia oxidation and methanation in this reactor system.

  4. Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in mediterranean urban stream biofilms.

    Science.gov (United States)

    Merbt, Stephanie N; Auguet, Jean-Christophe; Blesa, Alba; Martí, Eugènia; Casamayor, Emilio O

    2015-01-01

    Streams affected by wastewater treatment plant (WWTP) effluents are hotspots of nitrification. We analyzed the influence of WWTP inputs on the abundance, distribution, and composition of epilithic ammonia-oxidizing (AO) assemblages in five Mediterranean urban streams by qPCR and amoA gene cloning and sequencing of both archaea (AOA) and bacteria (AOB). The effluents significantly modified stream chemical parameters, and changes in longitudinal profiles of both NH(4)(+) and NO(3)(-) indicated stimulated nitrification activity. WWTP effluents were an allocthonous source of both AOA, essentially from the Nitrosotalea cluster, and mostly of AOB, mainly Nitrosomonas oligotropha, Nitrosomonas communis, and Nitrosospira spp. changing the relative abundance and the natural composition of AO assemblages. Under natural conditions, Nitrososphaera and Nitrosopumilus AOA dominated AO assemblages, and AOB were barely detected. After the WWTP perturbation, epilithic AOB increased by orders of magnitude whereas AOA did not show quantitative changes but a shift in population composition to dominance of Nitrosotalea spp. The foraneous AOB successfully settled in downstream biofilms and probably carried out most of the nitrification activity. Nitrosotalea were only observed downstream and only in biofilms exposed to either darkness or low irradiance. In addition to other potential environmental limitations for AOA distribution, this result suggests in situ photosensitivity as previously reported for Nitrosotalea under laboratory conditions.

  5. Ammonia Oxidation by Abstraction of Three Hydrogen Atoms from a Mo–NH 3 Complex

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Papri; Heiden, Zachariah M.; Wiedner, Eric S.; Raugei, Simone; Piro, Nicholas A.; Kassel, W. Scott; Bullock, R. Morris; Mock, Michael T.

    2017-02-15

    We report ammonia oxidation by homolytic cleavage of all three H atoms from a Mo-15NH3 complex using the 2,4,6-tri-tert-butylphenoxyl radical to afford a Mo-alkylimido (Mo=15NR) complex (R = 2,4,6-tri-t-butylcyclohexa-2,5-dien-1-one). Reductive cleavage of Mo=15NR generates a terminal Mo≡N nitride, and a [Mo-15NH]+ complex is formed by protonation. Computational analysis describes the energetic profile for the stepwise removal of three H atoms from the Mo-15NH3 complex and the formation of Mo=15NR. Acknowledgment. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Re-search Center funded by the U.S. Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences. EPR and mass spectrometry experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. The authors thank Dr. Eric D. Walter and Dr. Rosalie Chu for assistance in performing EPR and mass spectroscopy analysis, respectively. Computational resources provided by the National Energy Re-search Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific North-west National Laboratory is operated by Battelle for the U.S. DOE.

  6. Utilization of organic nitrogen by arbuscular mycorrhizal fungi-is there a specific role for protists and ammonia oxidizers?

    Science.gov (United States)

    Bukovská, Petra; Bonkowski, Michael; Konvalinková, Tereza; Beskid, Olena; Hujslová, Martina; Püschel, David; Řezáčová, Veronika; Gutiérrez-Núñez, María Semiramis; Gryndler, Milan; Jansa, Jan

    2018-04-01

    Arbuscular mycorrhizal (AM) fungi can significantly contribute to plant nitrogen (N) uptake from complex organic sources, most likely in concert with activity of soil saprotrophs and other microbes releasing and transforming the N bound in organic forms. Here, we tested whether AM fungus (Rhizophagus irregularis) extraradical hyphal networks showed any preferences towards certain forms of organic N (chitin of fungal or crustacean origin, DNA, clover biomass, or albumin) administered in spatially discrete patches, and how the presence of AM fungal hyphae affected other microbes. By direct 15 N labeling, we also quantified the flux of N to the plants (Andropogon gerardii) through the AM fungal hyphae from fungal chitin and from clover biomass. The AM fungal hyphae colonized patches supplemented with organic N sources significantly more than those receiving only mineral nutrients, organic carbon in form of cellulose, or nothing. Mycorrhizal plants grew 6.4-fold larger and accumulated, on average, 20.3-fold more 15 N originating from the labeled organic sources than their nonmycorrhizal counterparts. Whereas the abundance of microbes (bacteria, fungi, or Acanthamoeba sp.) in the different patches was primarily driven by patch quality, we noted a consistent suppression of the microbial abundances by the presence of AM fungal hyphae. This suppression was particularly strong for ammonia oxidizing bacteria. Our results indicate that AM fungi successfully competed with the other microbes for free ammonium ions and suggest an important role for the notoriously understudied soil protists to play in recycling organic N from soil to plants via AM fungal hyphae.

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

    Science.gov (United States)

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

    2017-11-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-15

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

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

    Science.gov (United States)

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

    2014-12-01

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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2015-05-01

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

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

    Science.gov (United States)

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

    2014-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Yuan Liu

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

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

    Science.gov (United States)

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

    2011-06-01

    Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of 'deep-sea' clades distinct from 'shallow' representatives. Measured deep-sea dark CO(2) fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [(14)C]HCO(3) incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance.

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

    Science.gov (United States)

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

    2018-06-01

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

  17. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil

    Directory of Open Access Journals (Sweden)

    Jie Chen

    2017-07-01

    Full Text Available Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD and extending the dry-season duration (ED but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08 was much lower than that of the net N transformation rate (0.55 ± 0.02 throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA and denitrifying genes (nirK, nirS, and nosZ, while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+ and dissolved organic carbon concentrations] during the experiment.

  18. Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers.

    Science.gov (United States)

    Courtens, Emilie N P; Vandekerckhove, Tom; Prat, Delphine; Vilchez-Vargas, Ramiro; Vital, Marius; Pieper, Dietmar H; Meerbergen, Ken; Lievens, Bart; Boon, Nico; Vlaeminck, Siegfried E

    2016-04-01

    Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2014-02-01

    Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Zhu Chen

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

  2. Distributions and activities of ammonia oxidizing bacteria and polyphosphate accumulating organisms in a pumped-flow biofilm reactor.

    Science.gov (United States)

    Wu, Guangxue; Nielsen, Michael; Sorensen, Ketil; Zhan, Xinmin; Rodgers, Michael

    2009-10-01

    The spatial distributions and activities of ammonia oxidizing bacteria (AOB) and polyphosphate accumulating organisms (PAOs) were investigated for a novel laboratory-scale sequencing batch pumped-flow biofilm reactor (PFBR) system that was operated for carbon, nitrogen and phosphorus removal. The PFBR comprised of two 16.5l tanks (Reactors 1 and 2), each with a biofilm module of 2m(2) surface area. To facilitate the growth of AOB and PAOs in the reactor biofilms, the influent wastewater was held in Reactor 1 under stagnant un-aerated conditions for 6 h after feeding, and was then pumped over and back between Reactors 1 and 2 for 12 h, creating aerobic conditions in the two reactors during this period; as a consequence, the biofilm in Reactor 2 was in an aerobic environment for almost all the 18.2 h operating cycle. A combination of micro-sensor measurements, molecular techniques, batch experiments and reactor studies were carried out to analyse the performance of the PFBR system. After 100 days operation at a filtered chemical oxygen demand (COD(f)) loading rate of 3.46 g/m(2) per day, the removal efficiencies were 95% COD(f), 87% TN(f) and 74% TP(f). While the PFBR microbial community structure and function were found to be highly diversified with substantial AOB and PAO populations, about 70% of the phosphorus release potential and almost 100% of the nitrification potential were located in Reactors 1 and 2, respectively. Co-enrichment of AOB and PAOs was realized in the Reactor 2 biofilm, where molecular analyses revealed unexpected microbial distributions at micro-scale, with population peaks of AOB in a 100-250 microm deep sub-surface zone and of PAOs in the 0-150 microm surface zone. The micro-distribution of AOB coincided with the position of the nitrification peak identified during micro-sensor analyses. The study demonstrates that enrichment of PAOs can be realized in a constant or near constant aerobic biofilm environment. Furthermore, the findings suggest

  3. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

    Science.gov (United States)

    Zhou, Xingang; Wang, Zhilin; Jia, Huiting; Li, Li; Wu, Fengzhi

    2018-01-01

    Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA , nirS , and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity ( P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile ( P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria , Planctomycetes , and Cyanobacteria , the first cropping of JA with Actinobacteria , the second cropping of JA with Acidobacteria , Armatimonadetes , Gemmatimonadetes , and Proteobacteria . At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms

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

    Directory of Open Access Journals (Sweden)

    Michele C ePereira e Silva

    2012-03-01

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

  5. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances

    Directory of Open Access Journals (Sweden)

    Xingang Zhou

    2018-04-01

    Full Text Available Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA, nirS, and nirK genes. Results showed that 1–2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity (P < 0.05. Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile (P < 0.001. At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria, Planctomycetes, and Cyanobacteria, the first cropping of JA with Actinobacteria, the second cropping of JA with Acidobacteria, Armatimonadetes, Gemmatimonadetes, and Proteobacteria. At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO

  6. Stable isotope probing and dynamic loading experiments provide insight into the ecophysiology of novel ammonia oxidizers in rapid gravity sand filters

    DEFF Research Database (Denmark)

    Fowler, Jane; Palomo, Alejandro; Gülay, Arda

    to elucidate the differences in ecophysiology between the ammonia oxidizing clades that enable them to co-exist in this unique environment. Experiments were conducted using sand columns designed and operated to mimic the conditions in the full-scale parent RSF. RNA and DNA stable isotope probing based on 13C......-bicarbonate incorporation during continuous feeding with either ammonium or nitrite as sole energy source implicated Nitrospira spp. and certain ‘heterotrophic’ bacteria in addition to Nitrosomonas spp. in autotrophy during ammonium oxidation in RSFs. Further experimentation aimed to elucidate the ecophysiology of each...

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

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    Curtis J Hayden

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

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

    Science.gov (United States)

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

    2013-01-01

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

  9. Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives.

    Science.gov (United States)

    Restrepo-Ortiz, C X; Merbt, S N; Barrero-Canossa, J; Fuchs, B M; Casamayor, E O

    2018-04-28

    The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N. devanaterra, as well as the non-target ammonia-oxidizing archaeon Nitrosopumilus maritimus. Probe specificity was improved with a competitor oligonucleotide, and fluorescence intensity and cell visualization were enhanced by the design and application of two adjacent helpers. Probe performance was tested in soil samples along a pH gradient, and counting results matched the expected in situ distributions. Probe SAG357 and the CARD-FISH protocol developed in the present study will help to improve the current understanding of the ecology and physiology of N. devanaterra and its relatives in natural environments. Copyright © 2018 Elsevier GmbH. All rights reserved.

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

    Science.gov (United States)

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

    2016-12-01

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

  11. Comparison of different two-pathway models for describing the combined effect of DO and nitrite on the nitrous oxide production by ammonia-oxidizing bacteria.

    Science.gov (United States)

    Lang, Longqi; Pocquet, Mathieu; Ni, Bing-Jie; Yuan, Zhiguo; Spérandio, Mathieu

    2017-02-01

    The aim of this work is to compare the capability of two recently proposed two-pathway models for predicting nitrous oxide (N 2 O) production by ammonia-oxidizing bacteria (AOB) for varying ranges of dissolved oxygen (DO) and nitrite. The first model includes the electron carriers whereas the second model is based on direct coupling of electron donors and acceptors. Simulations are confronted to extensive sets of experiments (43 batches) from different studies with three different microbial systems. Despite their different mathematical structures, both models could well and similarly describe the combined effect of DO and nitrite on N 2 O production rate and emission factor. The model-predicted contributions for nitrifier denitrification pathway and hydroxylamine pathway also matched well with the available isotopic measurements. Based on sensitivity analysis, calibration procedures are described and discussed for facilitating the future use of those models.

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

    Science.gov (United States)

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

    2014-03-01

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

  13. Isotope signatures of N2O emitted from vegetable soil: Ammonia oxidation drives N2O production in NH4(+)-fertilized soil of North China.

    Science.gov (United States)

    Zhang, Wei; Li, Yuzhong; Xu, Chunying; Li, Qiaozhen; Lin, Wei

    2016-07-08

    Nitrous oxide (N2O) is a potent greenhouse gas. In North China, vegetable fields are amended with high levels of N fertilizer and irrigation water, which causes massive N2O flux. The aim of this study was to determine the contribution of microbial processes to N2O production and characterize isotopic signature effects on N2O source partitioning. We conducted a microcosm study that combined naturally abundant isotopologues and gas inhibitor techniques to analyze N2O flux and its isotopomer signatures [δ(15)N(bulk), δ(18)O, and SP (intramolecular (15)N site preference)] that emitted from vegetable soil after the addition of NH4(+) fertilizers. The results show that ammonia oxidation is the predominant process under high water content (70% water-filled pore space), and nitrifier denitrification contribution increases with increasing N content. δ(15)N(bulk) and δ(18)O of N2O may not provide information about microbial processes due to great shifts in precursor signatures and atom exchange, especially for soil treated with NH4(+) fertilizer. SP and associated two end-member mixing model are useful to distinguish N2O source and contribution. Further work is needed to explore isotopomer signature stability to improve N2O microbial process identification.

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

    Science.gov (United States)

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

    2011-11-01

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

  15. Detection of Ammonia-Oxidizing Bacteria (AOB) Using a Porous Silicon Optical Biosensor Based on a Multilayered Double Bragg Mirror Structure.

    Science.gov (United States)

    Zhang, Hongyan; Lv, Jie; Jia, Zhenhong

    2018-01-01

    We successfully demonstrate a porous silicon (PS) double Bragg mirror by electrochemical etching at room temperature as a deoxyribonucleic acid (DNA) label-free biosensor for detecting ammonia-oxidizing bacteria (AOB). Compared to various other one-dimension photonic crystal configurations of PS, the double Bragg mirror structure is quite easy to prepare and exhibits interesting optical properties. The width of high reflectivity stop band of the PS double Bragg mirror is about 761 nm with a sharp and deep resonance peak at 1328 nm in the reflectance spectrum, which gives a high sensitivity and distinguishability for sensing performance. The detection sensitivity of such a double Bragg mirror structure is illustrated through the investigation of AOB DNA hybridization in the PS pores. The redshifts of the reflectance spectra show a good linear relationship with both complete complementary and partial complementary DNA. The lowest detection limit for complete complementary DNA is 27.1 nM and the detection limit of the biosensor for partial complementary DNA is 35.0 nM, which provides the feasibility and effectiveness for the detection of AOB in a real environment. The PS double Bragg mirror structure is attractive for widespread biosensing applications and provides great potential for the development of optical applications.

  16. Bacterium oxidizing carbon monoxide

    Energy Technology Data Exchange (ETDEWEB)

    Kistner, A

    1953-01-01

    Present-day knowledge of the microbiological oxidation of carbon monoxide is based on doubtful observations and imperfect experimental procedures. By making use of shake cultures in contact with gas mixtures containing high concentrations of CO and by employing liquid enrichment media with a low content of organic matter and solid media of the same composition with not more than 1.2% agar, it proved possible to isolate a co-oxidizing bacterium of the genus hydrogenomonas from sewage sludge. For the first time irrefutable proof has been given of the oxidation of carbon monoxide by a pure culture of a bacterium, both in growing cultures and in resting cell suspensions. 12 references.

  17. [Abundances of ammonia-oxidizing archaeal accA and amoA genes in response to NO2 - and NO3 - of hot springs in Yunnan province].

    Science.gov (United States)

    Song, Zhaoqi; Wang, Li; Zhou, Enmin; Wang, Fengping; Xiao, Xiang; Zhang, Chuanlun; Li, Wenjun

    2014-12-04

    Yunnan hot springs have highly diverseammonia-oxidizing archaea (AOA), which are autotrophic and can fix CO2 using the 3-hydroxypropionate/ 4-hydroxybutyrate (HP/HD) pathway. In this study, we investigated the abundances of prokaryotic 16S rRNA gene and archaeal accA and amoA genes in the sediments of hot springs of Yunnan Province, and analysed the correlations between the above gene abundances and environmental factors. We selected the sediments of twenty representative hot springs, and detected the gene abundances by quantitative polymerase chain reaction (qPCR). The principal component analysis (PCA) and the Mantel test in the R software package were performed for the correlations of gene abundance and environmental variables. The bacterial and archaeal 16S rRNA gene abundances were from 6.6 x 10(7) to 4.19 x 10(11) and from 1.27 x 10(6) to 1.51 x 10(11) copies/g sediment, respectively; Archaeal accA and amoA genes were from 8.89 x 10(3) to 6.49 x 10(5) and from 7.64 x 10(3) to 4.36 x 10(5) copies/g sediment, respectively. The results of mantel test showed that accA gene was significantly (R = 0.98, P < 0.001) correlated with amoA gene; Both of them also were correlated significantly with NO2- and NO3 -, but not with pH. The abundances of bacterial and archaeal 16S rRNA genes and the ratio between them varied significantly among Yunnan hot springs. The archaealaccA and amoA genes showed significant correlation with each other, validating our previous finding that AOA in terrestrial hot springs might acquire energy from ammonia oxidation coupled with CO2 fixation using the 3-hydroxypropionate/4-hydroxybutyrate pathway.

  18. Differential Responses of Dinitrogen Fixation, Diazotrophic Cyanobacteria and Ammonia Oxidation Reveal a Potential Warming-Induced Imbalance of the N-Cycle in Biological Soil Crusts.

    Directory of Open Access Journals (Sweden)

    Xiaobing Zhou

    Full Text Available N2 fixation and ammonia oxidation (AO are the two most important processes in the nitrogen (N cycle of biological soil crusts (BSCs. We studied the short-term response of acetylene reduction assay (ARA rates, an indicator of potential N2 fixation, and AO rates to temperature (T, -5°C to 35°C in BSC of different successional stages along the BSC ecological succession and geographic origin (hot Chihuahuan and cooler Great Basin deserts. ARA in all BSCs increased with T until saturation occurred between 15 and 20°C, and declined at 30-35°C. Culture studies using cyanobacteria isolated from these crusts indicated that the saturating effect was traceable to their inability to grow well diazotrophically within the high temperature range. Below saturation, temperature response was exponential, with Q10 significantly different in the two areas (~ 5 for Great Basin BSCs; 2-3 for Chihuahuan BSCs, but similar between the two successional stages. However, in contrast to ARA, AO showed a steady increase to 30-35°C in Great Basin, and Chihuhuan BSCs showed no inhibition at any tested temperature. The T response of AO also differed significantly between Great Basin (Q10 of 4.5-4.8 and Chihuahuan (Q10 of 2.4-2.6 BSCs, but not between successional stages. Response of ARA rates to T did not differ from that of AO in either desert. Thus, while both processes scaled to T in unison until 20°C, they separated to an increasing degree at higher temperature. As future warming is likely to occur in the regions where BSCs are often the dominant living cover, this predicted decoupling is expected to result in higher proportion of nitrates in soil relative to ammonium. As nitrate is more easily lost as leachate or to be reduced to gaseous forms, this could mean a depletion of soil N over large landscapes globally.

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

    Science.gov (United States)

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

    2016-01-01

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

  20. Differential responses of dinitrogen fixation, diazotrophic cyanobacteria and ammonia oxidation reveal a potential warming-induced imbalance of the N-cycle in biological soil crusts

    Science.gov (United States)

    Zhou, Xiaobing; Smith, Hilda J.; Giraldo Silva, Ana; Belnap, Jayne; Garcia-Pichel, Ferran

    2017-01-01

    N2 fixation and ammonia oxidation (AO) are the two most important processes in the nitrogen (N) cycle of biological soil crusts (BSCs). We studied the short-term response of acetylene reduction assay (ARA) rates, an indicator of potential N2 fixation, and AO rates to temperature (T, -5°C to 35°C) in BSC of different successional stages along the BSC ecological succession and geographic origin (hot Chihuahuan and cooler Great Basin deserts). ARA in all BSCs increased with T until saturation occurred between 15 and 20°C, and declined at 30–35°C. Culture studies using cyanobacteria isolated from these crusts indicated that the saturating effect was traceable to their inability to grow well diazotrophically within the high temperature range. Below saturation, temperature response was exponential, with Q10 significantly different in the two areas (~ 5 for Great Basin BSCs; 2–3 for Chihuahuan BSCs), but similar between the two successional stages. However, in contrast to ARA, AO showed a steady increase to 30–35°C in Great Basin, and Chihuhuan BSCs showed no inhibition at any tested temperature. The T response of AO also differed significantly between Great Basin (Q10 of 4.5–4.8) and Chihuahuan (Q10 of 2.4–2.6) BSCs, but not between successional stages. Response of ARA rates to T did not differ from that of AO in either desert. Thus, while both processes scaled to T in unison until 20°C, they separated to an increasing degree at higher temperature. As future warming is likely to occur in the regions where BSCs are often the dominant living cover, this predicted decoupling is expected to result in higher proportion of nitrates in soil relative to ammonium. As nitrate is more easily lost as leachate or to be reduced to gaseous forms, this could mean a depletion of soil N over large landscapes globally.

  1. 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▿ †

    Science.gov (United States)

    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

  2. Lactococcus lactis - a diploid bacterium

    DEFF Research Database (Denmark)

    Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

    the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...... milk products, is born with two complete non-replicating chromosomes. L. lactis therefore remain diploid throughout its entire life cycle....

  3. Potential coupling effects of ammonia-oxidizing and anaerobic ammonium-oxidizing bacteria on completely autotrophic nitrogen removal over nitrite biofilm formation induced by the second messenger cyclic diguanylate.

    Science.gov (United States)

    Wang, Chao; Liu, Sitong; Xu, Xiaochen; Zhao, Chuanqi; Yang, Fenglin; Wang, Dong

    2017-05-01

    The objective of this study was to investigate the influence of extracellular polymeric substance (EPS) on the coupling effects between ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria for the completely autotrophic nitrogen removal over nitrite (CANON) biofilm formation in a moving bed biofilm reactor (MBBR). Analysis of the quantity of EPS and cyclic diguanylate (c-di-GMP) confirmed that the contents of polysaccharides and c-di-GMP were correlated in the AOB sludge, anammox sludge, and CANON biofilm. The anammox sludge secreted more EPS (especially polysaccharides) than AOB with a markedly higher c-di-GMP content, which could be used by the bacteria to regulate the synthesis of exopolysaccharides that are ultimately used as a fixation matrix, for the adhesion of biomass. Indeed, increased intracellular c-di-GMP concentrations in the anammox sludge enhanced the regulation of polysaccharides to promote the adhesion of AOB and formation of the CANON biofilm. Overall, the results of this study provide new comprehensive information regarding the coupling effects of AOB and anammox bacteria for the nitrogen removal process.

  4. Molecular identification of phosphate solubilizing bacterium ...

    African Journals Online (AJOL)

    A phosphate solubilizing bacterium was isolated from the rhizosphere soil of upland rice and identified by 16S rRNA gene sequencing. The gene sequence showed 99% homology with Alcaligenes faecalis. Based on the gene sequence homology, it was identified as A. faecalis. Interaction effect of this bacterium on growth ...

  5. RESULTS OF INITIAL AMMONIA OXIDATION TESTING

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-12-30

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

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

    Science.gov (United States)

    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

  7. Zymomonas mobilis: a bacterium for ethanol production

    Energy Technology Data Exchange (ETDEWEB)

    Baratti, J.C.; Bu' Lock, J.D.

    1986-01-01

    Zymomonas mobilis is a facultative anaerobic gram negative bacterium first isolated in tropical countries from alcoholic beverages like the African palm wine, the Mexican pulque and also as a contaminant of cider (cider sickness) or beer in the European countries. It is one of the few facultative anaerobic bacteria degrading glucose by the Entner-Doudoroff pathway usually found in strictly aerobic microorganisms. Some work was devoted to this bacterium in the 50s and 60s and was reviewed by Swings and De Ley in their classical paper published in 1977. During the 70s there was very little work on the bacterium until 1979 and the first report by the Australian group of P.L. Rogers on the great potentialities of Z. mobilis for ethanol production. At that time the petroleum crisis had led the developed countries to search for alternative fuel from renewable resources. The Australian group clearly demonstrated the advantages of the bacterium compared to the yeasts traditionally used for the alcoholic fermentation. As a result, there was a considerable burst in the Zymomonas literature which started from nearly zero in the late 70s to attain 70 papers published in the field in 1984. In this article, papers published from 1982 to 1986 are reviewed.

  8. Microflora of urogenital tract in pregnancy with asymptomatic bacterium

    International Nuclear Information System (INIS)

    Abdullaeva, R.A.

    2006-01-01

    The article contains results of research interrelationship from colonization of vagina and urinary tract diseases. E.coli one of the main factors in development asymptomatic bacterium. Presented high effects of penicillin medicaments and nitrofurans in treatment of asymptomatic bacterium

  9. Engineering a wild fast-growing Mycoplasma bacterium to generate ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2018-01-12

    Jan 12, 2018 ... The CCPP bacterium causes sick animals to experience severe symptoms ... because antibiotic treatment does not eliminate the responsible bacterium. ... To develop a fast growing CCPP vaccine for cheaper production and ...

  10. Agrobacterium tumefaciens is a diazotrophic bacterium

    International Nuclear Information System (INIS)

    Kanvinde, L.; Sastry, G.R.K.

    1990-01-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate 15 N supplied as 15 N 2 . As with most other well-characterized diazotrophic bacteria, the presence of NH 4 + in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship

  11. Agrobacterium tumefaciens is a diazotrophic bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Kanvinde, L.; Sastry, G.R.K. (Univ. of Leeds (England))

    1990-07-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship.

  12. The chemical formula of a magnetotactic bacterium.

    Science.gov (United States)

    Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

    2012-05-01

    Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life. Copyright © 2011 Wiley Periodicals, Inc.

  13. Ethanologenic potential of the bacterium Bacillus cereus NB-19 in ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-12-01

    Dec 1, 2009 ... Ethanologenic bacterium was cultivated in a suspension of sugarcane ... bagasse is very useful for obtaining yields of the different products including cell mass and ethanol as ... the resources for the green fuel generation.

  14. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    Energy Technology Data Exchange (ETDEWEB)

    Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  15. Extreme Ionizing-Radiation-Resistant Bacterium

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2013-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  16. Formation of Hydroxylamine on Dust Grains via Ammonia Oxidation

    Science.gov (United States)

    He, Jiao; Vidali, Gianfranco; Lemaire, Jean-Louis; Garrod, Robin T.

    2015-01-01

    The quest to detect prebiotic molecules in space, notably amino acids, requires an understanding of the chemistry involving nitrogen atoms. Hydroxylamine (NH2OH) is considered a precursor to the amino acid glycine. Although not yet detected, NH2OH is considered a likely target of detection with ALMA. We report on an experimental investigation of the formation of hydroxylamine on an amorphous silicate surface via the oxidation of ammonia. The experimental data are then fed into a simulation of the formation of NH2OH in dense cloud conditions. On ices at 14 K and with a modest activation energy barrier, NH2OH is found to be formed with an abundance that never falls below a factor 10 with respect to NH3. Suggestions of conditions for future observations are provided.

  17. FORMATION OF HYDROXYLAMINE ON DUST GRAINS VIA AMMONIA OXIDATION

    Energy Technology Data Exchange (ETDEWEB)

    He, Jiao; Vidali, Gianfranco [Physics Department, Syracuse University, Syracuse, NY 13244 (United States); Lemaire, Jean-Louis [Paris Observatory, F-75014 Paris (France); Garrod, Robin T., E-mail: gvidali@syr.edu [Center for Radiophysics and Space Research, Cornell University, Ithaca, NY 14853 (United States)

    2015-01-20

    The quest to detect prebiotic molecules in space, notably amino acids, requires an understanding of the chemistry involving nitrogen atoms. Hydroxylamine (NH{sub 2}OH) is considered a precursor to the amino acid glycine. Although not yet detected, NH{sub 2}OH is considered a likely target of detection with ALMA. We report on an experimental investigation of the formation of hydroxylamine on an amorphous silicate surface via the oxidation of ammonia. The experimental data are then fed into a simulation of the formation of NH{sub 2}OH in dense cloud conditions. On ices at 14 K and with a modest activation energy barrier, NH{sub 2}OH is found to be formed with an abundance that never falls below a factor 10 with respect to NH{sub 3}. Suggestions of conditions for future observations are provided.

  18. Anaerobic ammonia oxidation in a fertilized paddy soil

    DEFF Research Database (Denmark)

    Zhu, Guibing; Wang, Shanyun; Wang, Yu

    2011-01-01

    Evidence for anaerobic ammonium oxidation in a paddy field was obtained in Southern China using an isotope-pairing technique, quantitative PCR assays and 16S rRNA gene clone libraries, along with nutrient profiles of soil cores. A paddy field with a high load of slurry manure as fertilizer...... was selected for this study and was shown to contain a high amount of ammonium (6.2–178.8 mg kg−1). The anaerobic oxidation of ammonium (anammox) rates in this paddy soil ranged between 0.5 and 2.9 nmolN per gram of soil per hour in different depths of the soil core, and the specific cellular anammox activity...

  19. Hotspots of anaerobic ammonia oxidation in land - freshwater interfaces

    DEFF Research Database (Denmark)

    Zhu, Guibing; Wang, Shanyun; Wang, Weidong

    2013-01-01

    sampled fromlake riparian zones in North China. Laboratory incubations in the presence of ammonium or nitrate—at concentrations equivalent to no more than 10% of those detected in situ—yielded some of the highest potential anammox activities reported for natural environments to date. Potential rates......For decades, the conversion of organic nitrogen to dinitrogen gas by heterotrophic bacteria, termed heterotrophic denitrification, was assumed to be the main pathway of nitrogen loss in natural ecosystems. Recently, however, autotrophic bacteria have been shown to oxidize ammonium in the absence...

  20. Ammonia oxidation at high pressure and intermediate temperatures

    DEFF Research Database (Denmark)

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

    2016-01-01

    were interpreted in terms of a detailed chemical kinetic model. The rate constant for the reaction of the important intermediate H2NO with O2 was determined from ab initio calculations to be 2.3 × 102 T2.994 exp (−9510 K/T) cm3 mol−1 s−1. The agreement between experimental results and model work...

  1. Catalytic Ammonia Oxidation on Noble Metal Surfaces: A Theoretical Study

    OpenAIRE

    Novell Leruth, Gerard

    2008-01-01

    Esta tesis se basa en el estudio de la oxidación de amoniaco sobre el grupo del platino. El objetivo de esta tesis es descartar o aceptar los diversos mecanismos propuestos. Incluso proponer el más correcto según los datos obtenidos. Para llevar a cabo esta acometida es necesario conocer cada geometría de las diferentes especies que pueden existir sobre la superficie del catalizador, así como los estados de transición entre las reacciones que lleven de una especie (o combinación de especies)...

  2. The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater.

    Science.gov (United States)

    Cui, You-Wei; Zhang, Hong-Yu; Ding, Jie-Ran; Peng, Yong-Zhen

    2016-04-25

    With annual increases in the generation and use of saline wastewater, the need to avoid environmental problems such as eutrophication is critical. A previous study identified ways to start up a halophilic sludge domesticated from estuarine sediments to remove nitrogen from wastewater with a salinity of 30 g/L. This investigation expands that work to explore the impact of salinity on nitrogen removal. This study demonstrated that the mixed halophilic consortia removed nitrogen from wastewater with a salinity of 30-85 g/L. A kinetic analysis showed that halophilic nitrifiers selected based on hypersalinity were characterized by low Ks, μmax and specific ammonium oxidization rates. This explains the decrease in ammonium removal efficiency in the high salinity operational phases. Salinity inhibited ammonia oxidizing bacteria (AOB) activity, as well as the number of dominant AOB, but did not significantly affect the AOB dominant species. Three most dominant AOB lineages in the halophilic sludge were Nitrosomonas marina, Nitrosomonas europaea, and Nitrosococcus mobilis. Nitrosomonas europaea and Nitrosococcus mobilis were mainly affected by salinity, while nitrite accumulation and ammonia loading played the key role in determining the abundance of Nitrosococcus mobilis and Nitrosococcus europaea. The study contributes insights about shifts in halophilic nitrifying bacterial populations.

  3. Antagonistic bioactivity of an endophytic bacterium isolated from ...

    African Journals Online (AJOL)

    Antagonistic bioactivity of an endophytic bacterium isolated from Epimedium brevicornu Maxim. R He, G Wang, X Liu, C Zhang, F Lin. Abstract. Endophytic bacteria are one of the most potential biological control agents in plant disease protection. The aim of this work was to evaluate the antimicrobial activities of a strain of ...

  4. The physiology of the filamentous bacterium Microthrix parvicella

    NARCIS (Netherlands)

    Slijkhuis, H.

    1983-01-01

    A study has been made of the physiology of Microthrix parvicella. This filamentous bacterium often causes poor settleability of activated sludge in oxidation ditches supplied with domestic sewage. The organism was found to utilize only long chain fatty acids (preferably in

  5. The Bacterium That Got Infected by a Cow! - Horizontal Gene

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 1. The Bacterium That Got Infected by a Cow! - Horizontal Gene Transfer and Evolution. Saurabh Dhawan Tomás John Ryan. General Article Volume 12 Issue 1 January 2007 pp 49-59 ...

  6. Monitoring of a novel bacterium, Lactobacillus thermotolerans , in ...

    African Journals Online (AJOL)

    Abstract. We successfully established fluorescence in situ hybridization (FISH) method for specific detection and enumeration of a novel bacterium, Lactobacillus thermotolerans, in chicken feces. The specific FISH probes were designed based on the L. thermotolerans 16S rRNA gene sequences, and these sequences were ...

  7. methoxyethanol by a new bacterium isolate Pseudomonas sp. Strain

    African Journals Online (AJOL)

    Michael Horsfall

    A 2-methoxyethanol degrading bacterium was isolated from anaerobic sludge of a municipal sewage from ... Stoichiometrically, the strain utilized one mole of oxygen per one mole of 2-methoxyethanol instead of ... physiological and biochemical characterization of the .... observed with acetate and the intact resting cells.

  8. Non-obligate predatory bacterium burkholderia casidaeand uses thereof

    OpenAIRE

    1998-01-01

    A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

  9. Non-obligate predatory bacterium Burkholderia casidae and uses thereof

    OpenAIRE

    2001-01-01

    A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

  10. Biosorption of heavy metals by a marine bacterium

    International Nuclear Information System (INIS)

    Iyer, Anita; Mody, Kalpana; Jha, Bhavanath

    2005-01-01

    Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here

  11. Biosorption of heavy metals by a marine bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Iyer, Anita [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India); Mody, Kalpana [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India)]. E-mail: khmody@csmcri.org; Jha, Bhavanath [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India)

    2005-03-01

    Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here.

  12. Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

    OpenAIRE

    Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

    1983-01-01

    A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and c...

  13. Antibacterial marine bacterium deter luminous vibriosis in shrimp larvae

    OpenAIRE

    Abraham, T.J.

    2004-01-01

    Inhibitory activity of a marine pigmented bacterium - Alteromonas sp. - isolated from Penaeus monodon Fabricius larva against pathogenic and environmental isolates of Vibrio harveyi was studied. All the isolates were inhibited to varying degrees by Alteromonas sp. in vitro. The antibacterial substance produced by the Alteromonas sp. was soluble in organic solvent and closely bound to the external surface of bacterial cells. The antibacterial Alteromonas sp., when allowed to colonize on shrimp...

  14. Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

    Directory of Open Access Journals (Sweden)

    Lukasz Makowski

    2016-11-01

    Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

  15. MODELING OF MIXED CHEMOSTAT CULTURES OF AN AEROBIC BACTERIUM, COMAMONAS-TESTOSTERONI, AND AN ANAEROBIC BACTERIUM, VEILLONELLA-ALCALESCENS - COMPARISON WITH EXPERIMENTAL-DATA

    NARCIS (Netherlands)

    GERRITSE, J; SCHUT, F; GOTTSCHAL, JC

    A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation Of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the

  16. Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

    NARCIS (Netherlands)

    Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

    1998-01-01

    The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

  17. Chitin utilization by the insect-transmitted bacterium Xylella fastidiosa.

    Science.gov (United States)

    Killiny, Nabil; Prado, Simone S; Almeida, Rodrigo P P

    2010-09-01

    Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa.

  18. Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

    Science.gov (United States)

    Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

    2016-04-21

    Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain.

  19. Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

    Energy Technology Data Exchange (ETDEWEB)

    Daniel P. Molloy

    2004-02-24

    The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

  20. Biological Control of Meloidogyne hapla Using an Antagonistic Bacterium

    Directory of Open Access Journals (Sweden)

    Jiyeong Park

    2014-09-01

    Full Text Available We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN Meloidogyne hapla in carrot (Daucus carota subsp. sativus and tomato (Solanum lycopersicum. Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla.

  1. Hydrogen production by co-cultures of Lactobacillus and a photosynthetic bacterium, Rhodobacter sphaeroides RV

    Energy Technology Data Exchange (ETDEWEB)

    Asada, Yasuo; Ishimi, Katsuhiro [Department of General Education, College of Science and Technology, Nihon University, Narashinodai, Chiba 274-8501 (Japan); Tokumoto, Masaru; Aihara, Yasuyuki; Oku, Masayo; Kohno, Hideki [Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Izumi-cho, Chiba 275-8575 (Japan); Wakayama, Tatsuki; Miyake, Jun [Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology, Nakoji, Amagasaki, Hyogo 661-0974 (Japan); Tomiyama, Masamitsu [Genetic Diversity Department, National Institute of Agrobiological Science, Tsukuba, Ibaraki 305-8602 (Japan)

    2006-09-15

    Hydrogen production with glucose by using co-immobilized cultures of a lactic acid bacterium, Lactobacillus delbrueckii NBRC13953, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. Glucose was converted to hydrogen gas in a yield of 7.1mol of hydrogen per mole of glucose at a maximum under illuminated conditions. (author)

  2. Isolation and characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium

    DEFF Research Database (Denmark)

    Mladenovska, Zuzana; Mathrani, Indra M.; Ahring, Birgitte Kiær

    1995-01-01

    An anaerobic, extremely thermophilic, cellulolytic, non-spore-forming bacterium, strain 6A, was isolated from an alkaline hot spring in Hverageroi, Iceland. The bacterium was non-motile, rod-shaped (1.5-3.5 x 0.7 mu m) and occurred singly, in pairs or in chains and stained gram-negative. The growth...

  3. Dense populations of a giant sulfur bacterium in Namibian shelf sediments

    DEFF Research Database (Denmark)

    Schulz, HN; Brinkhoff, T.; Ferdelman, TG

    1999-01-01

    A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA...

  4. Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii.

    Directory of Open Access Journals (Sweden)

    Konstantinos Mavromatis

    Full Text Available Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

  5. Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

    Energy Technology Data Exchange (ETDEWEB)

    Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui; Kunin, Victor; Lapidus, Alla; Hugenholtz, Philip; Patel, Bharat; Kyrpides, Nikos C.

    2008-11-03

    Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

  6. Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

    Science.gov (United States)

    Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

    1983-01-01

    A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and contained cytochrome c3 and desulfoviridin. Except for furfural degradation, the characteristics of the furfural isolate were remarkably similar to those of the sulfate reducer Desulfovibrio gigas. The furfural isolate has been tentatively identified as Desulfovibrio sp. strain F-1. Images PMID:16346423

  7. A bacterium that degrades and assimilates poly(ethylene terephthalate).

    Science.gov (United States)

    Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

    2016-03-11

    Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. Copyright © 2016, American Association for the Advancement of Science.

  8. The O-antigen structure of bacterium Comamonas aquatica CJG.

    Science.gov (United States)

    Wang, Xiqian; Kondakova, Anna N; Zhu, Yutong; Knirel, Yuriy A; Han, Aidong

    2017-11-01

    Genus Comamonas is a group of bacteria that are able to degrade a variety of environmental waste. Comamonas aquatica CJG (C. aquatica) in this genus is able to absorb low-density lipoprotein but not high-density lipoprotein of human serum. Using 1 H and 13 C NMR spectroscopy, we found that the O-polysaccharide (O-antigen) of this bacterium is comprised of a disaccharide repeat (O-unit) of d-glucose and 2-O-acetyl-l-rhamnose, which is shared by Serratia marcescens O6. The O-antigen gene cluster of C. aquatica, which is located between coaX and tnp4 genes, contains rhamnose synthesis genes, glycosyl and acetyl transferase genes, and ATP-binding cassette transporter genes, and therefore is consistent with the O-antigen structure determined here.

  9. Complete genome sequence of the photoautotrophic and bacteriochlorophyll e-synthesizing green sulfur bacterium Chlorobaculum limnaeum DSM 1677T

    DEFF Research Database (Denmark)

    Tank, Marcus; Liu, Zhenfeng; Frigaard, Niels-Ulrik

    2017-01-01

    Chlorobaculum limnaeum DSM 1677T is a mesophilic, brown-colored, chlorophototrophic green sulfur bacterium that produces bacteriochlorophyll e and the carotenoid isorenieratene as major pigments. This bacterium serves as a model organism in molecular research on photosynthesis, sulfur metabolism...

  10. Characterization of the radioresistance in the radioresistant bacterium deinococcus radiodurans

    International Nuclear Information System (INIS)

    Kong Xiangrong; Du Zeji

    1999-01-01

    The radioresistance of wild type Deinococcus radiodurans KD8301 and the factors affecting the radioresistance were investigated. KH3111 which was a DNA repair mutant of KD8301 (Zeji Du, 1998) was used to be compared with KD8301. Deinococcus radiodurans was discovered by Anderson et al (1956) in X-ray sterilized canned meat that was found to have undergone spoilage. this bacterium and other species of this genus share extreme resistance to ionizing radiation and other agents that damage DNA. Wild type KD8301 and its sensitive mutant KH3111 were irradiated with 60 Co γ-ray at the dose range 0.5 ∼ 10 kGy. Dose-survival fraction curves were made and the radio resistances were determined by LD 99 . The relative contents of DNA in cells were measured by Fluorescence Spectrophotometry (Freedman and Bruce, 1971). The results indicated that wild type KD8301 possesses more radioresistant than its mutant KH3111, LD99 were 9.5 kGy and 2.4 kGy respectively. KD8301 grown at exponential phase showed a decreased resistance to radiation, and the LD99 was 5.1 kGy. No differences of DNA/protein in cells were found between the exponential phase and the stationary phase. The results could be concluded that wild type KD8301 possesses remarkable radioresistance, but this ability was decreased or disappeared after mutation (in KH3111). None DNA relative content other than the growth stages were determinant factors of radioresistance in Deinococcus radiodurans. This results were different from other report (Dickie N et al, 1990). The cellular mechanisms might be the deference's of the bacterium cell morphology between the exponential phase and the stationary phase. Recently, the mutation site of KH3111 which was mutated chemically from wild type KD8301 was identified (Zeji Du, 1998). One base pair changed in the novel gene pprA which was isolated from KD8301 genomic DNA. This point mutation was confirmed to be responsible for the sensitivity of KH3111 to γ-ray and other DNA

  11. Electromicrobiology of Dissimilatory Sulfur Reducing Bacterium Desulfuromonas acetexigens

    KAUST Repository

    Bin Bandar, Khaled

    2014-12-01

    Bioelectrochmical systems (BES) are engineered electrochemical devices that harness hidden chemical energy of the wastewater in to the form of electricity or hydrogen. Unique microbial communities enrich in these systems for oxidation of organic matter as well as transfer of resulted electron to anode, known them as “electricigens” communities. Exploring novel electricigenesis microbial communities in the nature and understanding their electromicrobiology is one the important aspect for BES systems scale up. Herein, we report first time the electricigenesis property of an anaerobic, fresh water sediment, sulfur reducing bacterium Desulfuromona acetexigens. The electrochemical behavior of D. acetexigens biofilms grown on graphite-rod electrodes in batch-fed mode under an applied potential was investigated with traditional electroanalytical tools, and correlate the electron transfer from biofilms to electrode with a model electricigen Geobacter sulfurreducens electrochemical behavior. Research findings suggest that D. acetexigens has the ability to use electrode as electron acceptor in BES systems through establishing the direct contact with anode by expressing the membrane bound redox proteins, but not due to the secretion of soluble redox mediators. Preliminary results revealed that D. acetexigens express three distinct redox proteins in their membranes for turnover of the electrons from biofilm to electrode, and the 4 whole electricigenesis process observed to be unique in the D. acetexigens compared to that of well-studied model organism G. sulfurreducens.

  12. Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

    Science.gov (United States)

    Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

    1978-01-01

    Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

  13. Characterization of a Neochlamydia-like Bacterium Associated with Epitheliocystis in Cultured Artic Char Salvelinus alpinus

    Science.gov (United States)

    Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic char (Salvelinus alpinus). To characterize a bacterium associated with epitheliocystis in cultured char, gills were sampled for histopathologic examination, conventional...

  14. Echinicola shivajiensis sp. nov., a novel bacterium of the family "Cyclobacteriaceae" isolated from brackish water pond

    Digital Repository Service at National Institute of Oceanography (India)

    Srinivas, T.N.R.; Tryambak, B.K.; AnilKumar, P.

    Strain AK12 sup(T), an orange pigmented Gramnegative, rod shaped, non-motile bacterium, was isolated fromamud sample collected froma brackishwater pond at Rampur of West Bengal, India. The strain was positive for oxidase, catalase and phosphatase...

  15. Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium

    Czech Academy of Sciences Publication Activity Database

    Moon, C. D.; Pacheco, D. M.; Kelly, W. J.; Leahy, S. C.; Li, D.; Kopečný, Jan; Attwood, G. T.

    2008-01-01

    Roč. 58, - (2008), s. 2041-2045 ISSN 1466-5026 Institutional research plan: CEZ:AV0Z50450515 Keywords : Butyrivibrio * ruminal bacterium Subject RIV: EE - Microbiology, Virology Impact factor: 2.222, year: 2008

  16. Septicemia caused by the gram-negative bacterium CDC IV c-2 in an immunocompromised human.

    OpenAIRE

    Dan, M; Berger, S A; Aderka, D; Levo, Y

    1986-01-01

    A 37-year-old man with plasma cell leukemia developed nonfatal septicemia caused by the gram-negative bacterium CDC IV c-2. Recovery followed appropriate treatment with antibiotics. The biochemical features of this organism are reviewed.

  17. Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences

    NARCIS (Netherlands)

    Vanfossen, A.L.; Verhaart, M.R.A.; Kengen, S.W.M.; Kelly, R.M.

    2009-01-01

    Co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on

  18. Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium.

    Science.gov (United States)

    Cui, Changzheng; Li, Zhijie; Qian, Jiangchao; Shi, Jie; Huang, Ling; Tang, Hongzhi; Chen, Xin; Lin, Kuangfei; Xu, Ping; Liu, Yongdi

    2016-05-10

    Martelella sp. strain AD-3, a moderate halophilic bacterium, was isolated from a petroleum-contaminated soil with high salinity in China. Here, we report the complete genome of strain AD-3, which contains one circular chromosome and two circular plasmids. An array of genes related to metabolism of polycyclic aromatic hydrocarbons and halophilic mechanism in this bacterium was identified by the whole genome analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte.

    Directory of Open Access Journals (Sweden)

    Michele T Hoffman

    Full Text Available Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA, often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales, but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales. Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.

  20. Luciferase inactivation in the luminous marine bacterium Vibrio harveyi.

    Science.gov (United States)

    Reeve, C A; Baldwin, T O

    1981-06-01

    Luciferase was rapidly inactivated in stationary-phase cultures of the wild type of the luminous marine bacterium Vibrio harveyi, but was stable in stationary-phase cultures of mutants of V. harveyi that are nonluminous without exogenous aldehyde, termed the aldehyde-deficient mutants. The inactivation in the wild type was halted by cell lysis and was slowed or stopped by O2 deprivation or by addition of KCN and NaF or of chloramphenicol. If KCN and NaF or chloramphenicol were added to a culture before the onset of luciferase inactivation, then luciferase inactivation did not occur. However, if these inhibitors were added after the onset of luciferase inactivation, then luciferase inactivation continued for about 2 to 3 h before the inactivation process stopped. The onset of luciferase inactivation in early stationary-phase cultures of wild-type cell coincided with a slight drop in the intracellular adenosine 5'-triphosphate (ATP) level from a relatively constant log-phase value of 20 pmol of ATP per microgram of soluble cell protein. Addition of KCN and NaF to a culture shortly after this drop in ATP caused a rapid decrease in the ATP level to about 4 pmol of ATP per microgram whereas chloramphenicol added at this same time caused a transient increase in ATP level to about 25 pmol/microgram. The aldehyde-deficient mutant (M17) showed a relatively constant log-phase ATP level identical with that of the wild-type cells, but rather than decreasing in early stationary phase, the ATP level increased to a value twice that in log-phase cells. We suggest that the inactivation of luciferase is dependent on the synthesis of some factor which is produced during stationary phase and is itself unstable, and whose synthesis is blocked by chloramphenicol or cyanide plus fluoride.

  1. A Genetic System for the Thermophilic Acetogenic Bacterium Thermoanaerobacter kivui.

    Science.gov (United States)

    Basen, Mirko; Geiger, Irina; Henke, Laura; Müller, Volker

    2018-02-01

    Thermoanaerobacter kivui is one of the very few thermophilic acetogenic microorganisms. It grows optimally at 66°C on sugars but also lithotrophically with H 2 + CO 2 or with CO, producing acetate as the major product. While a genome-derived model of acetogenesis has been developed, only a few physiological or biochemical experiments regarding the function of important enzymes in carbon and energy metabolism have been carried out. To address this issue, we developed a method for targeted markerless gene deletions and for integration of genes into the genome of T. kivui The strain naturally took up plasmid DNA in the exponential growth phase, with a transformation frequency of up to 3.9 × 10 -6 A nonreplicating plasmid and selection with 5-fluoroorotate was used to delete the gene encoding the orotate phosphoribosyltransferase ( pyrE ), resulting in a Δ pyrE uracil-auxotrophic strain, TKV002. Reintroduction of pyrE on a plasmid or insertion of pyrE into different loci within the genome restored growth without uracil. We subsequently studied fructose metabolism in T. kivui The gene fruK (TKV_c23150) encoding 1-phosphofructosekinase (1-PFK) was deleted, using pyrE as a selective marker via two single homologous recombination events. The resulting Δ fruK strain, TKV003, did not grow on fructose; however, growth on glucose (or on mannose) was unaffected. The combination of pyrE as a selective marker and the natural competence of the strain for DNA uptake will be the basis for future studies on CO 2 reduction and energy conservation and their regulation in this thermophilic acetogenic bacterium. IMPORTANCE Acetogenic bacteria are currently the focus of research toward biotechnological applications due to their potential for de novo synthesis of carbon compounds such as acetate, butyrate, or ethanol from H 2 + CO 2 or from synthesis gas. Based on available genome sequences and on biochemical experiments, acetogens differ in their energy metabolism. Thus, there is an

  2. Nitrogen transformation under different dissolved oxygen levels by the anoxygenic phototrophic bacterium Marichromatium gracile.

    Science.gov (United States)

    Hong, Xuan; Chen, Zhongwei; Zhao, Chungui; Yang, Suping

    2017-06-01

    Marichromatium gracile: YL28 (M. gracile YL28) is an anoxygenic phototrophic bacterial strain that utilizes ammonia, nitrate, or nitrite as its sole nitrogen source during growth. In this study, we investigated the removal and transformation of ammonium, nitrate, and nitrite by M. gracile YL28 grown in a combinatorial culture system of sodium acetate-ammonium, sodium acetate-nitrate and sodium acetate-nitrite in response to different initial dissolved oxygen (DO) levels. In the sodium acetate-ammonium system under aerobic conditions (initial DO = 7.20-7.25 mg/L), we detected a continuous accumulation of nitrate and nitrite. However, under semi-anaerobic conditions (initial DO = 4.08-4.26 mg/L), we observed a temporary accumulation of nitrate and nitrite. Interestingly, under anaerobic conditions (initial DO = 0.36-0.67 mg/L), there was little accumulation of nitrate and nitrite, but an increase in nitrous oxide production. In the sodium acetate-nitrite system, nitrite levels declined slightly under aerobic conditions, and nitrite was completely removed under semi-anaerobic and anaerobic conditions. In addition, M. gracile YL28 was able to grow using nitrite as the sole nitrogen source in situations when nitrogen gas produced by denitrification was eliminated. Taken together, the data indicate that M. gracile YL28 performs simultaneous heterotrophic nitrification and denitrification at low-DO levels and uses nitrite as the sole nitrogen source for growth. Our study is the first to demonstrate that anoxygenic phototrophic bacteria perform heterotrophic ammonia-oxidization and denitrification under anaerobic conditions.

  3. Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study)

    OpenAIRE

    OCKY KARNA RADJASA; TORBEN MARTENS; HANS-PETER GROSSART; AGUS SABDONO; MEINHARD SIMON; TONNY BACHTIAR

    2005-01-01

    A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved s...

  4. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  5. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  6. Moritella viscosa, a pathogenic bacterium affecting the fillet quality in fish

    DEFF Research Database (Denmark)

    Ingerslev, Hans-Christian; Nielsen, Michael Engelbrecht

    2011-01-01

    Moritella viscosa is a bacterium belonging to the family Moritellaceae and was formerly known as Vibrio viscosus. The name ‘viscosa’ originates from the slimy nature of the bacterium. M. viscosa is considered to be the main causative agent of the phenomenon ‘winter ulcer’ or ‘cold-water ulcer......’ which affects various fish species in seawater during cold periods (Lunder et al. 1995). The bacterium is mainly a problem for farmed salmonid species, such as Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but has also been isolated from other fish species, including Atlantic...... market price because of a quality downgrade caused by textural changes in the fillet....

  7. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Science.gov (United States)

    Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

  8. Studies on the pathogenic bacterium of ulcer disease in Epinephelus awoara

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Studies were conducted to determine the cause of the acute mortality of cage-cultured Epinephelus awoara in the Tong'an Bay of Xiamen, China during the summer of 2002. Predominant bacteria strain TS-628 was isolated from the diseased grouper. The virulence test confirmed that TS-628 was the pathogenic bacterium. Biochemical characteristics of the isolates were determined using the automatic bacterial identification system and standard tube tests. To further confirm the identification, a 1 121 bp 16S rRNA gene sequence of the isolate was amplified by PCR, which had been deposited into Genbank (accession number: AY747308). According to the biochemical characteristics and by comparing the 16S rRNA gene homology of the isolate, the pathogenic bacterium was identified as Vibrio harveyi. Drug sensitivity tests showed that this pathogenic bacterium was sensitive to 16 antibacterials, especially to chloramphenicol and actinospectacin, but completely resistant to antibacterials likes vancomycin, penicillin, lincomycin, and so on.

  9. Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest.

    Science.gov (United States)

    Llamas, Inmaculada; del Moral, Ana; Martínez-Checa, Fernando; Arco, Yolanda; Arias, Soledad; Quesada, Emilia

    2006-01-01

    Halomonas maura is a bacterium of great metabolic versatility. We summarise in this work some of the properties that make it a very interesting microorganism both from an ecological and biotechnological point of view. It plays an active role in the nitrogen cycle, is capable of anaerobic respiration in the presence of nitrate and has recently been identified as a diazotrophic bacterium. Of equal interest is mauran, the exopolysaccharide produced by H. maura, which contributes to the formation of biofilms and thus affords the bacterium advantages in the colonisation of its saline niches. Mauran is highly viscous, shows thixotropic and pseudoplastic behaviour, has the capacity to capture heavy metals and exerts a certain immunomodulator effect in medicine. All these attributes have prompted us to make further investigations into its molecular characteristics. To date we have described 15 open reading frames (ORF's) related to exopolysaccharide production, nitrogen fixation and nitrate reductase activity among others.

  10. Description of a bacterium associated with redmouth disease of rainbow trout (Salmo gairdneri)

    Science.gov (United States)

    Ross, A.J.; Rucker, R.R.; Ewing, W.H.

    1966-01-01

    A description was given of a gram-negative, peritrichously flagellated, fermentative bacterium that was isolated on numerous occasions from kidney tissues of rainbow trout (Salmo gairdneri) afflicted with redmouth disease. Although the bacteria apparently were members of the family Enterobacteriaceae, it was impossible to determine their taxonomic position within the family with certainty. Hence it was recommended that their taxonomic position remain sub judice for the present. As a temporary designation RM bacterium was used. Redmouth disease was transmitted from infected to normal fish through the medium of water.

  11. From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus Subtilis

    Science.gov (United States)

    Crawshaw, Samuel G.; Wipat, Anil

    2001-01-01

    Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression of Bacillus genes in situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere. PMID:18628943

  12. Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.

    Science.gov (United States)

    El Kafsi, Hela; Binesse, Johan; Loux, Valentin; Buratti, Julien; Boudebbouze, Samira; Dervyn, Rozenn; Hammani, Amal; Maguin, Emmanuelle; van de Guchte, Maarten

    2014-07-17

    Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory properties both in vitro and in vivo. Here, we report the genome sequence of this bacterium, which appears to contain no less than 215 insertion sequence (IS) elements, an exceptionally high number regarding the small genome size of the strain. Copyright © 2014 El Kafsi et al.

  13. Intestinimonas butyriciproducens gen. nov., sp. nov., a novel butyrate-producing bacterium from the mouse intestine

    NARCIS (Netherlands)

    Kläring, K.; Hanske, L.; Bui, T.P.N.; Charrier, C.; Blaut, M.; Haller, D.; Plugge, C.M.; Clavel, T.

    2013-01-01

    Whilst creating a bacterial collection of strains from the mouse intestine, we isolated a Gram-negative, spore-forming, non-motile and strictly anaerobic rod-shaped bacterium from the caecal content of a TNFdeltaARE mouse. The isolate, referred to as strain SRB-521-5-IT, was originally cultured on a

  14. Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

    KAUST Repository

    Katuri, Krishna

    2017-03-03

    Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

  15. Design of semi industrial radium separator by a new bacterium MGF-48

    International Nuclear Information System (INIS)

    Ghafourian, H.; Emami, M.R.; Farazmand, A.

    1998-01-01

    Following of a research work which has been recently published in AEOI scientific Bulletin no. 14, a semi industrial bioreactor has been designed for separation of radium using a new bacterium MGF-48. This bioreactor could be utilized for a high rate separation of radium in semi industrial scale. (author)

  16. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    Science.gov (United States)

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

    DEFF Research Database (Denmark)

    Tanaka, Reiji; Kawaichi, Satoshi; Nishimura, Hiroshi

    2006-01-01

    A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52-78°C (optimum, 70°C), pH 5-8 (optimum, pH 7...

  18. Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater

    Digital Repository Service at National Institute of Oceanography (India)

    Nupur; Bhumika, V.; Srinivas, T.N.R.; AnilKumar, P.

    A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1 sup(T), was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate...

  19. Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water

    Digital Repository Service at National Institute of Oceanography (India)

    Bhumika, V.; Ravinder, K.; Korpole, S.; Srinivas, T.N.R.; AnilKumar, P.

    A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21T , was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, L-proline arylamidase...

  20. Aliidiomarina haloalkalitolerans sp. nov., a marine bacterium isolated from coastal surface seawater

    Digital Repository Service at National Institute of Oceanography (India)

    Srinivas, T.N.R.; Nupur; AnilKumar, P.

    A novel Gram-negative, rod shaped, motile, non-sporing strictly aerobic bacterium, designated strain AK5 sup(T), was isolated from a sea water sample collected near Visakhapatnam coast, Bay of Bengal, India. Colonies on marine agar were circular, 3...

  1. Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

    Science.gov (United States)

    Jin, Decai; Zhou, Lisha; Wu, Liang; An, Wei; Zhao, Lin

    2014-01-01

    Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated marine sediments. Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment. PMID:24482505

  2. Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

    KAUST Repository

    Katuri, Krishna; Albertsen, Mads; Saikaly, Pascal

    2017-01-01

    Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

  3. Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila

    OpenAIRE

    Hammer, Austin J.; Walters, Amber; Carroll, Courtney; Newell, Peter D.; Chaston, John M.

    2017-01-01

    ABSTRACT The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429?bp, with 3,454 predicted genes.

  4. Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.

    Science.gov (United States)

    Hammer, Austin J; Walters, Amber; Carroll, Courtney; Newell, Peter D; Chaston, John M

    2017-07-06

    The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429 bp, with 3,454 predicted genes. Copyright © 2017 Hammer et al.

  5. Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4

    OpenAIRE

    Masuda, Shinji; Hori, Koichi; Maruyama, Fumito; Ren, Shukun; Sugimoto, Saori; Yamamoto, Nozomi; Mori, Hiroshi; Yamada, Takuji; Sato, Shusei; Tabata, Satoshi; Ohta, Hiroyuki; Kurokawa, Ken

    2013-01-01

    We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum. The photosynthesis gene cluster comprises two segments?a unique feature among photosynthesis gene clusters of purple bacteria. The genome information will be useful for further analysis of bacterial photosynthesis.

  6. Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

    Science.gov (United States)

    Liu, Jin-liang; Hu, Xiao-min

    2013-01-01

    Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

  7. Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium

    Science.gov (United States)

    Joshi, M. N.; Sharma, A. C.; Pandya, R. V.; Patel, R. P.; Saiyed, Z. M.; Saxena, A. K.

    2012-01-01

    Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

  8. The 2015 Nobel Prize in Physiology or Medicine: A Soil Bacterium ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 4. The 2015 Nobel Prize in Physiology or Medicine: A Soil Bacterium and a Chinese Herb Steal the Show. Pundi N Rangarajan. General Article Volume 21 Issue 4 April 2016 pp 315-326 ...

  9. Exo- and surface proteomes of the probiotic bacterium Lactobacillus acidophilus NCFM

    DEFF Research Database (Denmark)

    Celebioglu, Hasan Ufuk; Svensson, Birte

    2017-01-01

    Lactobacillus acidophilus NCFM is a well-known probiotic bacterium extensively studied for its beneficial health effects. Exoproteome (proteins exported into culture medium) and surface proteome (proteins attached to S-layer) of this probiotic were identified by using 2DE followed by MALDI TOF MS...

  10. Isolation and Structure Elucidation of a Novel Yellow Pigment from the Marine Bacterium Pseudoalteromonas tunicata

    Directory of Open Access Journals (Sweden)

    N. Kumar

    2005-10-01

    Full Text Available The marine environment is a major source for many novel natural compounds. A new yellow pigment has been isolated from the marine bacterium P. tunicata and identified as a new member of the tambjamine class of compounds. The structural identification was achieved by a combination of 1D and 2D-NMR spectroscopy and high resolution mass spectrometry data.

  11. Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater

    Science.gov (United States)

    A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50**T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rDNA sequences revealed that the novel isolate represented...

  12. Oceanospirillum nioense sp. nov., a marine bacterium isolated from sediment sample of Palk bay, India

    Digital Repository Service at National Institute of Oceanography (India)

    Krishna, K.K.; Bhumika, V.; Thomas, M.; AnilKumar, P.; Srinivas, T.N.R.

    A novel Gram-negative, spiral shaped, motile bacterium, designated strain NIO-S6T, was isolated from a sediment sample collected from Offshore Rameswaram, Tamilnadu, India. Strain NIO-S6 sup(T) was found to be positive for oxidase, DNase and lysine...

  13. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

    NARCIS (Netherlands)

    Sirota-Madi, A.; Olender, T.; Helman, Y.; Ingham, C.; Brainis, I.; Roth, D.; Hagi, E.; Brodsky, L.; Leshkowitz, D.; Galatenko, V.; Nikolaev, V.; Mugasimangalam, R.C.; Bransburg-Zabary, S.; Gutnick, D.L.; Lancet, D.; Ben-Jacob, E.

    2010-01-01

    Background: The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae)

  14. Removal of zinc from aqueous solution by metal resistant symbiotic bacterium Mesorhizobium amorphae

    DEFF Research Database (Denmark)

    Hao, Xiuli; Mohamad, Osama Abdalla; Xie, Pin

    2014-01-01

    Biosorption of zinc by living biomasses of metal resistant symbiotic bacterium Mesorhizobium amorphae CCNWGS0123 was investigated under optimal conditions at pH 5.0, initial metal concentrations of 100 mg L-1, and a dose of 1.0 g L-1. M. amorphae exhibited an efficient removal of Zn2+ from aqueous...

  15. Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

    Science.gov (United States)

    Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

    2011-05-01

    The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

  16. Two-dimensional gel-based alkaline proteome of the probiotic bacterium Lactobacillus acidophilus NCFM

    DEFF Research Database (Denmark)

    Majumder, Avishek; Cai, Liyang; Ejby, Morten

    2012-01-01

    Lactobacillus acidophilus NCFM (NCFM) is a well‐documented probiotic bacterium isolated from human gut. Detailed 2D gel‐based NCFM proteomics addressed the so‐called alkaline range, i.e., pH 6–11. Proteins were identified in 150 of the 202 spots picked from the Coomassie Brilliant Blue stained 2D...

  17. New recombinant bacterium comprises a heterologous gene encoding glycerol dehydrogenase and/or an up-regulated native gene encoding glycerol dehydrogenase, useful for producing ethanol

    DEFF Research Database (Denmark)

    2010-01-01

    dehydrogenase encoding region of the bacterium, or is inserted into a phosphotransacetylase encoding region of the bacterium, or is inserted into an acetate kinase encoding region of the bacterium. It is operably linked to an inducible, a regulated or a constitutive promoter. The up-regulated glycerol......TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preparation (claimed): Producing recombinant bacterium having enhanced ethanol production characteristics when cultivated in growth medium comprising glycerol comprises: (a) transforming a parental bacterium by (i) the insertion of a heterologous gene encoding...... glycerol dehydrogenase; and/or (ii) up-regulating a native gene encoding glycerol dehydrogenase; and (b) obtaining the recombinant bacterium. Preferred Bacterium: In the recombinant bacterium above, the inserted heterologous gene and/or the up-regulated native gene is encoding a glycerol dehydrogenase...

  18. Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

    KAUST Repository

    Narita, Yuko; Zhang, Lei; Kimura, Zen-ichiro; Ali, Muhammad; Fujii, Takao; Okabe, Satoshi

    2017-01-01

    Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

  19. Isolation, identification, and biocontrol of antagonistic bacterium against Botrytis cinerea after tomato harvest

    Directory of Open Access Journals (Sweden)

    Jun-Feng Shi

    Full Text Available ABSTRACT Tomato is one of the most important vegetables in the world. Decay after harvest is a major issue in the development of tomato industry. Currently, the most effective method for controlling decay after harvest is storage of tomato at low temperature combined with usage of chemical bactericide; however, long-term usage of chemical bactericide not only causes pathogen resistance but also is harmful for human health and environment. Biocontrol method for the management of disease after tomato harvest has great practical significance. In this study, antagonistic bacterium B-6-1 strain was isolated from the surface of tomato and identified as Enterobacter cowanii based on morphological characteristics and physiological and biochemical features combined with sequence analysis of 16SrDNA and ropB gene and construction of dendrogram. Effects of different concentrations of antagonistic bacterium E. cowanii suspension on antifungal activity after tomato harvest were analyzed by mycelium growth rate method. Results revealed that antifungal activity was also enhanced with increasing concentrations of antagonistic bacterium; inhibitory rates of 1 × 105 colony-forming units (cfu/mL antagonistic bacterial solution on Fusarium verticillioides, Alternaria tenuissima, and Botrytis cinerea were 46.31%, 67.48%, and 75.67%, respectively. By using in vivo inoculation method, it was further confirmed that antagonistic bacterium could effectively inhibit the occurrence of B. cinerae after tomato harvest, biocontrol effect of 1 × 109 cfu/mL zymotic fluid reached up to 95.24%, and antagonistic bacterium E. cowanii has biocontrol potential against B. cinerea after harvest of fruits and vegetables.

  20. Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

    KAUST Repository

    Narita, Yuko

    2017-08-18

    Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

  1. Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

    KAUST Repository

    Wang, Yong

    2016-07-01

    Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

  2. Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

    Science.gov (United States)

    Tago, Damian; Meyer, Damien F

    2016-01-01

    Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria.

  3. The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian

    2011-01-01

    A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...... the bacterium to adhere to human red blood cells (RBCs) and thereby evade attack by circulating phagocytes. On incubation with normal human serum, the P. gingivalis strain efficiently fixed complement component 3 (C3). Incubation of bacteria with washed whole blood cells suspended in autologous serum resulted...... in a dose- and time-dependent adherence to RBCs. The adherence required functionally intact complement receptor 1 (CR1; also called CD35) on the RBCs and significantly inhibited the uptake of P. gingivalis by neutrophils and B cells within 1 min of incubation (by 64% and 51%, respectively...

  4. Framing in the Spanish press about the health crisis because of the E. coli bacterium

    Directory of Open Access Journals (Sweden)

    Paloma López Villafranca

    2013-12-01

    Full Text Available This research article analyses  the approach made by press media and other institutional advertising about the E. coli bacterium, most commonly known as cucumber crisis in Spain. While in the rest of Europe this crisis receives the same treatment as A Flu or mad cow disease in this country it is treated as a crisis that affects to the spanish economy and not to the health of the citizen. Economic interests prevail over public health and this is due to official information given. An analysis of contents of the most popular journals in Spain, according to OJD, is made to prove this hypothesis, El Pais, El Mundo and ABC, as well as a study of the main institutional advertising made about E. coli bacterium by official spanish organizations and the media.

  5. Mitigation of membrane biofouling by a quorum quenching bacterium for membrane bioreactors.

    Science.gov (United States)

    Ham, So-Young; Kim, Han-Shin; Cha, Eunji; Park, Jeong-Hoon; Park, Hee-Deung

    2018-06-01

    In this study, a quorum-quenching (QQ) bacterium named HEMM-1 was isolated at a membrane bioreactor (MBR) plant. HEMM-1 has diplococcal morphology and 99% sequence identity to Enterococcus species. The HEMM-1 cell-free supernatant (CFS) showed higher QQ activities than the CFS of other QQ bacteria, mostly by degrading N-acyl homoserine lactones (AHLs) with short acyl chains. Instrumental analyses revealed that HEMM-1 CFS degraded AHLs via lactonase activity. Under static, flow, and shear conditions, the HEMM-1 CFS was effective in reducing bacterial and activated-sludge biofilms formed on membrane surfaces. In conclusion, the HEMM-1 isolate is a QQ bacterium applicable to the control of biofouling in MBRs via inhibition of biofilm formation on membrane surfaces. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

    International Nuclear Information System (INIS)

    Aguayo, S; Bozec, L; Donos, N; Spratt, D

    2015-01-01

    The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine. (topical review)

  7. Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

    KAUST Repository

    Li, Yongxin; Xu, Ying; Liu, Lingli; Han, Zhuang; Lai, Pok Yui; Guo, Xiangrong; Zhang, Xixiang; Lin, Wenhan; Qian, Pei-Yuan

    2012-01-01

    Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

  8. Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

    KAUST Repository

    Harjes, Janno; Ryu, Tae Woo; Abdelmohsen, Usama Ramadan; Moitinho-Silva, Lucas; Horn, Hannes; Ravasi, Timothy; Hentschel, Ute

    2014-01-01

    The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

  9. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

    KAUST Repository

    Haroon, Mohamed; Thompson, Luke R.; Stingl, Ulrich

    2016-01-01

    A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

  10. Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

    KAUST Repository

    Harjes, Janno

    2014-03-06

    The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

  11. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

    KAUST Repository

    Haroon, Mohamed

    2016-02-11

    A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

  12. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

    OpenAIRE

    Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; Klenk, Hans-Peter; Spring, Stefan; G?ker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.

    2017-01-01

    © 2017 Kublanov, Sigalova, Gavrilov, Lebedinsky, Rinke, Kovaleva, Chernyh, Ivanova, Daum, Reddy, Klenk, Spring, Göker, Reva, Miroshnichenko, Kyrpides, Woyke, Gelfand, Bonch-Osmolovskaya. The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to impl...

  13. Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

    Science.gov (United States)

    Liu, Yang; Wang, Runping; Zeng, Runying

    2014-12-01

    Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

    KAUST Repository

    Li, Yongxin

    2012-02-03

    Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

  15. Alteration of the Canine Small-Intestinal Lactic Acid Bacterium Microbiota by Feeding of Potential Probiotics

    OpenAIRE

    Manninen, Titta J. K.; Rinkinen, Minna L.; Beasley, Shea S.; Saris, Per E. J.

    2006-01-01

    Five potentially probiotic canine fecal lactic acid bacterium (LAB) strains, Lactobacillus fermentum LAB8, Lactobacillus salivarius LAB9, Weissella confusa LAB10, Lactobacillus rhamnosus LAB11, and Lactobacillus mucosae LAB12, were fed to five permanently fistulated beagles for 7 days. The survival of the strains and their potential effects on the indigenous intestinal LAB microbiota were monitored for 17 days. Denaturing gradient gel electrophoresis (DGGE) demonstrated that the five fed LAB ...

  16. Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)".

    Science.gov (United States)

    Yang, Yu; Yang, Jun; Jiang, Lei

    2016-08-19

    Yoshida et al (Report, 11 March 2016, p. 1196) reported that the bacterium Ideonella sakaiensis 201-F6 can degrade and assimilate poly(ethylene terephthalate) (PET). However, the authors exaggerated degradation efficiency using a low-crystallinity PET and presented no straightforward experiments to verify depolymerization and assimilation of PET. Thus, the authors' conclusions are rather misleading. Copyright © 2016, American Association for the Advancement of Science.

  17. Two New Cholic Acid Derivatives from the Marine Ascidian-Associated Bacterium Hasllibacter halocynthiae

    Directory of Open Access Journals (Sweden)

    Sung Hun Kim

    2012-10-01

    Full Text Available The investigation of secondary metabolites in liquid cultures of a recently discovered marine bacterium, Hasllibacter halocynthiae strain KME 002T, led to the isolation of two new cholic acid derivatives. The structures of these compounds were determined to be 3,3,12-trihydroxy-7-ketocholanic acid (1 and 3,3,12-trihydroxy-7-deoxycholanic acid (2 through HRFABMS and NMR data analyses.

  18. Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium

    OpenAIRE

    Arif, Mohammad; Busot, Grethel Y.; Mann, Rachel; Rodoni, Brendan; Liu, Sanzhen; Stack, James P.

    2016-01-01

    Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of...

  19. A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium

    OpenAIRE

    Hoshi, Ayaka; Oshima, Kenro; Kakizawa, Shigeyuki; Ishii, Yoshiko; Ozeki, Johji; Hashimoto, Masayoshi; Komatsu, Ken; Kagiwada, Satoshi; Yamaji, Yasuyuki; Namba, Shigetou

    2009-01-01

    One of the most important themes in agricultural science is the identification of virulence factors involved in plant disease. Here, we show that a single virulence factor, tengu-su inducer (TENGU), induces witches' broom and dwarfism and is a small secreted protein of the plant-pathogenic bacterium, phytoplasma. When tengu was expressed in Nicotiana benthamiana plants, these plants showed symptoms of witches' broom and dwarfism, which are typical of phytoplasma infection. Transgenic Arabidop...

  20. Fourier transform infrared spectroscopic study of intact cells of the nitrogen-fixing bacterium Azospirillum brasilense

    Science.gov (United States)

    Kamnev, A. A.; Ristić, M.; Antonyuk, L. P.; Chernyshev, A. V.; Ignatov, V. V.

    1997-06-01

    The data of Fourier transform infrared (FTIR) spectroscopic measurements performed on intact cells of the soil nitrogen-fixing bacterium Azospirillum brasilense grown in a standard medium and under the conditions of an increased metal uptake are compared and discussed. The structural FTIR information obtained is considered together with atomic absorption spectrometry (AAS) data on the content of metal cations in the bacterial cells. Some methodological aspects concerning preparation of bacterial cell samples for FTIR measurements are also discussed.

  1. The Purine-Utilizing Bacterium Clostridium acidurici 9a: A Genome-Guided Metabolic Reconsideration

    OpenAIRE

    Hartwich, Katrin; Poehlein, Anja; Daniel, Rolf

    2012-01-01

    Clostridium acidurici is an anaerobic, homoacetogenic bacterium, which is able to use purines such as uric acid as sole carbon, nitrogen, and energy source. Together with the two other known purinolytic clostridia C. cylindrosporum and C. purinilyticum, C. acidurici serves as a model organism for investigation of purine fermentation. Here, we present the first complete sequence and analysis of a genome derived from a purinolytic Clostridium. The genome of C. acidurici 9a consists ...

  2. Sexual transmission of a plant pathogenic bacterium, Candidatus Liberibacter asiaticus, between conspecific insect vectors during mating.

    Directory of Open Access Journals (Sweden)

    Rajinder S Mann

    Full Text Available Candidatus Liberibacter asiaticus is a fastidious, phloem-inhabiting, gram-negative bacterium transmitted by Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae. The bacterium is the presumed causal agent of huanglongbing (HLB, one of the most destructive and economically important diseases of citrus. We investigated whether Las is transmitted between infected and uninfected D. citri adults during courtship. Our results indicate that Las was sexually transmitted from Las-infected male D. citri to uninfected females at a low rate (<4% during mating. Sexual transmission was not observed following mating of infected females and uninfected males or among adult pairs of the same sex. Las was detected in genitalia of both sexes and also in eggs of infected females. A latent period of 7 days or more was required to detect the bacterium in recipient females. Rod shaped as well as spherical structures resembling Las were observed in ovaries of Las-infected females with transmission electron microscopy, but were absent in ovaries from uninfected D. citri females. The size of the rod shaped structures varied from 0.39 to 0.67 µm in length and 0.19 to 0.39 µm in width. The spherical structures measured from 0.61 to 0.80 µm in diameter. This investigation provides convincing evidence that a plant pathogenic bacterium is sexually transmitted from male to female insects during courtship and established evidence that bacteria persist in reproductive organs. Moreover, these findings provide an alternative sexually horizontal mechanism for the spread of Las within populations of D. citri, even in the absence of infected host trees.

  3. DNA damage response in a radiation resistant bacterium Deinococcus radiodurans: a paradigm shift

    International Nuclear Information System (INIS)

    Misra, H.S.

    2015-01-01

    Deinococcusradiodurans is best known for its extraordinary resistance to gamma radiation with its D 10 12kGy, and several other DNA damaging agents including desiccation to less than 5% humidity and chemical xenotoxicants. An efficient DNA double strand break (DSB) repair and its ability to protect biomolecules from oxidative damage are a few mechanisms attributed to these phenotypes in this bacterium. Although it regulates its proteome and transcriptome in response to DNA damage for its growth and survival, it lacks LexA mediated classical SOS response mechanism. Since LexA mediated damages response mechanism is highly and perhaps only, characterized DNA damage response processes in prokaryotes, this bacterium keeps us guessing how it responds to extreme doses of DNA damage. Interestingly, this bacterium encodes a large number of eukaryotic type serine threonine/tyrosine protein kinases (eST/YPK), phosphatases and response regulators and roles of eST/YPKs in cellular response to DNA damage and cell cycle regulations are well established in eukaryotes. Here, we characterized an antioxidant and DNA damage inducible eST/YPK (RqkA) and established its role in extraordinary radioresistance and DSB repair in this bacterium. We identified native phosphoprotein substrates for this kinase and demonstrated the involvement of some of these proteins phosphorylation in the regulation of DSB repair and growth under radiation stress. Findings suggesting the possible existence of eST/YPK mediated DNA damage response mechanism as an alternate to classical SOS response in this prokaryote would be discussed. (author)

  4. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides.

    Science.gov (United States)

    Devendran, Saravanan; Abdel-Hamid, Ahmed M; Evans, Anton F; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I; Cann, Isaac

    2016-10-17

    Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.

  5. FtsZ from radiation resistant bacterium Deinococcus radiodurans is different from its characterized homologues

    International Nuclear Information System (INIS)

    Mehta, Kruti P.; Misra, H.S.

    2012-01-01

    Polymerization/depolymerization dynamics of FtsZ and its GTPase activity are interdependent and the regulation of these processes determines the growth rate in a bacterium. Deinococcus radiodurans R1 that is best known for its extraordinary radiation resistance and efficient DNA double strand break repair is a comparatively slow growing bacterium and its growth gets arrested in response to gamma radiation. Mechanisms of cell division and its regulation under gamma stressed growth condition would be worth investigating. Genome of this bacterium encodes at least all the known components of divisome. Recombinant FtsZ of D. radiodurans (drFtsZ) preferred Mg 2+ for its GTPase activity. Relatively a very low GTPase activity was observed in presence of Mn 2+ , Co 2+ and Ni 2+ while release of inorganic phosphate could not be detected in presence of other divalent ions including Ca 2+ . GTPase activity of drFtsZ was lower than E. coli but higher than Mycobacterium and it required both Mg 2+ and GTP for its polymerization. Its GTPase activity did not increase with increasing concentration of Mg 2+ and correlates with the bundling of protofilaments. Results obtained from transmission electron microscopy and sedimentation analysis supported the reciprocal correlation of polymerization/depolymerization with the levels of GTPase activity. Dynamic light scattering in presence of 5mM or higher concentration of Mg 2+ and Mn 2 showed a characteristic cyclic change in light scattering without addition of extra metal ion or GTP

  6. Antimicrobial polyketide furanoterpenoids from seaweed-associated heterotrophic bacterium Bacillus subtilis MTCC 10403.

    Science.gov (United States)

    Chakraborty, Kajal; Thilakan, Bini; Raola, Vamshi Krishna

    2017-10-01

    Brown seaweed Anthophycus longifolius (Turner) Kützing (family Sargassaceae) associated heterotrophic bacterium Bacillus subtilis MTCC 10403 was found to be a potent isolate with broad range of antibacterial activity against important perceptive food pathogens Vibrio parahaemolyticus, V. vulnificus, and Aeromonas hydrophila. This bacterium was positive for polyketide synthetase gene (KC589397), and therefore, was selected to bioprospect specialized metabolites bearing polyketide backbone. Bioactivity-guided chromatographic fractionation of the ethyl acetate extract of the seaweed-associated bacterium segregated four homologous polyketide furanoterpenoids with potential antibacterial activities against clinically important pathogens. The minimum inhibitory concentration (MIC) assay showed that the referral antibiotics tetracycline and ampicillin were active at 25 μg/mL against the test pathogens, whereas the previously undescribed (4E)-methyl 13-((16-(furan-2-yl) ethyl)-octahydro-7-hydroxy-4-((E)-23-methylbut-21-enyl)-2H-chromen-6-yl)-4-methylpent-4-enoate (compound 1) and methyl 3-(hexahydro-9-((E)-3-methylpent-1-enyl)-4H-furo[3,2-g]isochromen-6-yl) propanoate (compound 3) displayed antibacterial activities against the test pathogens at a lesser concentration (MIC subtilis MTCC 10403 demonstrated to represent a potential source of antimicrobial polyketides for pharmaceutical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes. Final Report

    International Nuclear Information System (INIS)

    Lidstrom, Mary E.

    2003-01-01

    Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions

  8. Purification and Characterization of Haloalkaline, Organic Solvent Stable Xylanase from Newly Isolated Halophilic Bacterium-OKH

    Science.gov (United States)

    Sanghvi, Gaurav; Jivrajani, Mehul; Patel, Nirav; Jivrajani, Heta; Bhaskara, Govinal Badiger; Patel, Shivani

    2014-01-01

    A novel, alkali-tolerant halophilic bacterium-OKH with an ability to produce extracellular halophilic, alkali-tolerant, organic solvent stable, and moderately thermostable xylanase was isolated from salt salterns of Mithapur region, Gujarat, India. Identification of the bacterium was done based upon biochemical tests and 16S rRNA sequence. Maximum xylanase production was achieved at pH 9.0 and 37°C temperature in the medium containing 15% NaCl and 1% (w/v) corn cobs. Sugarcane bagasse and wheat straw also induce xylanase production when used as carbon source. The enzyme was active over a range of 0–25% sodium chloride examined in culture broth. The optimum xylanase activity was observed at 5% sodium chloride. Xylanase was purified with 25.81%-fold purification and 17.1% yield. Kinetic properties such as Km and Vmax were 4.2 mg/mL and 0.31 μmol/min/mL, respectively. The enzyme was stable at pH 6.0 and 50°C with 60% activity after 8 hours of incubation. Enzyme activity was enhanced by Ca2+, Mn2+, and Mg2+ but strongly inhibited by heavy metals such as Hg2+, Fe3+, Ni2+, and Zn2+. Xylanase was found to be stable in organic solvents like glutaraldehyde and isopropanol. The purified enzyme hydrolysed lignocellulosic substrates. Xylanase, purified from the halophilic bacterium-OKH, has potential biotechnological applications. PMID:27350996

  9. The effect of Pseudoxanthomonas sp. as manganese oxidizing bacterium on the corrosion behavior of carbon steel

    International Nuclear Information System (INIS)

    Ashassi-Sorkhabi, H.; Moradi-Haghighi, M.; Zarrini, G.

    2012-01-01

    The present study investigated the role of manganese oxidizing bacterium (MOB), namely Pseudoxanthomonas sp. on the corrosion behavior of carbon steel. This bacterium was isolated from sewage treatment plants and identified by biochemical and molecular methods. The electrochemical techniques such as open circuit potentiometry, electrochemical impedance spectroscopy, potentiodynamic and cyclic polarization were used to measure the corrosion rate and observe the corrosion mechanism. Also, scanning electron microscopy and X-ray diffraction studies were applied to surface analysis. This study revealed the strong adhesion of the biofilm on the metal surface in the presence of Pseudoxanthomonas sp. that enhanced the corrosion of carbon steel. X-ray diffraction patterns identified a high content of MnO 2 deposition within these biofilms. This is the first report that discloses the involvement of Pseudoxanthomonas sp. as manganese oxidizing bacteria on the corrosion of carbon steel. - Highlights: ► A new type of manganese oxidizing bacteria, namely Pseudoxanthomonas sp. was indicated. ► This bacterium can create a biofilm on the part of metal surface and affect localized corrosion. ► In the presence of biofilm, the diffusion of oxygen vacancies and manganese ions has occurred.

  10. Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

    Science.gov (United States)

    Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

    2014-01-01

    Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production. PMID:24717418

  11. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin.

    Science.gov (United States)

    Svitil, A L; Chadhain, S; Moore, J A; Kirchman, D L

    1997-02-01

    Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products.

  12. The effect of Pseudoxanthomonas sp. as manganese oxidizing bacterium on the corrosion behavior of carbon steel

    Energy Technology Data Exchange (ETDEWEB)

    Ashassi-Sorkhabi, H., E-mail: habib_ashassi@yahoo.com [Electrochemistry Research Laboratory, Physical Chemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz (Iran, Islamic Republic of); Moradi-Haghighi, M. [Electrochemistry Research Laboratory, Physical Chemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz (Iran, Islamic Republic of); Zarrini, G. [Microbiology laboratory, Biology Department, Science Faculty, University of Tabriz, Tabriz (Iran, Islamic Republic of)

    2012-02-01

    The present study investigated the role of manganese oxidizing bacterium (MOB), namely Pseudoxanthomonas sp. on the corrosion behavior of carbon steel. This bacterium was isolated from sewage treatment plants and identified by biochemical and molecular methods. The electrochemical techniques such as open circuit potentiometry, electrochemical impedance spectroscopy, potentiodynamic and cyclic polarization were used to measure the corrosion rate and observe the corrosion mechanism. Also, scanning electron microscopy and X-ray diffraction studies were applied to surface analysis. This study revealed the strong adhesion of the biofilm on the metal surface in the presence of Pseudoxanthomonas sp. that enhanced the corrosion of carbon steel. X-ray diffraction patterns identified a high content of MnO{sub 2} deposition within these biofilms. This is the first report that discloses the involvement of Pseudoxanthomonas sp. as manganese oxidizing bacteria on the corrosion of carbon steel. - Highlights: Black-Right-Pointing-Pointer A new type of manganese oxidizing bacteria, namely Pseudoxanthomonas sp. was indicated. Black-Right-Pointing-Pointer This bacterium can create a biofilm on the part of metal surface and affect localized corrosion. Black-Right-Pointing-Pointer In the presence of biofilm, the diffusion of oxygen vacancies and manganese ions has occurred.

  13. Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

    Directory of Open Access Journals (Sweden)

    Bhagwan N. Rekadwad

    2016-01-01

    Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

  14. Photoproduction of hydrogen by a non-sulphur bacterium isolated from root zones of water fern Azolla pinnata

    Energy Technology Data Exchange (ETDEWEB)

    Singh, S.P.; Srivastava, S.C.; Pandey, K.D. (Banaras Hindu Univ., Varanasi (IN). Centre of Advanced Study in Botany)

    1990-01-01

    A photosynthetic bacterium Rhodopseudomonas sp. BHU strain 1 was isolated from the root zone of water fern Azolla pinnata. The bacterium was found to produce hydrogen with potato starch under phototrophic conditions. The immobilized bacterial cells showed sustained hydrogen production with a more than 4-fold difference over free cell suspensions. The data have been discussed in the light of possible utilization of relatively cheaper raw materials by non-sulphur bacteria to evolve hydrogen. (author).

  15. Thermophilic Anaerobic Degradation of Butyrate by a Butyrate-Utilizing Bacterium in Coculture and Triculture with Methanogenic Bacteria

    OpenAIRE

    Ahring, Birgitte K.; Westermann, Peter

    1987-01-01

    We studied syntrophic butyrate degradation in thermophilic mixed cultures containing a butyrate-degrading bacterium isolated in coculture with Methanobacterium thermoautotrophicum or in triculture with M. thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic bacterium. Butyrate was β-oxidized to acetate with protons as the electron acceptors. Acetate was used concurrently with its production in the triculture. We found a higher butyrate degradation rate in th...

  16. Understanding the interaction between an obligate hyperparasitic bacterium, Pasteuria penetrans and its obligate plant-parasitic nematode host, Meloidogyne spp.

    Science.gov (United States)

    Davies, Keith G

    2009-01-01

    Pasteuria penetrans is an endospore-forming bacterium, which is a hyperparasite of root-knot nematodes Meloidogyne spp. that are economically important pests of a wide range of crops. The life cycle of the bacterium and nematode are described with emphasis on the bacterium's potential as a biocontrol agent. Two aspects that currently prohibit the commercial development of the bacterium as a biocontrol agent are the inability to culture it outside its host and its host specificity. Vegetative growth of the bacterium is possible in vitro; however, getting the vegetative stages of the bacterium to enter sporogenesis has been problematic. Insights from genomic survey sequences regarding the role of cation concentration and the phosphorylation of Spo0F have proved useful in inducing vegetative bacteria to sporulate. Similarly, genomic data have also proved useful in understanding the attachment of endospores to the cuticle of infective nematode juveniles, and a Velcro-like model of spore attachment is proposed that involves collagen-like fibres on the surface of the endospore interacting with mucins on the nematode cuticle. Ecological studies of the interactions between Daphnia and Pasteuria ramosa are examined and similarities are drawn between the co-evolution of virulence in the Daphnia system and that of plant-parasitic nematodes.

  17. Traveling interface modulations and anisotropic front propagation in ammonia oxidation over Rh(110)

    Energy Technology Data Exchange (ETDEWEB)

    Rafti, Matías [Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Fac. Cs. Exactas, Universidad Nacional de La Plata, 64 y Diag. 113 (1900), La Plata (Argentina); Institut für Physikalische Chemie und Elektrochemie, Leibniz-Universität Hannover, Callinstr. 3-3a, D-30167 Hannover (Germany); Borkenhagen, Benjamin; Lilienkamp, Gerhard [Institut für Energieforschung und Physikalische Technologien, Technische Universität Clausthal, Leibnizstr. 4, 38678 Clausthal-Zellerfeld (Germany); Lovis, Florian; Smolinsky, Tim; Imbihl, Ronald, E-mail: imbihl@pci.uni-hannvover.de [Institut für Physikalische Chemie und Elektrochemie, Leibniz-Universität Hannover, Callinstr. 3-3a, D-30167 Hannover (Germany)

    2015-11-14

    The bistable NH{sub 3} + O{sub 2} reaction over a Rh(110) surface was explored in the pressure range 10{sup −6}–10{sup −3} mbar and in the temperature range 300–900 K using photoemission electron microscopy and low energy electron microscopy as spatially resolving methods. We observed a history dependent anisotropy in front propagation, traveling interface modulations, transitions with secondary reaction fronts, and stationary island structures.

  18. [Bacterial anaerobic ammonia oxidation (Anammox) in the marine nitrogen cycle--a review].

    Science.gov (United States)

    Hong, Yiguo; Li, Meng; Gu, Jidong

    2009-03-01

    Anaerobic ammonium oxidation (Anammox) is a microbial oxidation process of ammonium, with nitrite as the electron acceptor and dinitrogen gas as the main product, and is performed by a clade of deeply branched Planctomycetes, which possess an intracytoplasmic membrane-bounded organelle, the anammoxosome, for the Anammox process. The wide distribution of Anammox bacteria in different natural environments has been greatly modified the traditional view of biogeochemical cycling of nitrogen, in which microbial denitrifier is considered as the only organism to respire nitrate and nitrite to produce nitric and nitrous oxides, and eventually nitrogen gas. More evidences indicate that Anammox is responsible for the production of more than 50% of oceanic N2 and plays an important role in global nitrogen cycling. Moreover, due to the close relationship between nitrogen and carbon cycling, it is anticipated that Anammox process might also affect the concentration of CO2 in the atmosphere, and influence the global climate change. In addition, the simultaneous transformation of nitrite and ammonium in wastewater treatment by Anammox would allow a 90% reduction in operational costs and provide a much more effective biotechnological process for wastewater treatment.

  19. Development of a simultaneous partial nitrification and anaerobic ammonia oxidation process in a single reactor.

    Science.gov (United States)

    Cho, Sunja; Fujii, Naoki; Lee, Taeho; Okabe, Satoshi

    2011-01-01

    Up-flow oxygen-controlled biofilm reactors equipped with a non-woven fabric support were used as a single reactor system for autotrophic nitrogen removal based on a combined partial nitrification and anaerobic ammonium oxidation (anammox) reaction. The up-flow biofilm reactors were initiated as either a partial nitrifying reactor or an anammox reactor, respectively, and simultaneous partial nitrification and anammox was established by careful control of the aeration rate. The combined partial nitrification and anammox reaction was successfully developed in both biofilm reactors without additional biomass inoculation. The reactor initiated as the anammox reactor gave a slightly higher and more stable mean nitrogen removal rate of 0.35 (±0.19) kg-N m(-3) d(-1) than the reactor initiated as the partial nitrifying reactor (0.23 (±0.16) kg-N m(-3) d(-1)). FISH analysis revealed that the biofilm in the reactor started as the anammox reactor were composed of anammox bacteria located in inner anoxic layers that were surrounded by surface aerobic AOB layers, whereas AOB and anammox bacteria were mixed without a distinguishable niche in the biofilm in the reactor started as the partial nitrifying reactor. However, it was difficult to efficiently maintain the stable partial nitrification owing to inefficient aeration in the reactor, which is a key to development of the combined partial nitrification and anammox reaction in a single biofilm reactor. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater‐fed rapid sand filter communities

    DEFF Research Database (Denmark)

    Fowler, Susan Jane; Palomo, Alejandro; Dechesne, Arnaud

    2018-01-01

    quantification and diversity assessement of both comammox Nitrospira clades. The primers cover a wide range of comammox diversity, spanning all available high quality sequences. We applied these primers to 12 groundwater‐fed rapid sand filters, and found comammox Nitrospira to be abundant in all filters. Clade B...

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

    DEFF Research Database (Denmark)

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

    2010-01-01

     availability. In old natural crusts total potential NH3 oxidation rates were similar to reported fluxes of NH3 from slurry without surface crust. These results indicate that old, natural surface crusts may develop into a porous matrix with high O2 availability that harbors an active population of aerobic...

  2. Ammonia Oxidation and Nitrite Reduction in the Verrucomicrobial Methanotroph Methylacidiphilum fumariolicum SolV

    Directory of Open Access Journals (Sweden)

    Sepehr S. Mohammadi

    2017-09-01

    Full Text Available The Solfatara volcano near Naples (Italy, the origin of the recently discovered verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV was shown to contain ammonium (NH4+ at concentrations ranging from 1 to 28 mM. Ammonia (NH3 can be converted to toxic hydroxylamine (NH2OH by the particulate methane monooxygenase (pMMO, the first enzyme of the methane (CH4 oxidation pathway. Methanotrophs rapidly detoxify the intermediate NH2OH. Here, we show that strain SolV performs ammonium oxidation to nitrite at a rate of 48.2 nmol NO2-.h−1.mg DW−1 under O2 limitation in a continuous culture grown on hydrogen (H2 as an electron donor. In addition, strain SolV carries out nitrite reduction at a rate of 74.4 nmol NO2-.h−1.mg DW−1 under anoxic condition at pH 5–6. This range of pH was selected to minimize the chemical conversion of nitrite (NO2- potentially occurring at more acidic pH values. Furthermore, at pH 6, we showed that the affinity constants (Ks of the cells for NH3 vary from 5 to 270 μM in the batch incubations with 0.5–8% (v/v CH4, respectively. Detailed kinetic analysis showed competitive substrate inhibition between CH4 and NH3. Using transcriptome analysis, we showed up-regulation of the gene encoding hydroxylamine dehydrogenase (haoA cells grown on H2/NH4+ compared to the cells grown on CH4/NO3- which do not have to cope with reactive N-compounds. The denitrifying genes nirk and norC showed high expression in H2/NH4+ and CH4/NO3- grown cells compared to cells growing at μmax (with no limitation while the norB gene showed downregulation in CH4/NO3- grown cells. These cells showed a strong upregulation of the genes in nitrate/nitrite assimilation. Our results demonstrate that strain SolV can perform ammonium oxidation producing nitrite. At high concentrations of ammonium this may results in toxic effects. However, at low oxygen concentrations strain SolV is able to reduce nitrite to N2O to cope with this toxicity.

  3. Organic Nitrogen-Driven Stimulation of Arbuscular Mycorrhizal Fungal Hyphae Correlates with Abundance of Ammonia Oxidizers

    Science.gov (United States)

    Bukovská, Petra; Gryndler, Milan; Gryndlerová, Hana; Püschel, David; Jansa, Jan

    2016-01-01

    Large fraction of mineral nutrients in natural soil environments is recycled from complex and heterogeneously distributed organic sources. These sources are explored by both roots and associated mycorrhizal fungi. However, the mechanisms behind the responses of arbuscular mycorrhizal (AM) hyphal networks to soil organic patches of different qualities remain little understood. Therefore, we conducted a multiple-choice experiment examining hyphal responses to different soil patches within the root-free zone by two AM fungal species (Rhizophagus irregularis and Claroideoglomus claroideum) associated with Medicago truncatula, a legume forming nitrogen-fixing root nodules. Hyphal colonization of the patches was assessed microscopically and by quantitative real-time PCR (qPCR) using AM taxon-specific markers, and the prokaryotic and fungal communities in the patches (pooled per organic amendment treatment) were profiled by 454-amplicon sequencing. Specific qPCR markers were then designed and used to quantify the abundance of prokaryotic taxa showing the strongest correlation with the pattern of AM hyphal proliferation in the organic patches as per the 454-sequencing. The hyphal density of both AM fungi increased due to nitrogen (N)-containing organic amendments (i.e., chitin, DNA, albumin, and clover biomass), while no responses as compared to the non-amended soil patch were recorded for cellulose, phytate, or inorganic phosphate amendments. Abundances of several prokaryotes, including Nitrosospira sp. (an ammonium oxidizer) and an unknown prokaryote with affiliation to Acanthamoeba endosymbiont, which were frequently recorded in the 454-sequencing profiles, correlated positively with the hyphal responses of R. irregularis to the soil amendments. Strong correlation between abundance of these two prokaryotes and the hyphal responses to organic soil amendments by both AM fungi was then confirmed by qPCR analyses using all individual replicate patch samples. Further research is warranted to ascertain the causality of these correlations and particularly which direct roles (if any) do these prokaryotes play in the observed AM hyphal responses to organic N amendment, organic N utilization by the AM fungus and its (N-unlimited) host plant. Further, possible trophic dependencies between the different players in the AM hyphosphere needs to be elucidated upon decomposing the organic N sources. PMID:27242732

  4. Intact polar lipids of ammonia-oxidizing Archaea: Structural diversity anapplication inmolecular ecology

    NARCIS (Netherlands)

    Pitcher, A.

    2011-01-01

    Non-extremophilic Crenarchaeota are ubiquitous, and comprise a major component of the microbial assemblages in many modern-day systems. Several studies have analyzed glycerol dialkyl glycerol tetraether (GDGT) membrane lipids synthesized by Crenarchaeota to interpret the presence, distribution, and

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  6. Organic Nitrogen-Driven Stimulation of Arbuscular Mycorrhizal Fungal Hyphae Correlates with Abundance of Ammonia Oxidizers

    Czech Academy of Sciences Publication Activity Database

    Bukovská, Petra; Gryndler, Milan; Gryndlerová, Hana; Püschel, David; Jansa, Jan

    2016-01-01

    Roč. 4, MAY 12 (2016), s. 711 ISSN 1664-302X R&D Projects: GA ČR GAP504/12/1665; GA MŠk(CZ) LK11224 Institutional support: RVO:61388971 Keywords : soil heterogeneity * organic amendments * arbuscular mycorrhizal (AM) fungi Subject RIV: EE - Microbiology, Virology Impact factor: 4.076, year: 2016

  7. Linking isoprenoidal GDGT membrane lipid distributions with gene abundances of ammonia-oxidizing

    NARCIS (Netherlands)

    Buckles, L.K.; Villanueva, L.; Weijers, J.W.H.; Verschuren, D.; Sinninghe Damsté, J.S.

    2013-01-01

    Stratified lakes are important reservoirs of microbial diversity and provide habitats for niche differentiation of Archaea. In this study, we used a lipid biomarker/DNA-based approach to reveal the diversity and abundance of Archaea in the water column of Lake Challa (East Africa). Concentrations of

  8. Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

    International Nuclear Information System (INIS)

    Imam, S.H.; Greene, R.V.; Griffin, H.L.

    1990-01-01

    Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. 35 S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA [ethylene hlycol-bis(β-aminoethyl ether)-N,N,N'N'-tetraacetic acid] had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction

  9. ANALYSIS OF IMMUNE RESPONSES ON TRANSGENIC TIGER SHRIMP (Penaeus monodon AGAINST PATHOGENIC BACTERIUM Vibrio harveyi

    Directory of Open Access Journals (Sweden)

    Andi Parenrengi

    2014-06-01

    Full Text Available Vibriosis is one of main diseases of the black tiger shrimp Penaeus monodon infected by pathogenic bioluminous bacterium Vibrio harveyi that can cause mass mortalities in shrimp culture. The bacteria can also trigger the disease white spot syndrome virus (WSSV. An effort to produce shrimp disease-resistant strains has been done through transgenesis technology with antiviral gene transfection. By this technology, it is expected an increase in the immune response of shrimp in a variety of diseasecausing pathogens. This study aimed to determine the immune responses (total haemocytes, haemocyte differentiation, and phenoloxydase activity of transgenic tiger shrimp against pathogenic bacterium V. harveyi. Research using completely randomized design, which consists of two treatments and three replications. Test animals being used were transgenic and non-transgenic shrimp with size, weight 3.93±1.25 g and a total length of 7.59±0.87 cm. Treatments being tested were the injection of bacterium V. harveyi (density of 5x106 cfu/mL of 0.1 mL/individual on transgenic (A and non-transgenic shrimp (B. Immune response parameters such as total haemocytes, haemocyte differentiation, and phenoloxydase activity were observed on day 1, 3, and 6 days after challenging. Data were analyzed using t-test by SPSS software. The results showed that the total haemocyte of transgenic shrimp was not significantly different (P>0.05 from non-transgenic shrimp, but haemocyte differentiation and phenoloxydase activity were significantly different (P<0.05 especially on sixth days after being exposed to the bioluminescent bacteria. The study results implied that transgenic shrimp has a better immune response compared than non-transgenic shrimp.

  10. Cloning, sequencing, and sequence analysis of two novel plasmids from the thermophilic anaerobic bacterium Anaerocellum thermophilum

    DEFF Research Database (Denmark)

    Clausen, Anders; Mikkelsen, Marie Just; Schrøder, I.

    2004-01-01

    The nucleotide sequence of two novel plasmids isolated from the extreme thermophilic anaerobic bacterium Anaerocellum thermophilum DSM6725 (A. thermophilum), growing optimally at 70degreesC, has been determined. pBAS2 was found to be a 3653 bp plasmid with a GC content of 43%, and the sequence re...... with highest similarity to DNA repair protein from Campylobacter jejuni (25% aa). Orf34 showed similarity to sigma factors with highest similarity (28% aa) to the sporulation specific Sigma factor, Sigma 28(K) from Bacillus thuringiensis....

  11. A marine bacterium, Micrococcus MCCB 104, antagonistic to vibrios in prawn larval rearing systems.

    Science.gov (United States)

    Jayaprakash, N S; Pai, S Somnath; Anas, A; Preetha, R; Philip, Rosamma; Singh, I S Bright

    2005-12-30

    A marine bacterium, Micrococcus MCCB 104, isolated from hatchery water, demonstrated extracellular antagonistic properties against Vibrio alginolyticus, V. parahaemolyticus, V. vulnificus, V. fluviallis, V. nereis, V. proteolyticus, V. mediterranei, V cholerae and Aeromonas sp., bacteria associated with Macrobrachium rosenbergii larval rearing systems. The isolate inhibited the growth of V. alginolyticus during co-culture. The antagonistic component of the extracellular product was heat-stable and insensitive to proteases, lipase, catalase and alpha-amylase. Micrococcus MCCB 104 was demonstrated to be non-pathogenic to M. rosenbergii larvae.

  12. Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery

    DEFF Research Database (Denmark)

    Martinez, Virginia; Herencias, Cristina; Jurkevitch, Edouard

    2016-01-01

    This work examines the potential of the predatory bacterium Bdellovibrio bacteriovorus HD100, an obligate predator of other Gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. The bio-product targets to be recovered......% of that accumulated by the prey bacteria, even at high biomass concentrations. This innovative downstream process highlights how B. bacteriovorus can be used as a novel, biological lytic agent for the inexpensive, industrial scale recovery of intracellular products from different Gram-negative prey cultures....

  13. Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

    Directory of Open Access Journals (Sweden)

    Yunlong Yang

    Full Text Available ABSTRACT Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.

  14. A bacterium that can grow by using arsenic instead of phosphorus

    Energy Technology Data Exchange (ETDEWEB)

    Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

    2010-11-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

  15. A fatal endocarditis case due to an emerging bacterium: Moraxella nonliquefaciens

    Directory of Open Access Journals (Sweden)

    C. Duployez

    2017-01-01

    Full Text Available Moraxella nonliquefaciens is a Gram-negative coccobacillus considered as a commensal organism from the upper respiratory tract, with low pathogenic potential. The phenotypical conventional identification is difficult and the matrix-assisted laser desorption/ionization time-of-flight technology has increased the resolution of identification of this bacterium. We report a fatal case of endocarditis due to M. nonliquefaciens whose identification was confirmed by 16S rRNA, and we review the literature on this pathogen in endocarditis.

  16. Dissolution of Fe(III)(hydr)oxides by an Aerobic Bacterium

    International Nuclear Information System (INIS)

    Maurice, P.

    2004-01-01

    This project investigated the effects of an aerobic Pseudomonas mendocina bacterium on the dissolution of Fe(III)(hydr)oxides. The research is important because metals and radionuclides that adsorb to Fe(III)(hydr)oxides could potentially be remobilized by dissolving bacteria. We showed that P. mendocina is capable of dissolving Fe-bearing minerals by a variety of mechanisms, including production of siderophores, pH changes, and formation of reductants. The production of siderophores by P. mendocina was quantified under a variety of growth conditions. Finally, we demonstrated that microbial siderophores may adsorb to and enhance dissolution of clay minerals

  17. Isolation of an unidentified pink-pigmented bacterium in a clinical specimen.

    OpenAIRE

    Odugbemi, T; Nwofor, C; Joiner, K T

    1988-01-01

    An unidentified pink-pigmented bacterium isolated from a clinical specimen is reported. The organism was oxidase, urease, and catalase positive; it grew on Thayer-Martin and MacConkey media. The isolate is possibly similar to an unnamed taxon (G.L. Gilardi and Y.C. Faur, J. Clin. Microbiol. 20:626-629, 1984); however, it had unique characteristics of nonmotility with no flagellum detectable and was a gram-negative coccoid with a few rods in pairs and negative for starch hydrolysis.

  18. Isolation of an unidentified pink-pigmented bacterium in a clinical specimen.

    Science.gov (United States)

    Odugbemi, T; Nwofor, C; Joiner, K T

    1988-05-01

    An unidentified pink-pigmented bacterium isolated from a clinical specimen is reported. The organism was oxidase, urease, and catalase positive; it grew on Thayer-Martin and MacConkey media. The isolate is possibly similar to an unnamed taxon (G.L. Gilardi and Y.C. Faur, J. Clin. Microbiol. 20:626-629, 1984); however, it had unique characteristics of nonmotility with no flagellum detectable and was a gram-negative coccoid with a few rods in pairs and negative for starch hydrolysis.

  19. Illuminating the landscape of host–pathogen interactions with the bacterium Listeria monocytogenes

    Science.gov (United States)

    Cossart, Pascale

    2011-01-01

    Listeria monocytogenes has, in 25 y, become a model in infection biology. Through the analysis of both its saprophytic life and infectious process, new concepts in microbiology, cell biology, and pathogenesis have been discovered. This review will update our knowledge on this intracellular pathogen and highlight the most recent breakthroughs. Promising areas of investigation such as the increasingly recognized relevance for the infectious process, of RNA-mediated regulations in the bacterium, and the role of bacterially controlled posttranslational and epigenetic modifications in the host will also be discussed. PMID:22114192

  20. A bacterium that can grow by using arsenic instead of phosphorus.

    Science.gov (United States)

    Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

    2011-06-03

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

  1. Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

    Science.gov (United States)

    Abdoun, Hamid; McMillan, Mary; Pereg, Lily

    2016-04-01

    Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

  2. Mutagenesis and reparation processes in the methylotrophic bacterium Pseudomonas methanolica after UV irradiation

    International Nuclear Information System (INIS)

    Naumov, G.N.; Bokhan, I.K.; Multykh, I.G.

    1986-01-01

    High resistance of cells of methylotrophic bacterium Pseudomonas methanolica to bactericidal and mutagenous effects of ultraviolet irradiation is shown as well as activity of reparation processes after UV irradiation. The presence of low photoreactivating activity in P. methanolica is shown as well. Observed recovery in innutritious medium and decrease of irradiated cells survival rates under effect of reparation inhibitors (coffeine and acriflavine) testify to activity of excision reparation and, perhaps, recombination branch of postreplicative reparation. No manifestation of inducible reparation system is discovered. It is concluded that increased resistance of P. methanolica cells to bactericidal and mutagenous effects of short-wave ultraviolet radiation is related to activity of exact reparation systems

  3. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.

    Science.gov (United States)

    Han, Yejun; Agarwal, Vinayak; Dodd, Dylan; Kim, Jason; Bae, Brian; Mackie, Roderick I; Nair, Satish K; Cann, Isaac K O

    2012-10-12

    Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

  4. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

    KAUST Repository

    Balk, Melike; Mehboob, Farrakh; van Gelder, Antonie H; Rijpstra, W Irene C; Damsté , Jaap S Sinninghe; Stams, Alfons J M

    2010-01-01

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

  5. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

    KAUST Repository

    Balk, Melike

    2010-08-03

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

  6. Influence of yeast and lactic acid bacterium on the constituent profile of soy sauce during fermentation.

    Science.gov (United States)

    Harada, Risa; Yuzuki, Masanobu; Ito, Kotaro; Shiga, Kazuki; Bamba, Takeshi; Fukusaki, Eiichiro

    2017-02-01

    Soy sauce is a Japanese traditional seasoning composed of various constituents that are produced by various microbes during a long-term fermentation process. Due to the complexity of the process, the investigation of the constituent profile during fermentation is difficult. Metabolomics, the comprehensive study of low molecular weight compounds in biological samples, is thought to be a promising strategy for deep understanding of the constituent contribution to food flavor characteristics. Therefore, metabolomics is suitable for the analysis of soy sauce fermentation. Unfortunately, only few and unrefined studies of soy sauce fermentation using metabolomics approach have been reported. Therefore, we investigated changes in low molecular weight hydrophilic and volatile compounds of soy sauce using gas chromatography/mass spectrometry (GC/MS)-based non-targeted metabolic profiling. The data were analyzed by statistical analysis to evaluate influences of yeast and lactic acid bacterium on the constituent profile. Consequently, our results suggested a novel finding that lactic acid bacterium affected the production of several constituents such as cyclotene, furfural, furfuryl alcohol and methional in the soy sauce fermentation process. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  7. A highly infective plant-associated bacterium influences reproductive rates in pea aphids.

    Science.gov (United States)

    Hendry, Tory A; Clark, Kelley J; Baltrus, David A

    2016-02-01

    Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction.

  8. Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium.

    Science.gov (United States)

    Irisa, Tatsuya; Hira, Daisuke; Furukawa, Kenji; Fujii, Takao

    2014-12-01

    The hydroxylamine oxidoreductase (HAO) from the anammox bacterium, Candidatus Kuenenia stuttgartiensis has been reported to catalyze the oxidation of hydroxylamine (NH2OH) to nitric oxide (NO) by using bovine cytochrome c as an oxidant. In contrast, we investigated whether the HAO from anammox bacterium strain KSU-1 could catalyze the reduction of NO with reduced benzyl viologen (BVred) and the NO-releasing reagent, NOC 7. The reduction proceeded, resulting in the formation of NH2OH as a product. The oxidation rate of BVred was proportional to the concentration of BVred itself for a short period in each experiment, a situation that was termed quasi-steady state. The analyses of the states at various concentrations of HAO allowed us to determine the rate constant for the catalytic reaction, (2.85 ± 0.19) × 10(5) M(-1) s(-1), governing NO reduction by BVred and HAO, which was comparable to that reported for the HAO from the ammonium oxidizer, Nitrosomonas with reduced methyl viologen. These results suggest that the anammox HAO functions to adjust anammox by inter-conversion of NO and NH2OH depending on the redox potential of the physiological electron transfer protein in anammox bacteria. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  9. Removal of arsenic from groundwater by using a native isolated arsenite-oxidizing bacterium.

    Science.gov (United States)

    Kao, An-Chieh; Chu, Yu-Ju; Hsu, Fu-Lan; Liao, Vivian Hsiu-Chuan

    2013-12-01

    Arsenic (As) contamination of groundwater is a significant public health concern. In this study, the removal of arsenic from groundwater using biological processes was investigated. The efficiency of arsenite (As(III)) bacterial oxidation and subsequent arsenate (As(V)) removal from contaminated groundwater using bacterial biomass was examined. A novel As(III)-oxidizing bacterium (As7325) was isolated from the aquifer in the blackfoot disease (BFD) endemic area in Taiwan. As7325 oxidized 2300μg/l As(III) using in situ As(III)-contaminated groundwater under aerobic conditions within 1d. After the oxidation of As(III) to As(V), As(V) removal was further examined using As7325 cell pellets. The results showed that As(V) could be adsorbed efficiently by lyophilized As7325 cell pellets, the efficiency of which was related to lyophilized cell pellet concentration. Our study conducted the examination of an alternative technology for the removal of As(III) and As(V) from groundwater, indicating that the oxidation of As(III)-contaminated groundwater by native isolated bacterium, followed by As(V) removal using bacterial biomass is a potentially effective technology for the treatment of As(III)-contaminated groundwater. © 2013.

  10. The fate of a nitrobenzene-degrading bacterium in pharmaceutical wastewater treatment sludge.

    Science.gov (United States)

    Ren, Yuan; Yang, Juan; Chen, Shaoyi

    2015-12-01

    This paper describes the fate of a nitrobenzene-degrading bacterium, Klebsiella oxytoca NBA-1, which was isolated from a pharmaceutical wastewater treatment facility. The 90-day survivability of strain NBA-1 after exposure to sludge under anaerobic and aerobic conditions was investigated. The bacterium was inoculated into sludge amended with glucose and p-chloronitrobenzene (p-CNB) to compare the bacterial community variations between the modified sludge and nitrobenzene amendment. The results showed that glucose had no obvious effect on nitrobenzene biodegradation in the co-metabolism process, regardless of the presence/absence of oxygen. When p-CNB was added under anaerobic conditions, the biodegradation rate of nitrobenzene remained unchanged although p-CNB inhibited the production of aniline. The diversity of the microbial community increased and NBA-1 continued to be one of the dominant strains. Under aerobic conditions, the degradation rate of both nitrobenzene and p-CNB was only 20% of that under anaerobic conditions. p-CNB had a toxic effect on the microorganisms in the sludge so that most of the DGGE (denaturing gradient gel electrophoresis) bands, including that of NBA-1, began to disappear under aerobic conditions after 90days of exposure. These data show that the bacterial community was stable under anaerobic conditions and the microorganisms, including NBA-1, were more resistant to the adverse environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Expression and surface display of Cellulomonas endoglucanase in the ethanologenic bacterium Zymobacter palmae

    Energy Technology Data Exchange (ETDEWEB)

    Kojima, Motoki; Akahoshi, Tomohiro; Okamoto, Kenji; Yanase, Hideshi [Tottori Univ. (Japan). Dept. of Chemistry and Biotechnology

    2012-11-15

    In order to reduce the cost of bioethanol production from lignocellulosic biomass, we developed a tool for cell surface display of cellulolytic enzymes on the ethanologenic bacterium Zymobacter palmae. Z. palmae is a novel ethanol-fermenting bacterium capable of utilizing a broad range of sugar substrates, but not cellulose. Therefore, to express and display heterologous cellulolytic enzymes on the Z. palmae cell surface, we utilized the cell-surface display motif of the Pseudomonas ice nucleation protein Ina. The gene encoding Ina from Pseudomonas syringae IFO3310 was cloned, and its product was comprised of three functional domains: an N-terminal domain, a central domain with repeated amino acid residues, and a C-terminal domain. The N-terminal domain of Ina was shown to function as the anchoring motif for a green fluorescence protein fusion protein in Escherichia coli. To express a heterologous cellulolytic enzyme extracellularly in Z. palmae, we fused the N-terminal coding sequence of Ina to the coding sequence of an N-terminal-truncated Cellulomonas endoglucanase. Z. palmae cells carrying the fusion endoglucanase gene were shown to degrade carboxymethyl cellulose. Although a portion of the expressed fusion endoglucanase was released from Z. palmae cells into the culture broth, we confirmed the display of the protein on the cell surface by immunofluorescence microscopy. The results indicate that the N-terminal anchoring motif of Ina from P. syringae enabled the translocation and display of the heterologous cellulase on the cell surface of Z. palmae. (orig.)

  12. Extreme furfural tolerance of a soil bacterium Enterobacter cloacae GGT036.

    Science.gov (United States)

    Choi, Sun Young; Gong, Gyeongtaek; Park, Hong-Sil; Um, Youngsoon; Sim, Sang Jun; Woo, Han Min

    2015-01-10

    Detoxification process of cellular inhibitors including furfural is essential for production of bio-based chemicals from lignocellulosic biomass. Here we isolated an extreme furfural-tolerant bacterium Enterobacter cloacae GGT036 from soil sample collected in Mt. Gwanak, Republic of Korea. Among isolated bacteria, only E. cloacae GGT036 showed cell growth with 35 mM furfural under aerobic culture. Compared to the maximal half inhibitory concentration (IC50) of well-known industrial strains Escherichia coli (24.9 mM furfural) and Corynebacterium glutamicum (10 mM furfural) based on the cell density, IC50 of E. cloacae GGT036 (47.7 mM) was significantly higher after 24 h, compared to E. coli and C. glutamicum. Since bacterial cell growth was exponentially inhibited depending on linearly increased furfural concentrations in the medium, we concluded that E. cloacae GGT036 is an extreme furfural-tolerant bacterium. Recently, the complete genome sequence of E. cloacae GGT036 was announced and this could provide an insight for engineering of E. cloacae GGT036 itself or other industrially relevant bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age.

    Science.gov (United States)

    Murfin, Kristen E; Dillman, Adler R; Foster, Jeremy M; Bulgheresi, Silvia; Slatko, Barton E; Sternberg, Paul W; Goodrich-Blair, Heidi

    2012-08-01

    Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.

  14. A highly infective plant-associated bacterium influences reproductive rates in pea aphids

    Science.gov (United States)

    Hendry, Tory A.; Clark, Kelley J.; Baltrus, David A.

    2016-01-01

    Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction. PMID:26998321

  15. Application of agglomerative clustering for analyzing phylogenetically on bacterium of saliva

    Science.gov (United States)

    Bustamam, A.; Fitria, I.; Umam, K.

    2017-07-01

    Analyzing population of Streptococcus bacteria is important since these species can cause dental caries, periodontal, halitosis (bad breath) and more problems. This paper will discuss the phylogenetically relation between the bacterium Streptococcus in saliva using a phylogenetic tree of agglomerative clustering methods. Starting with the bacterium Streptococcus DNA sequence obtained from the GenBank, then performed characteristic extraction of DNA sequences. The characteristic extraction result is matrix form, then performed normalization using min-max normalization and calculate genetic distance using Manhattan distance. Agglomerative clustering technique consisting of single linkage, complete linkage and average linkage. In this agglomerative algorithm number of group is started with the number of individual species. The most similar species is grouped until the similarity decreases and then formed a single group. Results of grouping is a phylogenetic tree and branches that join an established level of distance, that the smaller the distance the more the similarity of the larger species implementation is using R, an open source program.

  16. Isolation, cloning and characterization of an azoreductase from the halophilic bacterium Halomonas elongata.

    Science.gov (United States)

    Eslami, Maryam; Amoozegar, Mohammad Ali; Asad, Sedigheh

    2016-04-01

    Azo dyes are a major class of colorants used in various industries including textile, paper and food. These dyes are regarded as pollutant since they are not readily reduced under aerobic conditions. Halomonas elongata, a halophilic bacterium, has the ability to decolorize different mono and di-azo dyes in anoxic conditions. In this study the putative azoreductase gene of H. elongata, formerly annotated as acp, was isolated, heterologously expressed in Escherichia coli, purified and characterized. The gene product, AzoH, was found to have a molecular mass of 22 kDa. The enzyme requires NADH, as an electron donor for its activity. The apparent Km was 63 μM for NADH and 12 μM for methyl red as a mono-azo dye substrate. The specific activity for methyl red was 0.27 μmol min(-1)mg(-1). The optimum enzyme activity was achieved in 50mM sodium phosphate buffer at pH 6. Although increased salinity resulted in reduced activity, AzoH could decolorize azo dye at NaCl concentrations up to 15% (w/v). The enzyme was also shown to be able to decolorize remazol black B as a representative of di-azo dyes. This is the first report describing the sequence and activity of an azo-reducing enzyme from a halophilic bacterium. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque.

    Science.gov (United States)

    Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

    2016-02-10

    Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.

  18. Enhanced Cadmium (Cd Phytoextraction from Contaminated Soil using Cd-Resistant Bacterium

    Directory of Open Access Journals (Sweden)

    Kunchaya Setkit

    2014-01-01

    Full Text Available A cadmium (Cd-resistant bacterium, Micrococcus sp. MU1, is able to produce indole-3-acetic acid and promotes root elongation and plant growth. The potential of this bacterium on enhancement of Cd uptake and bioaccumulation of Cd in Helianthus annuus L. planted in Cd-contaminated soil was evaluated in greenhouse condition. The results showed that Micrococcus sp. MU1promoted the growth of H. annuus L. by increasing the root length, stem height, dry biomass, root to shoot ratio and also significantly increased Cd accumulation in the root and above-ground tissues of H. annuus L. compared to uninoculated control. Re-inoculation with Micrococcus sp. MU1in contaminated soil helped in promoting plant growth and Cd phytoextraction throughout the cultivation period. In addition, phytoextraction coefficient and translocation factor (TF of H. annuus L. inoculated with Micrococcus sp. MU1were higher than that of uninoculated control and TF continuously increased with time. Our results suggested that Micrococcus sp. MU1 has an ability to enhance plant growth and Cd uptake in H. annuus L. Synergistic interaction between Micrococcus sp. MU1 and H. annuus L. could be further applied for Cd phytoextraction in polluted areas.

  19. Biofilm and capsule formation of the diatom Achnanthidium minutissimum are affected by a bacterium.

    Science.gov (United States)

    Windler, Miriam; Leinweber, Katrin; Bartulos, Carolina Rio; Philipp, Bodo; Kroth, Peter G

    2015-04-01

    Photoautotrophic biofilms play an important role in various aquatic habitats and are composed of prokaryotic and/or eukaryotic organisms embedded in extracellular polymeric substances (EPS). We have isolated diatoms as well as bacteria from freshwater biofilms to study organismal interactions between representative isolates. We found that bacteria have a strong impact on the biofilm formation of the pennate diatom Achnanthidium minutissimum. This alga produces extracellular capsules of insoluble EPS, mostly carbohydrates (CHO), only in the presence of bacteria (xenic culture). The EPS themselves also have a strong impact on the aggregation and attachment of the algae. In the absence of bacteria (axenic culture), A. minutissimum did not form capsules and the cells grew completely suspended. Fractionation and quantification of CHO revealed that the diatom in axenic culture produces large amounts of soluble CHO, whereas in the xenic culture mainly insoluble CHO were detected. For investigation of biofilm formation by A. minutissimum, a bioassay was established using a diatom satellite Bacteroidetes bacterium that had been shown to induce capsule formation of A. minutissimum. Interestingly, capsule and biofilm induction can be achieved by addition of bacterial spent medium, indicating that soluble hydrophobic molecules produced by the bacterium may mediate the diatom/bacteria interaction. With the designed bioassay, a reliable tool is now available to study the chemical interactions between diatoms and bacteria with consequences for biofilm formation. © 2015 Phycological Society of America.

  20. Characterization of carbon dioxide concentrating chemolithotrophic bacterium Serratia sp. ISTD04 for production of biodiesel.

    Science.gov (United States)

    Kumar, Manish; Morya, Raj; Gnansounou, Edgard; Larroche, Christian; Thakur, Indu Shekhar

    2017-11-01

    Proteomics and metabolomics analysis has become a powerful tool for characterization of microbial ability for fixation of Carbon dioxide. Bacterial community of palaeoproterozoic metasediments was enriched in the shake flask culture in the presence of NaHCO 3 . One of the isolate showed resistance to NaHCO 3 (100mM) and was identified as Serratia sp. ISTD04 by 16S rRNA sequence analysis. Carbon dioxide fixing ability of the bacterium was established by carbonic anhydrase enzyme assay along with proteomic analysis by LC-MS/MS. In proteomic analysis 96 proteins were identified out of these 6 protein involved in carbon dioxide fixation, 11 in fatty acid metabolism, indicating the carbon dioxide fixing potency of bacterium along with production of biofuel. GC-MS analysis revealed that hydrocarbons and FAMEs produced by bacteria within the range of C 13 -C 24 and C 11 -C 19 respectively. Presence of 59% saturated and 41% unsaturated organic compounds, make it a better fuel composition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Optimization of liquid media and biosafety assessment for algae-lysing bacterium NP23.

    Science.gov (United States)

    Liao, Chunli; Liu, Xiaobo; Shan, Linna

    2014-09-01

    To control algal bloom caused by nutrient pollution, a wild-type algae-lysing bacterium was isolated from the Baiguishan reservoir in Henan province of China and identified as Enterobacter sp. strain NP23. Algal culture medium was optimized by applying a Placket-Burman design to obtain a high cell concentration of NP23. Three minerals (i.e., 0.6% KNO3, 0.001% MnSO4·H2O, and 0.3% K2HPO4) were found to be independent factors critical for obtaining the highest cell concentration of 10(13) CFU/mL, which was 10(4) times that of the control. In the algae-lysing experiment, the strain exhibited a high lysis rate for the 4 algae test species, namely, Chlorella vulgari, Scenedesmus, Microcystis wesenbergii, and Chlorella pyrenoidosa. Acute toxicity and mutagenicity tests showed that the bacterium NP23 had no toxic and mutagenic effects on fish, even in large doses such as 10(7) or 10(9) CFU/mL. Thus, Enterobacter sp. strain NP23 has strong potential application in the microbial algae-lysing project.

  2. Adopt a Bacterium - an active and collaborative learning experience in microbiology based on social media.

    Science.gov (United States)

    Piantola, Marco Aurélio Floriano; Moreno, Ana Carolina Ramos; Matielo, Heloísa Alonso; Taschner, Natalia Pasternak; Cavalcante, Rafael Ciro Marques; Khan, Samia; Ferreira, Rita de Cássia Café

    2018-04-24

    The "Adopt a Bacterium" project is based on the use of social network as a tool in Microbiology undergraduate education, improving student learning and encouraging students to participate in collaborative learning. The approach involves active participation of both students and teachers, emphasizing knowledge exchange, based on widely used social media. Students were organized in groups and asked to adopt a specific bacterial genus and, subsequently, submit posts about "adopted genus". The formative assessment is based on posting information on Facebook®, and the summative assessment involves presentation of seminars about the adopted theme. To evaluate the project, students filled out three anonymous and voluntary surveys. Most of the students enjoyed the activities and positively evaluated the experience. A large amount of students declared a change in their attitude towards the way they processed information, especially regarding the use of scientific sources. Finally, we evaluated knowledge retention six months after the end of the course and students were able to recall relevant Microbiology concepts. Our results suggest that the "Adopt a Bacterium" project represents a useful strategy in Microbiology learning and may be applied to other academic fields. Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  3. Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.

    Science.gov (United States)

    Boutard, Magali; Cerisy, Tristan; Nogue, Pierre-Yves; Alberti, Adriana; Weissenbach, Jean; Salanoubat, Marcel; Tolonen, Andrew C

    2014-11-01

    Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.

  4. Production and characterization of bioemulsifier from a marine bacterium, Acinetobacter calcoaceticus subsp. anitratus SM7

    Directory of Open Access Journals (Sweden)

    Kulnaree Phetrong

    2008-05-01

    Full Text Available Marine bacterium strain SM7 was isolated as a bioemulsifier-producing bacterium from oil-spilled seawater in Songkhla lagoon, Thailand. It was identified as Acinetobacter calcoaceticus subsp. anitratus based on morphology, biochemicalcharacteristics and 16S rRNA sequence. A. calcoaceticus subsp. anitratus SM7 produced an extracellular emulsifying agent when grown in a minimal salt medium (pH 7.0 containing 0.3% (v/v n-heptadecane and 0.1% (w/v ammoniumhydrogen carbonate as carbon source and nitrogen source, respectively, at 30oC with agitation rate of 200 rpm. Crude bioemulsifier was recovered from the culture supernatant by ethanol precipitation with a yield of 2.94 g/l and had a criticalemulsifier concentration of 0.04 g/ml. The crude bioemulsifier was capable of emulsifying n-hexadecane in a broad pH range (6-12, temperatures (30-121oC and in the presence of NaCl up to 12% (w/v. The bioemulsifier was stable in saltsolution ranging from 0 to 0.1% (w/v of MgCl2 and CaCl2. The broad range of pH stability, thermostability and salt tolerance suggested that the bioemulsifier from A. calcoaceticus subsp. anitratus SM7 could be useful in environmentalapplication, especially bioremediation of oil-polluted seawater.

  5. Melanin from the nitrogen-fixing bacterium Azotobacter chroococcum: a spectroscopic characterization.

    Directory of Open Access Journals (Sweden)

    Aulie Banerjee

    Full Text Available Melanins, the ubiquitous hetero-polymer pigments found widely dispersed among various life forms, are usually dark brown/black in colour. Although melanins have variety of biological functions, including protection against ultraviolet radiation of sunlight and are used in medicine, cosmetics, extraction of melanin from the animal and plant kingdoms is not an easy task. Using complementary physicochemical techniques (i.e. MALDI-TOF, FTIR absorption and cross-polarization magic angle spinning solid-state (13C NMR, we report here the characterization of melanins extracted from the nitrogen-fixing non-virulent bacterium Azotobacter chroococcum, a safe viable source. Moreover, considering dihydroxyindole moiety as the main constituent, an effort is made to propose the putative molecular structure of the melanin hetero-polymer extracted from the bacterium. Characterization of the melanin obtained from Azotobacter chroococcum would provide an inspiration in extending research activities on these hetero-polymers and their use as protective agent against UV radiation.

  6. [Identification and function test of an alkali-tolerant denitrifying bacterium].

    Science.gov (United States)

    Wang, Ru; Zheng, Ping; Li, Wei; Chen, Hui; Chen, Tingting; Ghulam, Abbas

    2013-04-04

    We obtained an alkali-tolerant denitrifying bacterium, and determined its denitrifying activity and alkali-tolerance. An alkali-tolerant denitrifying bacterial strain was obtained by isolation and purification. We identified the bacterial strain by morphological observation, physiological test and 16S rRNA analysis. We determined the denitrifying activity and alkali-tolerance by effects of initial nitrate concentration and initial pH on denitrification. An alkali-tolerant denitrifier strain R9 was isolated from the lab-scale high-rate denitrifying reactor, and it was identified as Diaphorobater nitroreducens. The strain R9 grew heterotrophically with methanol as the electron donor and nitrate as the electron acceptor. The nitrate conversion was 93.25% when strain R9 was cultivated for 288 h with initial nitrate concentration 50 mg/L and initial pH 9.0. The denitrification activity could be inhibited at high nitrate concentration with a half inhibition constant of 202.73 mg N/L. Strain R9 showed a good alkali tolerance with the nitrate removal rate at pH 11.0 remained 86% of that at pH 9.0. Strain R9 was identified as Diaphorobater nitroreducens, and it was an alkali-tolerant denitrifying bacterium with optimum pH value of 9.0.

  7. Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study

    Directory of Open Access Journals (Sweden)

    OCKY KARNA RADJASA

    2005-06-01

    Full Text Available A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity, a multifunctional peptide synthetase from Nostoc sp. GSV224, and NdaB (44% identity, a peptide synthetase module of Nodularia spumigena

  8. Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study

    Directory of Open Access Journals (Sweden)

    OCKY KARNA RADJASA

    2005-06-01

    Full Text Available A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA.The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity, a multifunctional peptide synthetase from Nostoc sp. GSV224, and NdaB (44% identity, a peptide synthetase module of Nodularia spumigena.

  9. Bacterium-like Particles for efficient immune stimulation of existing vaccines and new subunit vaccines in mucosal applications

    Directory of Open Access Journals (Sweden)

    Natalija eVan Braeckel-Budimir

    2013-09-01

    Full Text Available The successful development of a mucosal vaccine critically depends on the use of a safe and effective immunostimulant and/or carrier system. This review describes the effectiveness and mode of action of an immunostimulating particle derived from bacteria in mucosal subunit vaccines. The non-living particles, designated Bacterium-like Particles (BLPs are based on the food-grade bacterium Lactococcus lactis. The focus of the overview is on the development of intranasal BLP-based vaccines to prevent diseases caused by influenza and respiratory syncytial virus, and includes a selection of Phase I clinical data for the intranasal FluGEM vaccine.

  10. The impact of a pathogenic bacterium on a social carnivore population.

    Science.gov (United States)

    Höner, Oliver P; Wachter, Bettina; Goller, Katja V; Hofer, Heribert; Runyoro, Victor; Thierer, Dagmar; Fyumagwa, Robert D; Müller, Thomas; East, Marion L

    2012-01-01

    1. The long-term ecological impact of pathogens on group-living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium, Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyena Crocuta crocuta population in the Ngorongoro Crater, Tanzania. 2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent ('outbreak') and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rate R(0) of the bacterium. 3. During the five pre-outbreak years, the mean annual hyena mortality rate was 0.088, and annual population growth was relatively high (13.6%). During the outbreak, mortality increased by 78% to a rate of 0.156, resulting in an annual population decline of 4.3%. After the outbreak, population size increased moderately (5.1%) during the first three post-outbreak years before resuming a growth similar to pre-outbreak levels (13.9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors. 4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females - the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimated R(0) for the bacterium to be 2.7, indicating relatively fast transmission. 5. Our results suggest that the short-term 'top-down' impact of S. equi ruminatorum during the outbreak was driven by 'bottom-up' effects on nutritionally disadvantaged age-sex classes, whereas the longer-term post-outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent

  11. A pathway closely related to the (D)-tagatose pathway of gram-negative enterobacteria identified in the gram-positive bacterium Bacillus licheniformis.

    Science.gov (United States)

    Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M; Galleni, Moreno; Joris, Bernard

    2013-06-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

  12. A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

    Science.gov (United States)

    Van der Heiden, Edwige; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

    2013-01-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. PMID:23524682

  13. A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

    OpenAIRE

    Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

    2013-01-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

  14. Heterotrophic ammonium removal characteristics of an aerobic heterotrophic nitrifying-denitrifying bacterium, Providencia rettgeri YL

    Institute of Scientific and Technical Information of China (English)

    TAYLOR Shauna M; HE Yiliang; ZHAO Bin; HUANG Jue

    2009-01-01

    Bacterium Providencia rettgeri YL was found to exhibit an unusual ability to heterotrophically nitrify and aerobically denitrify various concentrations of ammonium (NH4+-N). In order to further analyze its removal ability, several experiments were conducted to identify the growth and ammonium removal response in different carbon to nitrogen (C/N) mass ratios, shaking speeds, temperatures, ammonium concentrations and to qualitatively verify the production of nitrogen gas using gas chromatography techniques. Results showed that under optimum conditions (C/N 10, 30℃, 120 r/min), YL can significantly remove low and high concentrations of ammonium within 12 to 48 h of growth. The nitrification products hydroxylamine (NH2OH), nitrite (NO2-) and nitrate (NO3-) as well as the denitrification product, nitrogen gas (N2), were detected under completely aerobic conditions.

  15. Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118.

    Science.gov (United States)

    Lobley, Carina M C; Aller, Pierre; Douangamath, Alice; Reddivari, Yamini; Bumann, Mario; Bird, Louise E; Nettleship, Joanne E; Brandao-Neto, Jose; Owens, Raymond J; O'Toole, Paul W; Walsh, Martin A

    2012-12-01

    The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.

  16. Bioethanol production from mannitol by a newly isolated bacterium, Enterobacter sp. JMP3.

    Science.gov (United States)

    Wang, Jing; Kim, Young Mi; Rhee, Hong Soon; Lee, Min Woo; Park, Jong Moon

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Plague bacterium as a transformer species in prairie dogs and the grasslands of western North America

    Science.gov (United States)

    Eads, David A.; Biggins, Dean E.

    2015-01-01

    Invasive transformer species change the character, condition, form, or nature of ecosystems and deserve considerable attention from conservation scientists. We applied the transformer species concept to the plague bacterium Yersinia pestis in western North America, where the pathogen was introduced around 1900. Y. pestis transforms grassland ecosystems by severely depleting the abundance of prairie dogs (Cynomys spp.) and thereby causing declines in native species abundance and diversity, including threatened and endangered species; altering food web connections; altering the import and export of nutrients; causing a loss of ecosystem resilience to encroaching invasive plants; and modifying prairie dog burrows. Y. pestis poses an important challenge to conservation biologists because it causes trophic-level perturbations that affect the stability of ecosystems. Unfortunately, understanding of the effects of Y. pestis on ecosystems is rudimentary, highlighting an acute need for continued research.

  18. Polymicrobial infection and bacterium-mediated epigenetic modification of DNA tumor viruses contribute to pathogenesis.

    Science.gov (United States)

    Doolittle, J M; Webster-Cyriaque, J

    2014-04-29

    ABSTRACT The human body plays host to a wide variety of microbes, commensal and pathogenic. In addition to interacting with their host, different microbes, such as bacteria and viruses, interact with each other, sometimes in ways that exacerbate disease. In particular, gene expression of a number of viruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV), and human immunodeficiency virus (HIV), is known to be regulated by epigenetic modifications induced by bacteria. These viruses establish latent infection in their host cells and can be reactivated by bacterial products. Viral reactivation has been suggested to contribute to periodontal disease and AIDS. In addition, bacterium-virus interactions may play a role in cancers, such as Kaposi's sarcoma, gastric cancer, and head and neck cancer. It is important to consider the effects of coexisting bacterial infections when studying viral diseases in vivo.

  19. Molecular Mechanisms of Adaptation of the Moderately Halophilic Bacterium Halobacillis halophilus to Its Environment

    Directory of Open Access Journals (Sweden)

    Inga Hänelt

    2013-02-01

    Full Text Available The capability of osmoadaptation is a prerequisite of organisms that live in an environment with changing salinities. Halobacillus halophilus is a moderately halophilic bacterium that grows between 0.4 and 3 M NaCl by accumulating both chloride and compatible solutes as osmolytes. Chloride is absolutely essential for growth and, moreover, was shown to modulate gene expression and activity of enzymes involved in osmoadaptation. The synthesis of different compatible solutes is strictly salinity- and growth phase-dependent. This unique hybrid strategy of H. halophilus will be reviewed here taking into account the recently published genome sequence. Based on identified genes we will speculate about possible scenarios of the synthesis of compatible solutes and the uptake of potassium ion which would complete our knowledge of the fine-tuned osmoregulation and intracellular osmolyte balance in H. halophilus.

  20. A Marine Sulfate-Reducing Bacterium Producing Multiple Antibiotics: Biological and Chemical Investigation

    Directory of Open Access Journals (Sweden)

    Xiaoliang Wang

    2009-07-01

    Full Text Available A marine sulfate-reducing bacterium SRB-22 was isolated by means of the agar shake dilution method and identified as Desulfovibrio desulfuricans by morphological, physiological and biochemical characteristics and 16S rDNA analysis. In the bioassay, its extract showed broad-spectrum antimicrobial activity using the paper disc agar diffusion method. This isolate showed a different antimicrobial profile than either ampicillin or nystatin and was found to produce at least eight antimicrobial components by bioautography. Suitable fermentation conditions for production of the active constituents were determined to be 28 day cultivation at 25 °C to 30 °C with a 10% inoculation ratio. Under these conditions, the SRB-22 was fermented, extracted and chemically investigated. So far an antimicrobial compound, mono-n-butyl phthalate, and an inactive compound, thymine, have been isolated and characterized.

  1. Plague bacterium as a transformer species in prairie dogs and the grasslands of western North America.

    Science.gov (United States)

    Eads, David A; Biggins, Dean E

    2015-08-01

    Invasive transformer species change the character, condition, form, or nature of ecosystems and deserve considerable attention from conservation scientists. We applied the transformer species concept to the plague bacterium Yersinia pestis in western North America, where the pathogen was introduced around 1900. Y. pestis transforms grassland ecosystems by severely depleting the abundance of prairie dogs (Cynomys spp.) and thereby causing declines in native species abundance and diversity, including threatened and endangered species; altering food web connections; altering the import and export of nutrients; causing a loss of ecosystem resilience to encroaching invasive plants; and modifying prairie dog burrows. Y. pestis poses an important challenge to conservation biologists because it causes trophic-level perturbations that affect the stability of ecosystems. Unfortunately, understanding of the effects of Y. pestis on ecosystems is rudimentary, highlighting an acute need for continued research. © 2015 Society for Conservation Biology.

  2. Microbially influenced corrosion of stainless steel by marine bacterium Vibrio natriegens: (I) Corrosion behavior

    Energy Technology Data Exchange (ETDEWEB)

    Cheng Sha; Tian Jintao [Institute of Materials Science and Engineering, Ocean University of China, Qingdao 266100 (China); Chen Shougang, E-mail: sgchen@ouc.edu.cn [Institute of Materials Science and Engineering, Ocean University of China, Qingdao 266100 (China); Lei Yanhua; Chang Xueting; Liu Tao [Institute of Materials Science and Engineering, Ocean University of China, Qingdao 266100 (China); Yin Yansheng, E-mail: yys2006@ouc.edu.cn [Institute of Materials Science and Engineering, Ocean University of China, Qingdao 266100 (China)

    2009-04-30

    The microbially influenced corrosion of stainless steel (SS) by marine bacterium Vibrio natriegens (V. natriegens) was investigated using surface analysis (atomic force microscopy (AFM), scanning electron microscopy (SEM), and energy dispersive X-ray analysis (EDXA)) and electrochemical techniques (the open circuit potential, electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization curves ). AFM images corroborated the results from the EIS models which show biofilm attachment and subsequent detachment over time. The SEM images revealed the occurrence of micro-pitting corrosion underneath the biofilms on the metal surface after the biofilm removal. The presence of carbon, oxygen, phosphor and sulfur obtained from EDXA proved the formation of biofilm. The electrochemical results showed that the corrosion of SS was accelerated in the presence of V. natriegens based on the decrease in the resistance of the charge transfer resistance (R{sub ct}) obtained from EIS and the increase in corrosion current densities obtained from potentiodynamic polarization curves.

  3. Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118

    International Nuclear Information System (INIS)

    Lobley, Carina M. C.; Aller, Pierre; Douangamath, Alice; Reddivari, Yamini; Bumann, Mario; Bird, Louise E.; Nettleship, Joanne E.; Brandao-Neto, Jose; Owens, Raymond J.; O’Toole, Paul W.; Walsh, Martin A.

    2012-01-01

    The crystal structure of ribose 5-phosphate isomerase has been determined to 1.72 Å resolution and is presented with a brief comparison to other known ribose 5-phosphate isomerase A structures. The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β d-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography

  4. UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

    International Nuclear Information System (INIS)

    Murygina, V.P.

    1978-01-01

    UV-induced variability of a thermophilic bacterium Bacillus diastaticus 13 by amylase formation has been studied. It has been shown, that variability limits in amylase biosynthesis vary from 2.2 to 158.7% under UV irradiation. At 41.8x10 2 erg/mm 2 UV dose a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation two low-active in biosynthesis amylases of the mutant were prepared. Demands for growth factors of some mutant have been studied as well

  5. UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

    Energy Technology Data Exchange (ETDEWEB)

    Murygina, V P

    1978-03-01

    Ultroviolet-radioinduced variability in analyase biosynthesis of a thermophilic bacterium Bacillus diastaticus 13, has been studied. It has been shown that amylase biosynthesis varies from 2.2 to 158.7% under UV irradiation. At 41.8x10/sup 2/ erg/mm/sup 2/ UV dose, a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation, two mutants with reduced amylose biosynthesis activity were prepared. Demands for growth factors by some mutants have been studied as well.

  6. Pathogenic bacteriumVibrio harveyi: an endosymbiont in the marine parasitic ciliate protozoan Cryptocaryon irritans

    Institute of Scientific and Technical Information of China (English)

    QIAO Ying; WANG Jun; MAO Yong; LIU Min; CHEN Ruanni; SU Yongquan; KE Qiaozhen; HAN Kunhuang; ZHENG Weiqiang

    2017-01-01

    Vibrio harveyi, known as a pathogenic bacterium caused severe secondary bacterial infections of the large yellow croaker Larimichthys crocea, was identified as an endosymbiont in the marine parasitic ciliate protozoan Cryptocaryon irritans. Meta 16S sequencing method was used to identify the bacterial flora in C. irritans, and V. harveyi was isolated via culture-dependent method.Vibrio harveyi was observed in cytoplasm of C. irritans at the stage of tomont both by transmission electron microscopy and by Fluorescencein situ hybridization; no signal, however, was detected in nucleus area. The relationship betweenV. harveyi and C. irritans and the role of endosymbioticV. harveyi inC. irritans merit further investigation.

  7. Analysis of convergent gene transcripts in the obligate intracellular bacterium Rickettsia prowazekii.

    Directory of Open Access Journals (Sweden)

    Andrew Woodard

    2011-01-01

    Full Text Available Termination of transcription is an important component of bacterial gene expression. However, little is known concerning this process in the obligate intracellular pathogen and model for reductive evolution, Rickettsia prowazekii. To assess transcriptional termination in this bacterium, transcripts of convergent gene pairs, some containing predicted intrinsic terminators, were analyzed. These analyses revealed that, rather than terminating at a specific site within the intervening region between the convergent genes, most of the transcripts demonstrated either a lack of termination within this region, which generated antisense RNA, or a putative non-site-specific termination that occurred throughout the intervening sequence. Transcripts terminating at predicted intrinsic terminators, as well as at a putative Rho-dependant terminator, were also examined and found to vary based on the rickettsial host environment. These results suggest that transcriptional termination, or lack thereof, plays a role in rickettsial gene regulation.

  8. A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium

    Science.gov (United States)

    Hoshi, Ayaka; Oshima, Kenro; Kakizawa, Shigeyuki; Ishii, Yoshiko; Ozeki, Johji; Hashimoto, Masayoshi; Komatsu, Ken; Kagiwada, Satoshi; Yamaji, Yasuyuki; Namba, Shigetou

    2009-01-01

    One of the most important themes in agricultural science is the identification of virulence factors involved in plant disease. Here, we show that a single virulence factor, tengu-su inducer (TENGU), induces witches' broom and dwarfism and is a small secreted protein of the plant-pathogenic bacterium, phytoplasma. When tengu was expressed in Nicotiana benthamiana plants, these plants showed symptoms of witches' broom and dwarfism, which are typical of phytoplasma infection. Transgenic Arabidopsis thaliana lines expressing tengu exhibited similar symptoms, confirming the effects of tengu expression on plants. Although the localization of phytoplasma was restricted to the phloem, TENGU protein was detected in apical buds by immunohistochemical analysis, suggesting that TENGU was transported from the phloem to other cells. Microarray analyses showed that auxin-responsive genes were significantly down-regulated in the tengu-transgenic plants compared with GUS-transgenic control plants. These results suggest that TENGU inhibits auxin-related pathways, thereby affecting plant development. PMID:19329488

  9. Novel Poly[(R-3-Hydroxybutyrate]-Producing Bacterium Isolated from a Bolivian Hypersaline Lake

    Directory of Open Access Journals (Sweden)

    María Soledad Marqués-Calvo

    2013-01-01

    Full Text Available Poly[(R-3-hydroxybutyrate] (PHB constitutes a biopolymer synthesized from renewable resources by various microorganisms. This work focuses on finding a new PHB-producing bacterium capable of growing in conventional media used for industrial biopolymer production, its taxonomical identification, and characterization of its biopolymer. Thus, a bacterial isolation process was carried out from environmental samples of water and mud. Among the isolates, strain S29 was selected and used in a fed-batch fermentation to generate a biopolymer. This biopolymer was recovered and identified as PHB homopolymer. Surprisingly, it featured several fractions of different molecular masses, and thermal properties unusual for PHB. Hence, the microorganism S29, genetically identified as a new strain of Bacillus megaterium, proved to be interesting not only due to its growth and PHB accumulation kinetics under the investigated cultivation conditions, but also due to the thermal properties of the produced PHB.

  10. Concentration and transport of nitrate by the mat-forming sulphur bacterium Thioploca

    Science.gov (United States)

    Fossing, H.; Gallardo, V. A.; Jørgensen, B. B.; Hüttel, M.; Nielsen, L. P.; Schulz, H.; Canfield, D. E.; Forster, S.; Glud, R. N.; Gundersen, J. K.; Küver, J.; Ramsing, N. B.; Teske, A.; Thamdrup, B.; Ulloa, O.

    1995-04-01

    MARINE species of Thioploca occur over 3,000 km along the continental shelf off Southern Peru and North and Central Chile1-4. These filamentous bacteria live in bundles surrounded by a common sheath and form thick mats on the sea floor under the oxygen-minimum zone in the upwelling region, at between 40 and 280 m water depth. The metabolism of this marine bacterium5,6 remained a mystery until long after its discovery1,7. We report here that Thioploca cells are able to concentrate nitrate to up to 500 mM in a liquid vacuole that occupies >80% of the cell volume. Gliding filaments transport this nitrate 5-10 cm down into the sediment and reduce it, with concomitant oxidation of hydrogen sulphide, thereby coupling the nitrogen and sulphur cycles in the sediment.

  11. Proteomic Profiling of the Dioxin-Degrading Bacterium Sphingomonas wittichii RW1

    Directory of Open Access Journals (Sweden)

    David R. Colquhoun

    2012-01-01

    Full Text Available Sphingomonas wittichii RW1 is a bacterium of interest due to its ability to degrade polychlorinated dioxins, which represent priority pollutants in the USA and worldwide. Although its genome has been fully sequenced, many questions exist regarding changes in protein expression of S. wittichii RW1 in response to dioxin metabolism. We used difference gel electrophoresis (DIGE and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS to identify proteomic changes induced by growth on dibenzofuran, a surrogate for dioxin, as compared to acetate. Approximately 10% of the entire putative proteome of RW1 could be observed. Several components of the dioxin and dibenzofuran degradation pathway were shown to be upregulated, thereby highlighting the utility of using proteomic analyses for studying bioremediation agents. This is the first global protein analysis of a microorganism capable of utilizing the carbon backbone of both polychlorinated dioxins and dibenzofurans as the sole source for carbon and energy.

  12. Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum

    DEFF Research Database (Denmark)

    Frigaard, Niels-Ulrik; Maresca, Julia A; Yunker, Colleen E

    2004-01-01

    The green sulfur bacterium Chlorobium tepidum is a strict anaerobe and an obligate photoautotroph. On the basis of sequence similarity with known enzymes or sequence motifs, nine open reading frames encoding putative enzymes of carotenoid biosynthesis were identified in the genome sequence of C....... tepidum, and all nine genes were inactivated. Analysis of the carotenoid composition in the resulting mutants allowed the genes encoding the following six enzymes to be identified: phytoene synthase (crtB/CT1386), phytoene desaturase (crtP/CT0807), zeta-carotene desaturase (crtQ/CT1414), gamma......-carotene desaturase (crtU/CT0323), carotenoid 1',2'-hydratase (crtC/CT0301), and carotenoid cis-trans isomerase (crtH/CT0649). Three mutants (CT0180, CT1357, and CT1416 mutants) did not exhibit a discernible phenotype. The carotenoid biosynthetic pathway in C. tepidum is similar to that in cyanobacteria and plants...

  13. Isolation and characterization of a new hydrogen-utilizing bacterium from the rumen.

    Science.gov (United States)

    Rieu-Lesme, F; Fonty, G; Doré, J

    1995-01-01

    A new H2/CO2-utilizing acetogenic bacterium was isolated from the rumen of a mature deer. This is the first report of a spore-forming Gram-negative bacterial species from the rumen. The organism was a strictly anaerobic, motile rod and was able to grow autotrophically on hydrogen and carbon dioxide. Acetate was the major product detected. Glucose, fructose and lactate were also fermented heterotrophically. The optimum pH for growth was 7.0-7.5, and the optimum temperature was 37-42 degrees C. Yeast extract was required for growth and rumen fluid was highly stimulatory. The DNA base ratio was 52.9 +/- 0.5 mol% G+C. On the basis of these characteristics and fermentation products, the isolate was considered to be different from acetogenic bacteria described previously.

  14. BOG: R-package for Bacterium and virus analysis of Orthologous Groups

    Directory of Open Access Journals (Sweden)

    Jincheol Park

    2015-01-01

    Full Text Available BOG (Bacterium and virus analysis of Orthologous Groups is a package for identifying groups of differentially regulated genes in the light of gene functions for various virus and bacteria genomes. It is designed to identify Clusters of Orthologous Groups (COGs that are enriched among genes that have gone through significant changes under different conditions. This would contribute to the detection of pathogens, an important scientific research area of relevance in uncovering bioterrorism, among others. Particular statistical analyses include hypergeometric, Mann–Whitney rank sum, and gene set enrichment. Results from the analyses are organized and presented in tabular and graphical forms for ease of understanding and dissemination of results. BOG is implemented as an R-package, which is available from CRAN or can be downloaded from http://www.stat.osu.edu/~statgen/SOFTWARE/BOG/.

  15. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress.

    Science.gov (United States)

    Chen, Yanmei; Chao, Yuanqing; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong; Qiu, Rongliang

    2016-01-04

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  16. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    Science.gov (United States)

    Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

    2010-01-01

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  17. Reduction of chalcogen oxyanions and generation of nanoprecipitates by the photosynthetic bacterium Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Baccolini, Chiara; Francia, Francesco [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Sabatino, Piera [Department of Chemistry G. Ciamician, University of Bologna (Italy); Turner, Raymond J. [Department of Biological Sciences, University of Calgary, Calgary, Alberta (Canada); Zannoni, Davide, E-mail: davide.zannoni@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy)

    2014-03-01

    Graphical abstract: - Highlights: • R. capsulatus cells produce extracellular chalcogens nanoprecipitates when lawsone is present. • Lawsone acts as a redox mediator from reducing equivalents to tellurite and selenite. • Nanoprecipitates production depends on carbon source and requires metabolically active cells. • Te{sup 0} and Se{sup 0} nanoprecipitates are identified by X-ray diffraction (XRD) spectroscopy. - Abstract: The facultative photosynthetic bacterium Rhodobacter capsulatus is characterized in its interaction with the toxic oxyanions tellurite (Te{sup IV}) and selenite (Se{sup IV}) by a highly variable level of resistance that is dependent on the growth mode making this bacterium an ideal organism for the study of the microbial interaction with chalcogens. As we have reported in the past, while the oxyanion tellurite is taken up by R. capsulatus cells via acetate permease and it is reduced to Te{sup 0} in the cytoplasm in the form of splinter-like black intracellular deposits no clear mechanism was described for Se{sup 0} precipitation. Here, we present the first report on the biotransformation of tellurium and selenium oxyanions into extracellular Te{sup 0} and Se{sup 0}nanoprecipitates (NPs) by anaerobic photosynthetically growing cultures of R. capsulatus as a function of exogenously added redox-mediator lawsone, i.e. 2-hydroxy-1,4-naphthoquinone. The NPs formation was dependent on the carbon source used for the bacterial growth and the rate of chalcogen reduction was constant at different lawsone concentrations, in line with a catalytic role for the redox mediator. X-ray diffraction (XRD) analysis demonstrated the Te{sup 0} and Se{sup 0} nature of the nanoparticles.

  18. Curiously modern DNA for a "250 million-year-old" bacterium.

    Science.gov (United States)

    Nickle, David C; Learn, Gerald H; Rain, Matthew W; Mullins, James I; Mittler, John E

    2002-01-01

    Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.

  19. Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium

    Directory of Open Access Journals (Sweden)

    Leong-Keat eChan

    2012-05-01

    Full Text Available Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC, a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ~50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium Ruegeria pomeroyi (a member of the Roseobacter clade under four element limitation regimes (C, N, P, and S. Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S-limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to 6-fold were measured in R. pomeroyi biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometery in R. pomeroyi may have implications for global carbon cycling. Strong homeostatic responses to N limitation by heterotrophic marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean.

  20. Extracellular polymer substance synthesized by a halophilic bacterium Chromohalobacter canadensis 28.

    Science.gov (United States)

    Radchenkova, Nadja; Boyadzhieva, Ivanka; Atanasova, Nikolina; Poli, Annarita; Finore, Ilaria; Di Donato, Paola; Nicolaus, Barbara; Panchev, Ivan; Kuncheva, Margarita; Kambourova, Margarita

    2018-04-03

    Halophilic microorganisms are producers of a lot of new compounds whose properties suggest promising perspectives for their biotechnological exploration. Moderate halophilic bacterium Chromohalobacter canadensis 28 was isolated from Pomorie salterns as an extracellular polymer substance (EP) producer. The best carbon source for extracellular polymer production was found to be lactose, a sugar received as a by-product from the dairy industry. After optimization of the culture medium and physicochemical conditions for cultivation, polymer biosynthesis increased more than 2-fold. The highest level of extracellular polymer synthesis by C. canadensis 28 was observed in an unusually high NaCl concentration (15% w/v). Chemical analysis of the purified polymer revealed the presence of an exopolysaccharide (EPS) fraction (14.3% w/w) and protein fraction (72% w/w). HPLC analysis of the protein fraction showed the main presence of polyglutamic acid (PGA) (75.7% w/w). EPS fraction analysis revealed the following sugar composition (% w/w): glucosamine 36.7, glucose 32.3, rhamnose 25.4, xylose 1.7, and not identified sugar 3.9. The hydrogel formed by PGA and EPS fractions showed high swelling behavior, very good emulsifying and stabilizing properties, and good foaming ability. This is the first report for halophilic bacterium able to synthesize a polymer containing PGA fraction. The synthesized biopolymer shows an extremely high hydrophilicity, due to the simultaneous presence of PGA and EPS. The analysis of its functional properties and the presence of glucosamine in the highest proportion in EPS fraction clearly determine the potential of EP synthesized by C. canadensis 28 for application in the cosmetics industry.

  1. Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology.

    Science.gov (United States)

    Kindzierski, Viktoria; Raschke, Silvia; Knabe, Nicole; Siedler, Frank; Scheffer, Beatrix; Pflüger-Grau, Katharina; Pfeiffer, Friedhelm; Oesterhelt, Dieter; Marin-Sanguino, Alberto; Kunte, Hans-Jörg

    2017-01-01

    Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem. However, as more of these reconstructions become available, it becomes clear that processes predicted by genome annotation may not reflect the processes that are active in vivo. As a case in point, E. coli is unable to grow aerobically on citrate in spite of having all the necessary genes to do it. It has also been shown that the realization of this genetic potential into an actual capability to metabolize citrate is an extremely unlikely event under normal evolutionary conditions. Moreover, many marine bacteria seem to have the same pathways to metabolize glucose but each species uses a different one. In this work, a metabolic network inferred from genomic annotation of the halophilic bacterium Halomonas elongata and proteomic profiling experiments are used as a starting point to motivate targeted experiments in order to find out some of the defining features of the osmoregulatory strategies of this bacterium. This new information is then used to refine the network in order to describe the actual capabilities of H. elongata, rather than its genetic potential.

  2. Serpentine endophytic bacterium Pseudomonas azotoformans ASS1 accelerates phytoremediation of soil metals under drought stress.

    Science.gov (United States)

    Ma, Ying; Rajkumar, Mani; Moreno, António; Zhang, Chang; Freitas, Helena

    2017-10-01

    This study evaluates the potential of serpentine endophytic bacterium to foster phytoremediation efficiency of Trifolium arvense grown on multi-metal (Cu, Zn and Ni) contaminated soils under drought stress. A drought resistant endophytic bacterial strain ASS1 isolated from the leaves of Alyssum serpyllifolium grown in serpentine soils was identified as Pseudomonas azotoformans based on biochemical tests and partial 16S rRNA gene sequencing. P. azotoformans ASS1 possessed abiotic stress resistance (heavy metals, drought, salinity, antibiotics and extreme temperature) and plant growth promoting (PGP) properties (phosphate solubilization, nitrogen fixation, production of 1-aminocyclopropane-1-carboxylate deaminase, siderophore and ammonia). Inoculation of T. arvense with ASS1 considerably increased the plant biomass and leaf relative water content in both roll towel assay and pot experiments in the absence and presence of drought stress (DS). In the pot experiments, ASS1 greatly enhanced chlorophyll content, catalase, peroxidase, superoxide dismutase activities, and proline content (only in the absence of drought) in plant leaves, whereas they decreased the concentrations of malondialdehyde. Irrespective of water stress, ASS1 significantly improved accumulation, total removal, bio-concentration factor and biological accumulation coefficient of metals (Cu, Zn and Ni), while decreased translocation factors of Cu. The effective colonization and survival in the rhizosphere and tissue interior assured improved plant growth and successful metal phytoremediation under DS. These results demonstrate the potential of serpentine endophytic bacterium ASS1 for protecting plants against abiotic stresses and helping plants to thrive in semiarid ecosystems and accelerate phytoremediation process in metal polluted soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Isolation and characterization of a radiation resistant thermophilic bacterium from radon hot spring

    International Nuclear Information System (INIS)

    Liang Xinle; Yang Long; Zhang Hong; Zhang Lei

    2011-01-01

    A radiation resistant and thermophilic bacterium strain R4-33 was isolated from radon hot spring water samples, pretreated with 60 Co γ-rays and UV irradiation. Tests on morphological, physiological and biochemical characters, fatty acid compositions, (G + C) mol% contents, and 16S rDNA sequencing were conducted. The results showed that strain R4-33 was of rod-shape, Gram-negative, atrichous, and endospore-forming. The optimum growth temperature and pH were 60 ℃ and 7.5, respectively. The strain utilized glucose, maltose and trehalose as carbon sources, and hydrolyzed casein and starch. Its catalase positive. The strain was sensitive to penicillin, neomycin, erythromycin, vancomycin, streptomycin, gentamycin, amikacin and ampicillin. The major cellular fatty acids were C 14:1 (48.8%) and C 15:1 (15.2%). The (G + C) mol% content of DNA was 58.2%. Phylogenetic tree based on 16S rDNA sequence showed R4-33 shared highly similarity to those of species in genus Anoxybacillus, especially to that of Anoxybacillus gonensis (99.5%). Based on the above, the strain R4-33 was proposed to the evolution branch of Anoxybacillus and designated as Anoxybacillu sp. R4-33. The UV and γ-radiation tests showed that the strain R4-33 had an ability of resistance to UV of 396 J/m 2 and 60 Co γ-rays irradiation of 14.0 kGy, indicating that the strain was a radiation resistant and thermophilic bacterium. (authors)

  4. Reduction of Mo(VI) by the bacterium Serratia sp. strain DRY5.

    Science.gov (United States)

    Rahman, M F A; Shukor, M Y; Suhaili, Z; Mustafa, S; Shamaan, N A; Syed, M A

    2009-01-01

    The need to isolate efficient heavy metal reducers for cost effective bioremediation strategy have resulted in the isolation of a potent molybdenum-reducing bacterium. The isolate was tentatively identified as Serratia sp. strain DRY5 based on the Biolog GN carbon utilization profiles and partial 16S rDNA molecular phylogeny. Strain DRY5 produced 2.3 times the amount of Mo-blue than S. marcescens strain Dr.Y6, 23 times more than E. coli K12 and 7 times more than E. cloacae strain 48. Strain DRY5 required 37 degrees C and pH 7.0 for optimum molybdenum reduction. Carbon sources such as sucrose, maltose, glucose and glycerol, supported cellular growth and molybdate reduction after 24 hr of static incubation. The most optimum carbon source that supported reduction was sucrose at 1.0% (w/v). Ammonium sulphate, ammonium chloride, glutamic acid, cysteine, and valine supported growth and molybdate reduction with ammonium sulphate as the optimum nitrogen source at 0. 2% (w/v). Molybdate reduction was optimally supported by 30 mM molybdate. The optimum concentration of phosphate for molybdate reduction was 5 mM when molybdate concentration was fixed at 30 mM and molybdate reduction was totally inhibited at 100 mM phosphate. Mo-blue produced by this strain shows a unique characteristic absorption profile with a maximum peak at 865 nm and a shoulder at 700 nm, Dialysis tubing experiment showed that 95.42% of Mo-blue was found in the dialysis tubing suggesting that the molybdate reduction seen in this bacterium was catalyzed by enzyme(s). The characteristics of isolate DRY5 suggest that it would be useful in the bioremediation ofmolybdenum-containing waste.

  5. A soluble fatty acyl-acyl carrier protein synthetase from the bioluminescent bacterium Vibrio harveyi.

    Science.gov (United States)

    Byers, D M; Holmes, C G

    1990-01-01

    An enzyme catalyzing the ligation of long chain fatty acids to bacterial acyl carrier protein (ACP) has been detected and partially characterized in cell extracts of the bioluminescent bacterium Vibrio harveyi. Acyl-ACP synthetase activity (optimal pH 7.5-8.0) required millimolar concentrations of ATP and Mg2+ and was slightly activated by Ca2+, but was inhibited at high ionic strength and by Triton X-100. ACP from either Escherichia coli (apparent Km = 20 microM) or V. harveyi was used as a substrate. Of the [14C]fatty acids tested as substrates (8-18 carbons), a preference for fatty acids less than or equal to 14 carbons in length was observed. Vibrio harveyi acyl-ACP synthetase appears to be a soluble hydrophilic enzyme on the basis of subcellular fractionation and Triton X-114 phase partition assay. The enzyme was not coinduced with luciferase activity or light emission in vivo during the late exponential growth phase in liquid culture. Acyl-ACP synthetase activity was also detected in extracts from the luminescent bacterium Vibrio fischeri, but not Photobacterium phosphoreum. The cytosolic nature and enzymatic properties of V. harveyi acyl-ACP synthetase indicate that it may have a different physiological role than the membrane-bound activity of E. coli, which has been implicated in phosphatidylethanolamine turnover. Acyl-ACP synthetase activity in V. harveyi could be involved in the intracellular activation and elongation of exogenous fatty acids that occurs in this species or in the reactivation of free myristic acid generated by luciferase.

  6. Virus-Bacterium Interactions in Water and Sediment of West African Inland Aquatic Systems

    Science.gov (United States)

    Bettarel, Yvan; Bouvy, Marc; Dumont, Claire; Sime-Ngando, Télesphore

    2006-01-01

    The ecology of virioplankton in tropical aquatic ecosystems is poorly documented, and in particular, there are no references concerning African continental waters in the literature. In this study, we examined virus-bacterium interactions in the pelagic and benthic zones of seven contrasting shallow inland waters in Senegal, including one hypersaline lake. SYBR Gold-stained samples revealed that in the surface layers of the sites, the numbers of viruses were in the same range as the numbers of viruses reported previously for productive temperate systems. Despite high bacterial production rates, the percentages of visibly infected cells (as determined by transmission electron microscopy) were similar to the lowest percentages (range, 0.3 to 1.1%; mean, 0.5%) found previously at pelagic freshwater or marine sites, presumably because of the local environmental and climatic conditions. Since the percentages of lysogenic bacteria were consistently less than 8% for pelagic and benthic samples, lysogeny did not appear to be a dominant strategy for virus propagation at these sites. In the benthic samples, viruses were highly concentrated, but paradoxically, no bacteria were visibly infected. This suggests that sediment provides good conditions for virus preservation but ironically is an unfavorable environment for proliferation. In addition, given the comparable size distributions of viruses in the water and sediment samples, our results support the paradigm that aquatic viruses are ubiquitous and may have moved between the two compartments of the shallow systems examined. Overall, this study provides additional information about the relevance of viruses in tropical areas and indicates that the intensity of virus-bacterium interactions in benthic habitats may lower than the intensity in the adjacent bodies of water. PMID:16885276

  7. Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

    Science.gov (United States)

    Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

    2015-09-01

    A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

  8. Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax

    Directory of Open Access Journals (Sweden)

    Guangli Wang

    2010-06-01

    Full Text Available Microbial degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenylethane (DDT is the most promising way to clean up DDT residues found in the environment. In this paper, a bacterium designated as wax, which was capable of co-metabolizing DDT with other carbon sources, was isolated from a long-term DDT-contaminated soil sample by an enrichment culture technique. The new isolate was identified as a member of the Pseudoxanthomonas sp., based on its morphological, physiological and biochemical properties, as well as by 16S rRNA gene analysis. In the presence of 100 mg l-1 glucose, the wax strain could degrade over 95% of the total DDT, at a concentration of 20 mg l-1, in 72 hours, and could degrade over 60% of the total DDT, at a concentration of 100 mg l-1, in 144 hours. The wax strain had the highest degradation efficiency among all of the documented DDT-degrading bacteria. The wax strain could efficiently degrade DDT at temperatures ranging from 20 to 37ºC, and with initial pH values ranging from 7 to 9. The bacterium could also simultaneously co-metabolize 1,1-dichloro-2,2-bis(p-chlorophenylethane (DDD, 2,2-bis(p-chlorophenyl-1,1-dichlorethylene (DDE, and other organochlorine compounds. The wax strain could also completely remove 20 mg kg-1 of DDT from both sterile and non-sterile soils in 20 days. This study demonstrates the significant potential use of Pseudoxanthomonas sp. wax for the bioremediation of DDT in the environment.

  9. Lethal Effect on Bacterium of Decay of Incorporated Radioactive Atoms (3H, 14C, 32P)

    International Nuclear Information System (INIS)

    Apelgot, Sonia

    1968-01-01

    The biological effect of decay of 3 H, 14 C and 32 P incorporated into a bacterium depends on the nature of the organic molecule labelled, on the position of the isotope within it and on the isotope itself. In sum, results obtained to date show that: The decay of 3 H atoms incorporated into certain macromolecules of a bacterium causes sterilization through ionization by the ß - particle emitted; transmutation is of negligible importance. This self-irradiation is comparable in effect with X-rays and is affected in a similar manner by the same factors: temperature, presence of a radioprotector, radiosensitivity of the strain. Decay of 14 C or 32 P atoms incorporated into bacterial DNA is lethal because of the transmutation effect; ionizations produced by emitted ß - particles may be disregarded. Survival curves for 32 P transmutations depend on the experimental conditions. Some of the results obtained with 32 P are similar to those obtained with X-rays, e.g. effects of temperature, radical capture and oxygen, while others are similar to those of u.v. light, e.g., effect of growth conditions. Comparative tests made with 32 P indicate that the recoil energy of transmutation is not the phenomenon responsible for the lethal effect observed. Comparison of the results obtained after X-irradiation or decay of 3 H or 32 P incorporated into the DNA of bacteria of the same strain of E. coli shows that the efficiency of a 32 P transmutation is about four times greater than that of an ionization produced at random within the same DNA. (author) [fr

  10. Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea

    KAUST Repository

    Lafi, Feras Fawzi; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

    2017-01-01

    Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth–promoting activity and environmental adaption.

  11. Draft genome sequence of Enterobacter sp. Sa187, an endophytic bacterium isolated from the desert plant Indigofera argentea

    NARCIS (Netherlands)

    Lafi, Feras F.; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged M.

    2017-01-01

    Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth-promoting activity and

  12. A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

    Science.gov (United States)

    Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

    2016-01-01

    Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS.

  13. First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974, a Butyrate-Producing Bacterium Isolated from Palm Wine.

    Science.gov (United States)

    Poehlein, Anja; Hettwer, Eva; Mohnike, Lennart; Daniel, Rolf

    2018-04-26

    Clostridium thermopalmarium is a moderate thermophilic, rod-shaped, and endospore-forming bacterium, which was isolated from palm wine in Senegal. Butyrate is produced from a broad variety of sugar substrates. Here, we present the draft genome sequence of C. thermopalmarium DSM 5974 (2.822 Mb) containing 2,665 predicted protein-encoding genes. Copyright © 2018 Poehlein et al.

  14. ‘Lactobacillus raoultii’ sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    B. Nicaise

    2018-01-01

    Full Text Available We report the isolation of a new bacterium species, ‘Lactobacillus raoultii’ strain Marseille P4006 (CSUR P4006, isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis. Keywords: Bacterial vaginosis, culturomics, emerging bacteria, human microbiota, Lactobacillus raoultii, vaginal microbiota

  15. Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air

    NARCIS (Netherlands)

    Khan, M. Tanweer; van Dijl, Jan Maarten; Harmsen, Hermie J M

    2014-01-01

    The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far

  16. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

    OpenAIRE

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Fran?oise; Loux, Valentin; Vidal, Marie; Passot, St?phanie; B?al, Catherine; Layec, S?verine; Fonseca, Fernanda

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes.

  17. Phosphorus uptake of an arbuscular mycorrhizal fungus is not effected by the biocontrol bacterium ¤Burkholderia cepacia¤

    DEFF Research Database (Denmark)

    Ravnskov, S.; Larsen, J.; Jakobsen, I.

    2002-01-01

    The biocontrol bacterium Burkholderia cepacia is known to suppress a broad range of root pathogenic fungi, while its impact on other beneficial non-target organisms such as arbuscular mycorrhizal (AM) fungi is unknown. Direct interactions between five B. cepacia strains and the AM fungus, Glomus ...

  18. Microbacter margulisiae gen. nov., sp. nov., a novel propionigenic bacterium isolated from sediments of an acid rock drainage pond

    NARCIS (Netherlands)

    Sanchez Andrea, I.; Luis Sanz, J.; Stams, A.J.M.

    2014-01-01

    A novel anaerobic propionigenic bacterium, strain ADRIT, was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6 x 1-1.7 µm), non-motile and non-spore forming rods. Cells possessed a Gram-negative cell wall structure and were vancomycin

  19. Differential proteome and cellular adhesion analyses of the probiotic bacterium Lactobacillus acidophilus NCFM grown on raffinose - an emerging prebiotic

    DEFF Research Database (Denmark)

    Celebioglu, Hasan Ufuk; Hansen, Morten Ejby; Majumder, Avishek

    2016-01-01

    Whole cell and surface proteomes were analyzed together with adhesive properties of the probiotic bacterium Lactobacillus acidophilus NCFM (NCFM) grown on the emerging prebiotic raffinose, exemplifying a synbiotic. Adhesion of NCFM to mucin and intestinal HT-29 cells increased three-fold after...

  20. Complete genome sequences of two strains of the meat spoilage bacterium Brochothrix thermosphacta isolated from ground chicken

    Science.gov (United States)

    Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT©) technology and are the first complete ...

  1. Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis

    NARCIS (Netherlands)

    van der Horst, M.A.; Stalcup, T.P.; Kaledhonkar, S.; Kumauchi, M.; Hara, M.; Xie, A.; Hellingwerf, K.J.; Hoff, W.D.

    2009-01-01

    Idiomarina loihiensis is a heterotrophic deep sea bacterium with no known photobiology. We show that light suppresses biofilm formation in this organism. The genome of I. loihiensis encodes a single photoreceptor protein: a homologue of photoactive yellow protein (PYP), a blue light receptor with

  2. Lactobacillus diolivorans sp nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage

    NARCIS (Netherlands)

    Krooneman, J; Faber, F; Alderkamp, AC; Elferink, SJHWO; Driehuis, F; Cleenwerck, [No Value; Swings, J; Gottschal, JC; Vancanneyt, M

    Inoculation of maize silage with Lactobacillus buchneri (5 x 10(5) c.f.u. g(-1) of maize silage) prior to ensiling results in the formation of aerobically stable silage. After 9 months, lactic acid bacterium counts are approximately 10(10) c.f.u. g(-1) in these treated silages. An important

  3. Thermotoga lettingae sp. nov. : a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor

    NARCIS (Netherlands)

    Balk, M.; Weijma, J.; Stams, A.J.M.

    2002-01-01

    A novel, anaerobic, non-spore-forming, mobile, Gram-negative, thermophilic bacterium, strain TMO(T), was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 degrees C with methanol as the sole substrate. The G C content of the DNA of strain TMO(T) was 39.2 molÐThe optimum pH,

  4. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment

    OpenAIRE

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant?Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, F?bio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M. P.

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.

  5. Genome Sequence of the Enterobacter mori Type Strain, LMG 25706, a Pathogenic Bacterium of Morus alba L. ▿

    Science.gov (United States)

    Zhu, Bo; Zhang, Guo-Qing; Lou, Miao-Miao; Tian, Wen-Xiao; Li, Bin; Zhou, Xue-Ping; Wang, Guo-Feng; Liu, He; Xie, Guan-Lin; Jin, Gu-Lei

    2011-01-01

    Enterobacter mori is a plant-pathogenic enterobacterium responsible for the bacterial wilt of Morus alba L. Here we present the draft genome sequence of the type strain, LMG 25706. To the best of our knowledge, this is the first genome sequence of a plant-pathogenic bacterium in the genus Enterobacter. PMID:21602328

  6. Characterization of cytochrome P450 monooxygenase CYP154H1 from the thermophilic soil bacterium Thermobifida fusca

    NARCIS (Netherlands)

    Schallmey, Anett; den Besten, Gijs; Teune, Ite G. P.; Kembaren, Roga F.; Janssen, Dick B.

    Cytochrome P450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. We have cloned the gene for a new cytochrome P450 monooxygenase, named CYP154H1, from the moderately thermophilic soil bacterium Thermobifida fusca. The

  7. Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea

    KAUST Repository

    Lafi, Feras Fawzi

    2017-02-17

    Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth–promoting activity and environmental adaption.

  8. Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site.

    Science.gov (United States)

    Lim, Yan-Lue; Ee, Robson; Yong, Delicia; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

    2015-11-20

    Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost

    Science.gov (United States)

    Tsujimoto, Yoshiyuki; Saito, Ryo; Sahara, Takehiko; Kimura, Nobutada; Tsuruoka, Naoki; Shigeri, Yasushi

    2017-01-01

    ABSTRACT Caenibacillus caldisaponilyticus B157T (= NBRC 111400T = DSM 101100T), in the family Sporolactobacillaceae, was isolated from acidulocompost as a thermophilic and phospholipid-degrading bacterium. Here, we report the 3.36-Mb draft genome sequence, with a G+C content of 51.8%, to provide the genetic information coding for phospholipases. PMID:28360164

  10. Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.

    Science.gov (United States)

    da Silva, Fábio Daniel Florêncio; Lima, Alex Ranieri Jerônimo; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Dall'Agnol, Leonardo Teixeira; Baraúna, Anna Rafaella Ferreira; Martins, Luisa Carício; Oliveira, Karol Guimarães; de Lima, Clayton Pereira Silva; Nunes, Márcio Roberto Teixeira; Vianez-Júnior, João Lídio Silva Gonçalves; Gonçalves, Evonnildo Costa

    2016-05-19

    Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here. Copyright © 2016 da Silva et al.

  11. Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria

    OpenAIRE

    da Silva, F?bio Daniel Flor?ncio; Lima, Alex Ranieri Jer?nimo; Moraes, Pablo Henrique Gon?alves; Siqueira, Andrei Santos; Dall?Agnol, Leonardo Teixeira; Bara?na, Anna Rafaella Ferreira; Martins, Luisa Car?cio; Oliveira, Karol Guimar?es; de Lima, Clayton Pereira Silva; Nunes, M?rcio Roberto Teixeira; Vianez-J?nior, Jo?o L?dio Silva Gon?alves; Gon?alves, Evonnildo Costa

    2016-01-01

    Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here.

  12. Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacterium Dinoroseobacter shibae

    Czech Academy of Sciences Publication Activity Database

    Piwosz, Kasia; Kaftan, David; Dean, Jason; Šetlík, Jiří; Koblížek, Michal

    2018-01-01

    Roč. 20, č. 2 (2018), s. 724-733 ISSN 1758-2229 R&D Projects: GA MŠk(CZ) LO1416 Institutional support: RVO:61388971 Keywords : PHOTOSYNTHETIC BACTERIUM * LEUCINE INCORPORATION * SOLAR-RADIATION Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.363, year: 2016

  13. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

    Science.gov (United States)

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

    2016-03-03

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. Copyright © 2016 Meneghel et al.

  14. ["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum].

    Science.gov (United States)

    Zhilina, T N; Zavarzina, D G; Kolganova, T V; Turova, T P; Zavarzin, G A

    2005-01-01

    From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum."

  15. Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures

    DEFF Research Database (Denmark)

    Nazir, Rashid; Hansen, Martin A.; Sorensen, Soren

    2012-01-01

    Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately...

  16. Successful split thickness skin grafting in the presence of heavy colonisation with rare bacterium Aeromonas hydrophila: A case report

    Directory of Open Access Journals (Sweden)

    S. Koschel

    2017-09-01

    Discussion: Contemporary literature is yet to make the distinction between colonisation and infection of this bacterium, with clinicians relying solely on the presence of infective stigmata and serum analysis. However, this is a critically important distinction when ascertaining the likelihood of success of wound healing.

  17. Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

    Directory of Open Access Journals (Sweden)

    Zhiping Wang

    Full Text Available Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

  18. Enhanced bactericidal potency of nanoliposomes by modification of the fusion activity between liposomes and bacterium

    Directory of Open Access Journals (Sweden)

    Ma YF

    2013-06-01

    Full Text Available Yufan Ma,1 Zhao Wang,1,2 Wen Zhao,1 Tingli Lu,1 Rutao Wang,1,2 Qibing Mei,1 Tao Chen1–3 1Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, People's Republic of China; 2Shaanxi Liposome Research Center, Xi'an, Shaanxi, People's Republic of China; 3Xi'an Libang Pharmaceuticals Co, Ltd, Xi'an, People's Republic of China Background: Pseudomonas aeruginosa represents a good model of antibiotic resistance. These organisms have an outer membrane with a low level of permeability to drugs that is often combined with multidrug efflux pumps, enzymatic inactivation of the drug, or alteration of its molecular target. The acute and growing problem of antibiotic resistance of Pseudomonas to conventional antibiotics made it imperative to develop new liposome formulations to overcome these mechanisms, and investigate the fusion between liposome and bacterium. Methods: The rigidity, stability and charge properties of phospholipid vesicles were modified by varying the cholesterol, 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE, and negatively charged lipids 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol sodium salt (DMPG, 1,2-dimyristoyl-sn-glycero-3-phopho-L-serine sodium salt (DMPS, 1,2-dimyristoyl-sn-glycero-3-phosphate monosodium salt (DMPA, nature phosphatidylserine sodium salt from brain and nature phosphatidylinositol sodium salt from soybean concentrations in liposomes. Liposomal fusion with intact bacteria was monitored using a lipid-mixing assay. Results: It was discovered that the fluid liposomes-bacterium fusion is not dependent on liposomal size and lamellarity. A similar degree of fusion was observed for liposomes with a particle size from 100 to 800 nm. The fluidity of liposomes is an essential pre-request for liposomes fusion with bacteria. Fusion was almost completely inhibited by incorporation of cholesterol into fluid liposomes. The increase in the

  19. Sphaerotilus natans, a neutrophilic iron-related filamentous bacterium : mechanisms of uranium scavenging

    International Nuclear Information System (INIS)

    Seder-Colomina, Marina

    2014-01-01

    Heavy metals and radionuclides are present in some ecosystems worldwide due to natural contaminations or anthropogenic activities. The use of microorganisms to restore those polluted ecosystems, a process known as bioremediation, is of increasing interest, especially under near-neutral pH conditions. Iron minerals encrusting neutrophilic iron-related bacteria, especially Bacterio-genic Iron Oxides (BIOS), have a poorly crystalline structure, which in addition to their large surface area and reactivity make them excellent scavengers for inorganic pollutants. In this PhD work we studied the different mechanisms of uranium scavenging by the neutrophilic bacterium Sphaerotilus natans, chosen as a model bacterium for iron-related sheath-forming filamentous microorganisms. S. natans can grow as single cells and filaments. The latter were used to investigate U(VI) bio-sorption and U(VI) sorption onto BIOS. In addition, uranium sorption onto the abiotic analogues of such iron minerals was assessed. In order to use S. natans filaments for U(VI) scavenging, it was necessary to identify factors inducing S. natans filamentation. The influence of oxygen was ascertained by using molecular biology techniques and our results revealed that while saturated oxygen conditions resulted in single cell growth, a moderate oxygen depletion to ∼ 3 mg O 2 .L -1 led to the desired filamentous growth of S. natans. BIOS attached to S. natans filaments as well as the abiotic analogues were analysed by XAS at Fe K-edge. Both materials were identified as amorphous iron(III) phosphates with a small component of Fe(II), with a high reactivity towards scavenging of inorganic pollutants. In addition, EXAFS at the U LIII-edge revealed a common structure for the O shells, while those for P, Fe and C were different for each sorbent. An integrated approach combining experimental techniques and speciation calculations made it possible to describe U(VI) adsorption isotherms by using a surface complexation

  20. Cold adaptation of the mononuclear molybdoenzyme periplasmic nitrate reductase from the Antarctic bacterium Shewanella gelidimarina

    International Nuclear Information System (INIS)

    Simpson, Philippa J.L.; Codd, Rachel

    2011-01-01

    Highlights: ► Cold-adapted phenotype of NapA from the Antarctic bacterium Shewanella gelidimarina. ► Protein homology model of NapA from S. gelidimarina and mesophilic homologue. ► Six amino acid residues identified as lead candidates governing NapA cold adaptation. ► Molecular-level understanding of designing cool-temperature in situ oxyanion sensors. -- Abstract: The reduction of nitrate to nitrite is catalysed in bacteria by periplasmic nitrate reductase (Nap) which describes a system of variable protein subunits encoded by the nap operon. Nitrate reduction occurs in the NapA subunit, which contains a bis-molybdopterin guanine dinucleotide (Mo–MGD) cofactor and one [4Fe–4S] iron–sulfur cluster. The activity of periplasmic nitrate reductase (Nap) isolated as native protein from the cold-adapted (psychrophilic) Antarctic bacterium Shewanella gelidimarina (Nap Sgel ) and middle-temperature adapted (mesophilic) Shewanella putrefaciens (Nap Sput ) was examined at varied temperature. Irreversible deactivation of Nap Sgel and Nap Sput occurred at 54.5 and 65 °C, respectively. When Nap Sgel was preincubated at 21–70 °C for 30 min, the room-temperature nitrate reductase activity was maximal and invariant between 21 and 54 °C, which suggested that Nap Sgel was poised for optimal catalysis at modest temperatures and, unlike Nap Sput , did not benefit from thermally-induced refolding. At 20 °C, Nap Sgel reduced selenate at 16% of the rate of nitrate reduction. Nap Sput did not reduce selenate. Sequence alignment showed 46 amino acid residue substitutions in Nap Sgel that were conserved in NapA from mesophilic Shewanella, Rhodobacter and Escherichia species and could be associated with the Nap Sgel cold-adapted phenotype. Protein homology modeling of Nap Sgel using a mesophilic template with 66% amino acid identity showed the majority of substitutions occurred at the protein surface distal to the Mo–MGD cofactor. Two mesophilic ↔ psychrophilic

  1. Evaluation of dna extraction methods of the Salmonella sp. bacterium in artificially infected chickens eggs

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    Ana Cristina dos Reis Ferreira

    2015-06-01

    Full Text Available ABSTRACT. Ferreira A.C.dosR. & dos Santos B.M. [Evaluation of dna extraction methods of the Salmonella sp. bacterium in artificially infected chickens eggs.] Avaliação de três métodos de extração de DNA de Salmonella sp. em ovos de galinhas contaminados artificialmente. Revista Brasileira de Medicina Veterinária, 37(2:115-119, 2015. Departamento de Veterinária, Universidade Federal de Viçosa, Campus Universitário, Av. Peter Henry Rolfs, s/n, Viçosa, MG 36571-000, Brasil. E-mail: bmsantos@ufv.br The present study evaluated the efficiency of different protocols for the genomic DNA extraction of Salmonella bacteria in chicken eggs free of specific pathogens – SPF. Seventy-five eggs were used and divided into five groups with fifteen eggs each. Three of the five groups of eggs were inoculated with enteric Salmonella cultures. One of the five groups was inoculated with Escherichia coli bacterium culture. And another group of eggs was the negative control that received saline solution 0.85% infertile. The eggs were incubated on a temperature that varied from 20 to 25°C during 24, 48 and 72 hours. Five yolks of each group were collected every 24 hours. These yolks were homogenized and centrifuged during 10 minutes. The supernatant was rejected. After the discard, PBS ph 7.2 was added and centrifuged again. The sediment obtained of each group was used for the extraction of bacterial genomic DNA. Silica particles and a commercial kit were utilized as the extraction methods. The extracted DNA was kept on a temperature of 20°C until the evaluation through PCR. The primers utilized were related with the invA gene and they were the following: 5’ GTA AAA TTA TCG CCA CGT TCG GGC AA 3’ and 5’ TCA TCG CAC CGT CAA AGG AAC C 3’. The amplification products were visualized in transilluminator with ultraviolet light. The obtained results through the bacterial DNA extractions demonstrated that the extraction method utilizing silica particles was

  2. Functional analyses of multiple lichenin-degrading enzymes from the rumen bacterium Ruminococcus albus 8.

    Science.gov (United States)

    Iakiviak, Michael; Mackie, Roderick I; Cann, Isaac K O

    2011-11-01

    Ruminococcus albus 8 is a fibrolytic ruminal bacterium capable of utilization of various plant cell wall polysaccharides. A bioinformatic analysis of a partial genome sequence of R. albus revealed several putative enzymes likely to hydrolyze glucans, including lichenin, a mixed-linkage polysaccharide of glucose linked together in β-1,3 and β-1,4 glycosidic bonds. In the present study, we demonstrate the capacity of four glycoside hydrolases (GHs), derived from R. albus, to hydrolyze lichenin. Two of the genes encoded GH family 5 enzymes (Ra0453 and Ra2830), one gene encoded a GH family 16 enzyme (Ra0505), and the last gene encoded a GH family 3 enzyme (Ra1595). Each gene was expressed in Escherichia coli, and the recombinant protein was purified to near homogeneity. Upon screening on a wide range of substrates, Ra0453, Ra2830, and Ra0505 displayed different hydrolytic properties, as they released unique product profiles. The Ra1595 protein, predicted to function as a β-glucosidase, preferred cleavage of a nonreducing end glucose when linked by a β-1,3 glycosidic bond to the next glucose residue. The major product of Ra0505 hydrolysis of lichenin was predicted to be a glucotriose that was degraded only by Ra0453 to glucose and cellobiose. Most importantly, the four enzymes functioned synergistically to hydrolyze lichenin to glucose, cellobiose, and cellotriose. This lichenin-degrading enzyme mix should be of utility as an additive to feeds administered to monogastric animals, especially those high in fiber.

  3. Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.

    Science.gov (United States)

    Hong, Pei-Ying; Iakiviak, Michael; Dodd, Dylan; Zhang, Meiling; Mackie, Roderick I; Cann, Isaac

    2014-04-01

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

  4. [Isolation and identification of Mn oxidizing bacterium Aminobacter sp. H1 and its oxidation mechanism].

    Science.gov (United States)

    Yan, Ping; Jiang, Li-Ying; Chen, Jian-Meng; He, Zhi-Min; Xiao, Shao-Dan; Jiang, Yi-Feng

    2014-04-01

    A bacterium with high manganese oxidizing activity was isolated from a biological manganese removal filter and named as H1. Based on its characteristics and the analysis of 16S rDNA sequence, the strain H1 belonged to the genus Aminobacter sp. and its manganese oxidizing ability had never been reported. In this paper, the microbiologic properties of the strain H1, the manganese oxidation mechanisms and characteristics of biogenic manganese oxides were investigated. The results showed that the maximal tolerant Mn concentration of strain H1 was 50 mmol x L(-1), and Mn(II) could be completely removed by strain H1 when the concentration was lower than 10 mmol x L(-1). Strain H1 could oxidize Mn2+ by both the production of manganese oxidizing activity factor and alkaline metabolites during growth, which were synthesized in the cell and then secreted into extracellular culture medium. During the oxidation process, the intermediate of soluble Mn(III) was detected. SEM showed that the biogenic manganese oxides were amorphous and poorly-crystalline, and it closely combined with bacteria. The components of the biogenic manganese oxides produced by strain H1 were identified as MnCO3, MnOOH, Mn3O4 and MnO2 by XRD, XPS and SEM-EDX.

  5. Novel heterotrophic nitrogen removal and assimilation characteristic of the newly isolated bacterium Pseudomonas stutzeri AD-1.

    Science.gov (United States)

    Qing, Hui; Donde, Oscar Omondi; Tian, Cuicui; Wang, Chunbo; Wu, Xingqiang; Feng, Shanshan; Liu, Yao; Xiao, Bangding

    2018-04-18

    AD-1, an aerobic denitrifier, was isolated from activated sludge and identified as Pseudomonas stutzeri. AD-1 completely removed NO 3 - or NO 2 - and removed 99.5% of NH 4 + during individual culturing in a broth medium with an initial nitrogen concentration of approximately 50 mg L -1 . Results showed that larger amounts of nitrogen were removed through assimilation by the bacteria. And when NH 4 + was used as the sole nitrogen source in the culture medium, neither NO 2 - nor NO 3 - was detected, thus indicating that AD-1 may not be a heterotrophic nitrifier. Only trace amount of N 2 O was detected during the denitrification process. Single factor experiments indicated that the optimal culture conditions for AD-1 were: a carbon-nitrogen ratio (C/N) of 15, a temperature of 25°C and sodium succinate or glucose as a carbon source. In conclusion, due to the ability of AD-1 to utilize nitrogen of different forms with high efficiencies for its growth while producing only trace emissions of N 2 O, the bacterium had outstanding potential to use in the bioremediation of high-nitrogen-containing wastewaters. Meanwhile, it may also be a proper candidate for biotreatment of high concentration organic wastewater. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  6. Enterobacter siamensis sp. nov., a transglutaminase-producing bacterium isolated from seafood processing wastewater in Thailand.

    Science.gov (United States)

    Khunthongpan, Suwannee; Bourneow, Chaiwut; H-Kittikun, Aran; Tanasupawat, Somboon; Benjakul, Soottawat; Sumpavapol, Punnanee

    2013-01-01

    A novel strain of Enterobacter, C2361(T), a Gram-negative, non-spore-forming, rod-shaped and facultative anaerobic bacterium with the capability to produce transglutaminase, was isolated from seafood processing wastewater collected from a treatment pond of a seafood factory in Songkhla Province, Thailand. Phylogenetic analyses and phenotypic characteristics, including chemotaxonomic characteristics, showed that the strain was a member of the genus Enterobacter. The 16S rRNA gene sequence similarities between strain C2361(T) and Enterobacter cloacae subsp. cloacae ATCC 13047(T) and Enterobacter cloacae subsp. dissolvens LMG 2683(T) were 97.5 and 97.5%, respectively. Strain C2361(T) showed a low DNA-DNA relatedness with the above-mentioned species. The major fatty acids were C16:0, C17:0cyclo and C14:0. The DNA G+C content was 53.0 mol%. On the basis of the polyphasic evidence gathered in this study, it should be classified as a novel species of the genus Enterobacter for which the name Enterobacter siamensis sp. nov. is proposed. The type strain is C2361(T) (= KCTC 23282(T) = NBRC 107138(T)).

  7. A novel radio-tolerant astaxanthin-producing bacterium reveals a new astaxanthin derivative: astaxanthin dirhamnoside.

    Science.gov (United States)

    Asker, Dalal; Awad, Tarek S; Beppu, Teruhiko; Ueda, Kenji

    2012-01-01

    Astaxanthin is a red ketocarotenoid that exhibits extraordinary health-promoting activities such as antioxidant, anti-inflammatory, antitumor, and immune booster. The recent discovery of the beneficial roles of astaxanthin against many degenerative diseases such as cancers, heart diseases, and exercise-induced fatigue has raised its market demand as a nutraceutical and medicinal ingredient in aquaculture, food, and pharmaceutical industries. To satisfy the growing demand for this high-value nutraceuticals ingredient and consumer interest in natural products, many research efforts are being made to discover novel microbial producers with effective biotechnological production of astaxanthin. Using a rapid screening method based on 16S rRNA gene, and effective HPLC-Diodearray-MS methods for carotenoids analysis, we succeeded to isolate a unique astaxanthin-producing bacterium (strain TDMA-17(T)) that belongs to the family Sphingomonadaceae (Asker et al., Appl Microbiol Biotechnol 77: 383-392, 2007). In this chapter, we provide a detailed description of effective HPLC-Diodearray-MS methods for rapid analysis and identification of the carotenoids produced by strain TDMA-17(T). We also describe the methods of isolation and identification for a novel bacterial carotenoid (astaxanthin derivative), a major carotenoid that is produced by strain TDMA-17(T). Finally, we describe the polyphasic taxonomic analysis of strain TDMA-17(T) and the description of a novel species belonging to genus Sphingomonas.

  8. Sorption of ferrous iron by EPS from the acidophilic bacterium Acidiphilium Sp.: A mechanism proposal

    Energy Technology Data Exchange (ETDEWEB)

    Tapia, J.M.; MuNoz, J.; Gonzlez, F.; Blazquez, M.L.; Ballester, A.

    2016-07-01

    The aim of this work was to assess the uptake of Fe(II) by extracellular polymeric substances (EPS) from the acidophilic bacterium Acidiphillium 3.2Sup(5). These EPS were extracted using EDTA. EPS of A. 3.2Sup(5) loaded in sorption tests with Fe(II), were characterized using the following experimental techniques: scanning electron microscopy (SEM) with energy dispersive X-ray microanalysis (EDX), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The experimental results indicate that EPS adsorb ferrous iron according to Freundlich model with a metal sorption uptake of K = 1.14 mg1−1/n L1/n g−1 and a sorption intensity of 1/n = 1.26. In addition, ferrous iron sorption by EPS took place by preferential interaction with the carboxyl group which promotes the formation of ferrous iron oxalates (FeC2O4). Since the interaction reaction was reversible (Log K = 0.77 ± 0.33), that means that the cation sorption can be reversed at convenience. (Author)

  9. The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4.

    Directory of Open Access Journals (Sweden)

    Jin Duan

    Full Text Available The plant growth-promoting bacterium (PGPB Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated "housekeeping" genes (16S rRNA, gyrB, rpoB and rpoD of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

  10. Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

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    Alvaro Banderas

    2013-08-01

    Full Text Available The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS, we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process.

  11. Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

    Science.gov (United States)

    Banderas, Alvaro; Guiliani, Nicolas

    2013-01-01

    The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS) cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS), we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME) to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase) might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process. PMID:23959118

  12. Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393

    KAUST Repository

    Hong, Pei-Ying

    2014-01-24

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

  13. Direct bioconversion of brown algae into ethanol by thermophilic bacterium Defluviitalea phaphyphila.

    Science.gov (United States)

    Ji, Shi-Qi; Wang, Bing; Lu, Ming; Li, Fu-Li

    2016-01-01

    Brown algae are promising feedstocks for biofuel production with inherent advantages of no structural lignin, high growth rate, and no competition for land and fresh water. However, it is difficult for one microorganism to convert all components of brown algae with different oxidoreduction potentials to ethanol. Defluviitalea phaphyphila Alg1 is the first characterized thermophilic bacterium capable of direct utilization of brown algae. Defluviitalea phaphyphila Alg1 can simultaneously utilize mannitol, glucose, and alginate to produce ethanol, and high ethanol yields of 0.47 g/g-mannitol, 0.44 g/g-glucose, and 0.3 g/g-alginate were obtained. A rational redox balance system under obligate anaerobic condition in fermenting brown algae was revealed in D. phaphyphila Alg1 through genome and redox analysis. The excess reducing equivalents produced from mannitol metabolism were equilibrated by oxidizing forces from alginate assimilation. Furthermore, D. phaphyphila Alg1 can directly utilize unpretreated kelp powder, and 10 g/L of ethanol was accumulated within 72 h with an ethanol yield of 0.25 g/g-kelp. Microscopic observation further demonstrated the deconstruction process of brown algae cell by D. phaphyphila Alg1. The integrated biomass deconstruction system of D. phaphyphila Alg1, as well as its high ethanol yield, provided us an excellent alternative for brown algae bioconversion at elevated temperature.

  14. Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137

    Science.gov (United States)

    Powell, Ryan J.

    2013-01-01

    Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

  15. Identification and characterization of a core fucosidase from the bacterium Elizabethkingia meningoseptica.

    Science.gov (United States)

    Li, Tiansheng; Li, Mengjie; Hou, Linlin; Guo, Yameng; Wang, Lei; Sun, Guiqin; Chen, Li

    2018-01-26

    All reported α-l-fucosidases catalyze the removal of nonreducing terminal l-fucoses from oligosaccharides or their conjugates, while having no capacity to hydrolyze core fucoses in glycoproteins directly. Here, we identified an α-fucosidase from the bacterium Elizabethkingia meningoseptica with catalytic activity against core α-1,3-fucosylated substrates, and we named it core fucosidase I (cFase I). Using site-specific mutational analysis, we found that three acidic residues (Asp-242, Glu-302, and Glu-315) in the predicted active pocket are critical for cFase I activity, with Asp-242 and Glu-315 acting as a pair of classic nucleophile and acid/base residues and Glu-302 acting in an as yet undefined role. These findings suggest a catalytic mechanism for cFase I that is different from known α-fucosidase catalytic models. In summary, cFase I exhibits glycosidase activity that removes core α-1,3-fucoses from substrates, suggesting cFase I as a new tool for glycobiology, especially for studies of proteins with core fucosylation. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Purification and Characterization of Catalase from Marine Bacterium Acinetobacter sp. YS0810

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    Xinhua Fu

    2014-01-01

    Full Text Available The catalase from marine bacterium Acinetobacter sp. YS0810 (YS0810CAT was purified and characterized. Consecutive steps were used to achieve the purified enzyme as follows: ethanol precipitation, DEAE Sepharose ion exchange, Superdex 200 gel filtration, and Resource Q ion exchange. The active enzyme consisted of four identical subunits of 57.256 kDa. It showed a Soret peak at 405 nm, indicating the presence of iron protoporphyrin IX. The catalase was not apparently reduced by sodium dithionite but was inhibited by 3-amino-1,2,4-triazole, hydroxylamine hydrochloride, and sodium azide. Peroxidase-like activity was not found with the substrate o-phenylenediamine. So the catalase was determined to be a monofunctional catalase. N-terminal amino acid of the catalase analysis gave the sequence SQDPKKCPVTHLTTE, which showed high degree of homology with those of known catalases from bacteria. The analysis of amino acid sequence of the purified catalase by matrix-assisted laser desorption ionization time-of-flight mass spectrometry showed that it was a new catalase, in spite of its high homology with those of known catalases from other bacteria. The catalase showed high alkali stability and thermostability.

  17. Experimental Infection and Detection of Necrotizing Hepatopancreatitis Bacterium in the American Lobster Homarus americanus

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    Luz A. Avila-Villa

    2012-01-01

    Full Text Available Necrotizing hepatopancreatitis bacterium (NHPB is an obligated intracellular bacteria causing severe hepatopancreatic damages and mass mortalities in penaeid shrimp. The worldwide distribution of penaeid shrimp as alien species threatens the life cycle of other crustacean species. The aim of the experiment was to evaluate the possibility of experimentally infecting the American lobster (Homarus americanus with NHPB extracted from shrimp hepatopancreas. Homogenates from infected shrimp were fed by force to lobsters. Other group of lobsters was fed with homogenates of NHPB-free hepatopancreas. After the 15th day from initial inoculation, the presence of NHPB was detected by polymerase chain reaction in feces and hepatopancreas from lobsters inoculated with infected homogenates. Necrotized spots were observed in the surface of lobster hepatopancreas. In contrast, lobsters fed on NHPB-free homogenates resulted negative for NHPB. Evidence suggests the plasticity of NHPB which can infect crustacean from different species and inhabiting diverse latitudes. Considering the results, the American lobster could be a good candidate to maintain available NHPB in vivo.

  18. Experimental Infection and Detection of Necrotizing Hepatopancreatitis Bacterium in the American Lobster Homarus americanus

    Science.gov (United States)

    Avila-Villa, Luz A.; Gollas-Galván, Teresa; Martínez-Porchas, Marcel; Mendoza-Cano, Fernando; Hernández-López, Jorge

    2012-01-01

    Necrotizing hepatopancreatitis bacterium (NHPB) is an obligated intracellular bacteria causing severe hepatopancreatic damages and mass mortalities in penaeid shrimp. The worldwide distribution of penaeid shrimp as alien species threatens the life cycle of other crustacean species. The aim of the experiment was to evaluate the possibility of experimentally infecting the American lobster (Homarus americanus) with NHPB extracted from shrimp hepatopancreas. Homogenates from infected shrimp were fed by force to lobsters. Other group of lobsters was fed with homogenates of NHPB-free hepatopancreas. After the 15th day from initial inoculation, the presence of NHPB was detected by polymerase chain reaction in feces and hepatopancreas from lobsters inoculated with infected homogenates. Necrotized spots were observed in the surface of lobster hepatopancreas. In contrast, lobsters fed on NHPB-free homogenates resulted negative for NHPB. Evidence suggests the plasticity of NHPB which can infect crustacean from different species and inhabiting diverse latitudes. Considering the results, the American lobster could be a good candidate to maintain available NHPB in vivo. PMID:22645497

  19. Bidirectional gene sequences with similar homology to functional proteins of alkane degrading bacterium pseudomonas fredriksbergensis DNA

    International Nuclear Information System (INIS)

    Megeed, A.A.

    2011-01-01

    The potential for two overlapping fragments of DNA from a clone of newly isolated alkanes degrading bacterium Pseudomonas frederiksbergensis encoding sequences with similar homology to two parts of functional proteins is described. One strand contains a sequence with high homology to alkanes monooxygenase (alkB), a member of the alkanes hydroxylase family, and the other strand contains a sequence with some homology to alcohol dehydrogenase gene (alkJ). Overlapping of the genes on opposite strands has been reported in eukaryotic species, and is now reported in a bacterial species. The sequence comparisons and ORFS results revealed that the regulation and the genes organization involved in alkane oxidation represented in Pseudomonas frederiksberghensis varies among the different known alkane degrading bacteria. The alk gene cluster containing homologues to the known alkane monooxygenase (alkB), and rubredoxin (alkG) are oriented in the same direction, whereas alcohol dehydrogenase (alkJ) is oriented in the opposite direction. Such genomes encode messages on both strands of the DNA, or in an overlapping but different reading frames, of the same strand of DNA. The possibility of creating novel genes from pre-existing sequences, known as overprinting, which is a widespread phenomenon in small viruses. Here, the origin and evolution of the gene overlap to bacteriophages belonging to the family Microviridae have been investigated. Such a phenomenon is most widely described in extremely small genomes such as those of viruses or small plasmids, yet here is a unique phenomenon. (author)

  20. The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

    Science.gov (United States)

    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R.

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup. PMID:23516524

  1. Colwellia polaris sp. nov., a psychrotolerant bacterium isolated from Arctic sea ice.

    Science.gov (United States)

    Zhang, De-Chao; Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Zhou, Pei-Jin; Zhou, Yu-Guang

    2008-08-01

    A novel psychrotolerant, Gram-negative, aerobic bacterium, designated strain 537T, was isolated from sea-ice samples from the Arctic. Strain 537T was able to grow at 4-26 degrees C, with optimum growth occurring at 20-21 degrees C. Strain 537T had Q-8 as the major respiratory quinone and contained iso-C15:0 2-OH and/or C16:1 omega7c (22.95 %), C15:1 (17.64 %) and C17:1 omega8c (13.74 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 38.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 537T formed a coherent cluster within the genus Colwellia. The highest level of 16S rRNA gene sequence similarity (97.5 %) exhibited by strain 537T was obtained with respect to the type strain of Colwellia aestuarii. On the basis of phenotypic, chemotaxonomic and phylogenetic properties and DNA-DNA relatedness data, strain 537T represents a novel species of the genus Colwellia, for which the name Colwellia polaris sp. nov. is proposed. The type strain is 537T (=CGMCC 1.6132T =JCM 13952T).

  2. Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments.

    Science.gov (United States)

    Vasconcellos, Rafael L F; Santos, Suikinai Nobre; Zucchi, Tiago Domingues; Silva, Fábio Sérgio Paulino; Souza, Danilo Tosta; Melo, Itamar Soares

    2017-10-01

    Strain CMAA 1215 T , a Gram-reaction-negative, aerobic, catalase positive, polarly flagellated, motile, rod-shaped (0.5-0.8 × 1.3-1.9 µm) bacterium, was isolated from mangrove sediments, Cananéia Island, Brazil. Analysis of the 16S rRNA gene sequences showed that strain CMAA 1215 T forms a distinct phyletic line within the Pseudomonas putida subclade, being closely related to P. plecoglossicida ATCC 700383 T , P. monteilii NBRC 103158 T , and P. taiwanensis BCRC 17751 T of sequence similarity of 98.86, 98.73, and 98.71%, respectively. Genomic comparisons of the strain CMAA 1215 T with its closest phylogenetic type strains using average nucleotide index (ANI) and DNA:DNA relatedness approaches revealed 84.3-85.3% and 56.0-63.0%, respectively. A multilocus sequence analysis (MLSA) performed concatenating 16S rRNA, gyrB and rpoB gene sequences from the novel species was related with Pseudomonas putida subcluster and formed a new phylogenetic lineage. The phenotypic, physiological, biochemical, and genetic characteristics support the assignment of CMAA 1215 T to the genus Pseudomonas, representing a novel species. The name Pseudomonas aestus sp.nov. is proposed, with CMAA 1215 T (=NRRL B-653100 T  = CBMAI 1962 T ) as the type strain.

  3. Cloning, sequencing, and expression of dnaK-operon proteins from the thermophilic bacterium Thermus thermophilus.

    Science.gov (United States)

    Osipiuk, J; Joachimiak, A

    1997-09-12

    We propose that the dnaK operon of Thermus thermophilus HB8 is composed of three functionally linked genes: dnaK, grpE, and dnaJ. The dnaK and dnaJ gene products are most closely related to their cyanobacterial homologs. The DnaK protein sequence places T. thermophilus in the plastid Hsp70 subfamily. In contrast, the grpE translated sequence is most similar to GrpE from Clostridium acetobutylicum, a Gram-positive anaerobic bacterium. A single promoter region, with homology to the Escherichia coli consensus promoter sequences recognized by the sigma70 and sigma32 transcription factors, precedes the postulated operon. This promoter is heat-shock inducible. The dnaK mRNA level increased more than 30 times upon 10 min of heat shock (from 70 degrees C to 85 degrees C). A strong transcription terminating sequence was found between the dnaK and grpE genes. The individual genes were cloned into pET expression vectors and the thermophilic proteins were overproduced at high levels in E. coli and purified to homogeneity. The recombinant T. thermophilus DnaK protein was shown to have a weak ATP-hydrolytic activity, with an optimum at 90 degrees C. The ATPase was stimulated by the presence of GrpE and DnaJ. Another open reading frame, coding for ClpB heat-shock protein, was found downstream of the dnaK operon.

  4. Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

    Science.gov (United States)

    Walker, Graham C.; Finan, Turlough M.; Mengoni, Alessio; Griffitts, Joel S.

    2018-01-01

    Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium Sinorhizobium meliloti, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons. Ten percent of chromosomal genes from diverse functional categories are shown to genetically interact with pSymA and pSymB. These results demonstrate the pervasive robustness provided by the extrachromosomal replicons, which is further supported by constraint-based metabolic modeling. A comprehensive picture of core S. meliloti metabolism was generated through a Tn-seq-guided in silico metabolic network reconstruction, producing a core network encompassing 726 genes. This integrated approach facilitated functional assignments for previously uncharacterized genes, while also revealing that Tn-seq alone missed over a quarter of wild-type metabolism. This work highlights the many functional dependencies and epistatic relationships that may arise between bacterial replicons and across a genome, while also demonstrating how Tn-seq and metabolic modeling can be used together to yield insights not obtainable by either method alone. PMID:29672509

  5. Physiological role of vitamin B12 in a methanol-utilizing bacterium, Protaminobacter ruber

    International Nuclear Information System (INIS)

    Shimizu, S.; Ueda, S.; Sato, K.

    1984-01-01

    The methanol-utilizing bacterium Protaminobacter ruber is able to produce a relatively large amount of vitamin B 12 . The present study aims at the physiological role of vitamin B 12 in P. ruber. P. ruber was found to contain the two sequential reactions of glutamate mutase with β-methylaspartase and propionyl-CoA carboxylase with methylmalonyl-CoA mutase. Considering the presence of these enzyme systems and the reaction from mesaconyl-CoA to glyoxylate and propionyl-CoA, it could be considered that the formation of glutamate from α-ketoglutarate, the conversion of glutamate to mesaconate via β-methylaspartate, the activation of mesaconate with CoA to form mesaconyl-CoA, the cleavage of mesaconyl-CoA to glyoxylate and propionyl-CoA, the carboxylation of propionyl-CoA to methylmalonyl-CoA, and the isomerization of methylmalonyl-CoA to succinyl-CoA require cobalamine as a cofactor. 29 refs., 2 figs., 2 tabs

  6. Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

    Directory of Open Access Journals (Sweden)

    Alexander B. Chase

    2017-11-01

    Full Text Available Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. The response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment.

  7. Microbial deposition of gold nanoparticles by the metal-reducing bacterium Shewanella algae

    International Nuclear Information System (INIS)

    Konishi, Y.; Tsukiyama, T.; Tachimi, T.; Saitoh, N.; Nomura, T.; Nagamine, S.

    2007-01-01

    Microbial reduction and deposition of gold nanoparticles was achieved at 25 deg. C over the pH range 2.0-7.0 using the mesophilic bacterium Shewanella algae in the presence of H 2 as the electron donor. The reductive deposition of gold by the resting cells of S. algae was a fast process: 1 mM AuCl 4 - ions were completely reduced to elemental gold within 30 min. At a solution pH of 7, gold nanoparticles 10-20 nm in size were deposited in the periplasmic space of S. algae cells. At pH 2.8, gold nanoparticles 15-200 nm in size were deposited on the bacterial cells, and the biogenic nanoparticles exhibited a variety of shapes that included nanotriangles: in particular, single crystalline gold nanotriangles 100-200 nm in size were microbially deposited. At a solution pH of 2.0, gold nanoparticles about 20 nm in size were deposited intracellularly, and larger gold particles approximately 350 nm in size were deposited extracellularly. The solution pH was an important factor in controlling the morphology of the biogenic gold particles and the location of gold deposition. Microbial deposition of gold nanoparticles is potentially attractive as an environmentally friendly alternative to conventional methods

  8. Interactions of protamine with the marine bacterium, Pseudoalteromonas sp. NCIMB 2021.

    Science.gov (United States)

    Pustam, A; Smith, C; Deering, C; Grosicki, K M T; Leng, T Y; Lin, S; Yang, J; Pink, D; Gill, T; Graham, L; Derksen, D; Bishop, C; Demont, M E; Wyeth, R C; Smith-Palmer, T

    2014-03-01

    Pseudoalteromonas sp. NCIMB 2021 (NCIMB 2021) was grown in synthetic seawater (SSW) containing pyruvate, in the presence (SSW(++) ) and absence (SSW(-) ) of divalent cations. Cultures contained single cells. Addition of the cationic antibacterial peptide (CAP), protamine, did not inhibit, but rather increased, the growth of NCIMB 2021 in SSW(++) and caused the bacteria to grow in chains. Bacterial growth was assessed using turbidity, cell counts and the sodium salt of resazurin. In SSW(-) , NCIMB 2021 was no longer resistant to protamine. The minimum inhibitory concentration (MIC) was 5 mg ml(-1) . Protamine is a cationic antimicrobial peptide (CAP), which is active against a variety of bacteria. This is the first in-depth study of the interaction of protamine with a marine bacterium, Pseudoalteromonas sp. NCIMB 2021. Our results show that protamine is only active in seawater in the absence of divalent cations. In the presence of the divalent cations, Mg(2+) and Ca(2+) , protamine enhances the growth of Pseudoalteromonas sp. NCIMB 2021 and produces chains rather than individual cells. These are important considerations when deciding on applications for protamine and in terms of understanding its mechanism of action. © 2013 The Society for Applied Microbiology.

  9. Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives

    Directory of Open Access Journals (Sweden)

    Servé W. M. Kengen

    2013-01-01

    Full Text Available Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit for dark fermentation of 4 mol hydrogen per mol hexose, this organism has proven itself to be an excellent candidate for biological hydrogen production. This review provides an overview of the research on C. saccharolyticus with respect to the hydrolytic capability, sugar metabolism, hydrogen formation, mechanisms involved in hydrogen inhibition, and the regulation of the redox and carbon metabolism. Analysis of currently available fermentation data reveal decreased hydrogen yields under non-ideal cultivation conditions, which are mainly associated with the accumulation of hydrogen in the liquid phase. Thermodynamic considerations concerning the reactions involved in hydrogen formation are discussed with respect to the dissolved hydrogen concentration. Novel cultivation data demonstrate the sensitivity of C. saccharolyticus to increased hydrogen levels regarding substrate load and nitrogen limitation. In addition, special attention is given to the rhamnose metabolism, which represents an unusual type of redox balancing. Finally, several approaches are suggested to improve biohydrogen production by C. saccharolyticus.

  10. Extracellular proteases of Halobacillus blutaparonensis strain M9, a new moderately halophilic bacterium.

    Science.gov (United States)

    Santos, Anderson F; Valle, Roberta S; Pacheco, Clarissa A; Alvarez, Vanessa M; Seldin, Lucy; Santos, André L S

    2013-12-01

    Halophilic microorganisms are source of potential hydrolytic enzymes to be used in industrial and/or biotechnological processes. In the present study, we have investigated the ability of the moderately halophilic bacterium Halobacillus blutaparonensis (strain M9), a novel species described by our group, to release proteolytic enzymes. This bacterial strain abundantly proliferated in Luria-Bertani broth supplemented with 2.5% NaCl as well as secreted proteases to the extracellular environment. The production of proteases occurred in bacterial cells grown under different concentration of salt, ranging from 0.5% to 10% NaCl, in a similar way. The proteases secreted by H. blutaparonensis presented the following properties: (i) molecular masses ranging from 30 to 80 kDa, (ii) better hydrolytic activities under neutral-alkaline pH range, (iii) expression modulated according to the culture age, (iv) susceptibility to phenylmethylsulphonyl fluoride, classifying them as serine-type proteases, (v) specific cleavage over the chymotrypsin substrate, and (vi) enzymatic stability in the presence of salt (up to 20% NaCl) and organic solvents (e.g., ether, isooctane and cyclohexane). The proteases described herein are promising for industrial practices due to its haloalkaline properties.

  11. Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake.

    Science.gov (United States)

    Guan, Tong-Wei; Tian, Lei; Li, En-Yuan; Tang, Shu-Kun; Zhang, Xiao-Ping

    2017-11-01

    A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001 T . Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C 15:0 , anteiso C 17:0 , iso C 15:0 . The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8 T (96.84%), followed by Gracilibacillus saliphilus YIM 91119 T (96.78%) and Gracilibacillus ureilyticus MF38 T (96.57%), thus confirming the affiliation of strain YIM 98001 T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001 T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001 T (=KCTC 42683 T  = DSMZ 104330 T ).

  12. Purification and characterization of an extreme halothermophilic protease from a halophilic bacterium Chromohalobacter sp. TVSP101

    Directory of Open Access Journals (Sweden)

    Malashetty Vidyasagar

    2009-03-01

    Full Text Available An extreme halophilic bacterium was isolated from solar saltern samples and identified based on biochemical tests and 16S r RNA sequencing as Chromohalobacter sp. strain TVSP101. The halophilic protease was purified using ultrafiltration, ethanol precipitation, hydrophobic interaction column chromatography and gel permeation chromatography to 180 fold with 22% yield. The molecular mass of the protease determined by SDS PAGE was 66 kDa. The purified enzyme was salt dependent for its activity and stability with an optimum of 4.5 M NaCl. The optimum temperature for maximum protease activity was 75°C. The protease was optimally active at pH 8 and retained more than 80% of its activity in the range of pH 7-10. Sucrose and glycine at 10% (w/v were the most effective osmolytes, retained 100% activity in the absence of NaCl. The activity was completely inhibited by ZnCl2 (2 mM, 0.1% SDS and PMSF (1mM. The enzyme was not inhibited by 1mM of pepstatin, EDTA and PCMB. The protease was active and retained 100% it activity in 10% (v/v DMSO, DMF, ethanol and acetone.

  13. New crystal forms of NTPDase1 from the bacterium Legionella pneumophila

    International Nuclear Information System (INIS)

    Zebisch, Matthias; Schäfer, Petra; Lauble, Peter; Sträter, Norbert

    2013-01-01

    The soluble NTPDase1 from L. pneumophila was crystallized in six crystal forms and the structure was solved using a sulfur SAD approach. Nucleoside triphosphate diphosphohydrolases (NTPDases) are a large class of nucleotidases that hydrolyze the (γ/β)- and (β/α)-anhydride bonds of nucleoside triphosphates and diphosphates, respectively. NTPDases are found throughout the eukaryotic domain. In addition, a very small number of members can be found in bacteria, most of which live as parasites of eukaryotic hosts. NTPDases of intracellular and extracellular parasites are emerging as important regulators for the survival of the parasite. To deepen the knowledge of the structure and function of this enzyme class, recombinant production of the NTPDase1 from the bacterium Legionella pneumophila has been established. The protein could be crystallized in six crystal forms, of which one has been described previously. The crystals diffracted to resolutions of between 1.4 and 2.5 Å. Experimental phases determined by a sulfur SAD experiment using an orthorhombic crystal form produced an interpretable electron-density map

  14. Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates

    International Nuclear Information System (INIS)

    Jeffrey, W.H.; Paul, J.H.

    1990-01-01

    One assumption made in bacterial production estimates from [ 3 H]thymidine incorporation is that all heterotrophic bacteria can incorporate exogenous thymidine into DNA. Heterotrophic marine bacterium isolates from Tampa Bay, Fla., Chesapeake Bay, Md., and a coral surface microlayer were examined for thymidine uptake (transport), thymidine incorporation, the presence of thymidine kinase genes, and thymidine kinase enzyme activity. Of the 41 isolates tested, 37 were capable of thymidine incorporation into DNA. The four organisms that could not incorporate thymidine also transported the thymidine poorly and lacked thymidine kinase activity. Attempts to detect thymidine kinase genes in the marine isolates by molecular probing with gene probes made from Escherichia coli and herpes simplex virus thymidine kinase genes proved unsuccessful. To determine if the inability to incorporate thymidine was due to the lack of thymidine kinase, one organism, Vibro sp. strain DI9, was transformed with a plasmid (pGQ3) that contained an E. coli thymidine kinase gene. Although enzyme assays indicated high levels of thymidine kinase activity in transformants, these cells still failed to incorporate exogenous thymidine into DNA or to transport thymidine into cells. These results indicate that the inability of certain marine bacteria to incorporate thymidine may not be solely due to the lack of thymidine kinase activity but may also be due to the absence of thymidine transport systems

  15. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal

    Science.gov (United States)

    Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W.

    2000-10-01

    Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10 9.

  16. Low-temperature chemotaxis, halotaxis and chemohalotaxis by the psychrophilic marine bacterium Colwellia psychrerythraea 34H.

    Science.gov (United States)

    Showalter, G M; Deming, J W

    2018-02-01

    A variety of ecologically important processes are driven by bacterial motility and taxis, yet these basic bacterial behaviours remain understudied in cold habitats. Here, we present a series of experiments designed to test the chemotactic ability of the model marine psychrophilic bacterium Colwellia psychrerythraea 34H, when grown at optimal temperature and salinity (8°C, 35 ppt) or its original isolation conditions (-1°C, 35 ppt), towards serine and mannose at temperatures from -8°C to 27°C (above its upper growth temperature of 18°C), and at salinities of 15, 35 and 55 ppt (at 8°C and -1°C). Results indicate that C. psychrerythraea 34H is capable of chemotaxis at all temperatures tested, with strongest chemotaxis at the temperature at which it was first grown, whether 8°C or -1°C. This model marine psychrophile also showed significant halotaxis towards 15 and 55 ppt solutions, as well as strong substrate-specific chemohalotaxis. We suggest that such patterns of taxis may enable bacteria to colonize sea ice, position themselves optimally within its extremely cold, hypersaline and temporally fluctuating microenvironments, and respond to various chemical signals therein. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and JohnWiley & Sons Ltd.

  17. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

    KAUST Repository

    Tian, Renmao

    2014-08-29

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  18. A thermostable serralysin inhibitor from marine bacterium Flavobacterium sp. YS-80-122

    Science.gov (United States)

    Liang, Pengjuan; Li, Shangyong; Wang, Kun; Wang, Fang; Xing, Mengxin; Hao, Jianhua; Sun, Mi

    2018-03-01

    Serralysin inhibitors have been proposed as potent drugs against many diseases and may help to prevent further development of antibiotic-resistant pathogenic bacteria. In this study, a novel serralysin inhibitor gene, lupI, was cloned from the marine bacterium Flavobacterium sp. YS-80-122 and expressed in Escherichia coli. The deduced serralysin inhibitor, LupI, shows <40% amino acid identity to other reported serralysin inhibitors. Multiple sequence alignment and phylogenetic analysis of LupI with other serralysin inhibitors indicated that LupI was a novel type of serralysin inhibitor. The inhibitory constant for LupI towards its target metalloprotease was 0.64 μmol/L. LupI was thermostable at high temperature, in which 35.6%-90.7% of its inhibitory activity was recovered after treatment at 100°C for 1-60 min followed by incubation at 0°C. This novel inhibitor may represent a candidate drug for the treatment of serralysin-related infections.

  19. The endosymbiotic bacterium Wolbachia induces resistance to dengue virus in Aedes aegypti.

    Directory of Open Access Journals (Sweden)

    Guowu Bian

    2010-04-01

    Full Text Available Genetic strategies that reduce or block pathogen transmission by mosquitoes have been proposed as a means of augmenting current control measures to reduce the growing burden of vector-borne diseases. The endosymbiotic bacterium Wolbachia has long been promoted as a potential vehicle for introducing disease-resistance genes into mosquitoes, thereby making them refractory to the human pathogens they transmit. Given the large overlap in tissue distribution and intracellular localization between Wolbachia and dengue virus in mosquitoes, we conducted experiments to characterize their interactions. Our results show that Wolbachia inhibits viral replication and dissemination in the main dengue vector, Aedes aegypti. Moreover, the virus transmission potential of Wolbachia-infected Ae. aegypti was significantly diminished when compared to wild-type mosquitoes that did not harbor Wolbachia. At 14 days post-infection, Wolbachia completely blocked dengue transmission in at least 37.5% of Ae. aegypti mosquitoes. We also observed that this Wolbachia-mediated viral interference was associated with an elevated basal immunity and increased longevity in the mosquitoes. These results underscore the potential usefulness of Wolbachia-based control strategies for population replacement.

  20. Exopolysaccharides play a role in the swarming of the benthic bacterium Pseudoalteromonas sp. SM9913

    Directory of Open Access Journals (Sweden)

    Ang eLiu

    2016-04-01

    Full Text Available Most marine bacteria secrete exopolysaccharide (EPS, which is important for bacterial survival in the marine environment. However, it is still unclear whether the self-secreted EPS is involved in marine bacterial motility. Here we studied the role of EPS in the lateral flagella-driven swarming motility of benthic bacterium Pseudoalteromonas sp. SM9913 (SM9913 by a comparison of wild SM9913 and ΔepsT, an EPS synthesis defective mutant. Reduction of EPS production in ΔepsT did not affect the growth rate or the swimming motility, but significantly decreased the swarming motility on a swarming plate, suggesting that the EPS may play a role in SM9913 swarming. However, the expression and assembly of lateral flagella in ΔepsT were not affected. Instead, ΔepsT had a different swarming behavior from wild SM9913. The swarming of ΔepsT did not have an obvious rapid swarming period, and its rate became much lower than that of wild SM9913 after 35 h incubation. An addition of surfactin or SM9913 EPS on the surface of the swarming plate could rescue the swarming level. These results indicate that the self-secreted EPS is required for the swarming of SM9913. This study widens our understanding of the function of the EPS of benthic bacteria.

  1. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus

    Energy Technology Data Exchange (ETDEWEB)

    Saw, Jimmy H [Los Alamos National Laboratory; Mountain, Bruce W [NEW ZEALAND; Feng, Lu [NANKAI UNIV; Omelchenko, Marina V [NCBI/NLM/NIH; Hou, Shaobin [UNIV OF HAWAII; Saito, Jennifer A [UNIV OF HAWAII; Stott, Matthew B [NEW ZEALAND; Li, Dan [NANKAI UNIV; Zhao, Guang [NANKAI UNIV; Wu, Junli [NANKAI UNIV; Galperin, Michael Y [NCBI/NLM/NIH; Koonin, Eugene V [NCBI/NLM/NIH; Makarova, Kira S [NCBI/NLM/NIH; Wolf, Yuri I [NCBI/NLM/NIH; Rigden, Daniel J [UNIV OF LIVERPOOL; Dunfield, Peter F [UNIV OF CALGARY; Wang, Lei [NANKAI UNIV; Alam, Maqsudul [UNIV OF HAWAII

    2008-01-01

    Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.

  2. Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil.

    Science.gov (United States)

    Cunha, Sofia; Tiago, Igor; Paiva, Gabriel; Nobre, Fernanda; da Costa, Milton S; Veríssimo, António

    2012-03-01

    A Gram-staining-positive, motile, rod-shaped, spore-forming bacterium, designated P9(T), was isolated from soil in Portugal. This organism was aerobic and catalase- and oxidase-positive. It had an optimum growth temperature of about 35 °C and an optimum growth pH of about 8.0-8.5, and grew in medium with 0-9% (w/v) NaCl. The cell-wall peptidoglycan was of the A1α type, with L-lysine as the diagnostic diamino acid. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C(15:0) (45.4%), iso-C(15:0) (22.0%) and anteiso-C(17:0) (11.2%). The genomic DNA G+C content was about 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P9(T) was most closely related to Jeotgalibacillus campisalis DSM 18983(T) (96.8%) and Jeotgalibacillus marinus DSM 1297(T) (96.5%). These two recognized species formed a coherent cluster with strain P9(T) that was supported by a bootstrap value of 99%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, strain P9(T) (=DSM 23228(T)=LMG 25523(T)) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus soli sp. nov. is proposed.

  3. A self-lysis pathway that enhances the virulence of a pathogenic bacterium.

    Science.gov (United States)

    McFarland, Kirsty A; Dolben, Emily L; LeRoux, Michele; Kambara, Tracy K; Ramsey, Kathryn M; Kirkpatrick, Robin L; Mougous, Joseph D; Hogan, Deborah A; Dove, Simon L

    2015-07-07

    In mammalian cells, programmed cell death (PCD) plays important roles in development, in the removal of damaged cells, and in fighting bacterial infections. Although widespread among multicellular organisms, there are relatively few documented instances of PCD in bacteria. Here we describe a potential PCD pathway in Pseudomonas aeruginosa that enhances the ability of the bacterium to cause disease in a lung infection model. Activation of the system can occur in a subset of cells in response to DNA damage through cleavage of an essential transcription regulator we call AlpR. Cleavage of AlpR triggers a cell lysis program through de-repression of the alpA gene, which encodes a positive regulator that activates expression of the alpBCDE lysis cassette. Although this is lethal to the individual cell in which it occurs, we find it benefits the population as a whole during infection of a mammalian host. Thus, host and pathogen each may use PCD as a survival-promoting strategy. We suggest that activation of the Alp cell lysis pathway is a disease-enhancing response to bacterial DNA damage inflicted by the host immune system.

  4. Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori

    International Nuclear Information System (INIS)

    Han Cong; Wang Qi; Dong Lei; Sun Haifang; Peng Shuying; Chen Jing; Yang Yiming; Yue Jianmin; Shen Xu; Jiang Hualiang

    2004-01-01

    Helicobacter pylori is a gram-negative pathogenic bacterium, which is associated with peptic ulcer disease and gastric cancer. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. In bacteria, peptide deformylase (PDF) catalyzes the removal of a formyl group from the N-termini of nascent polypeptides. Due to its essentiality and absence in mammalian cells, PDF has been considered as an attractive target for the discovery of novel antibiotics. In this work, a new PDF gene (def) from H. pylori strain SS1 was cloned, expressed, and purified in Escherichia coli system. Sequence alignment shows that H. pylori PDF (HpPDF) shares about 40% identity to E. coli PDF (EcPDF). The enzymatic properties of HpPDF demonstrate its relatively high activity toward formyl-Met-Ala-Ser, with K cat of 3.4 s -1 , K m of 1.7 mM, and K cat /K m of 2000 M -1 s -1 . HpPDF enzyme appears to be fully active at pH between 8.0 and 9.0, and temperature 50 deg. C. The enzyme activity of Co 2+ -containing HpPDF is apparently higher than that of Zn 2+ -containing HpPDF. This present work thereby supplies a potential platform that facilitates the discovery of novel HpPDF inhibitors and further of possible antimicrobial agents against H. pylori

  5. Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori.

    Science.gov (United States)

    Han, Cong; Wang, Qi; Dong, Lei; Sun, Haifang; Peng, Shuying; Chen, Jing; Yang, Yiming; Yue, Jianmin; Shen, Xu; Jiang, Hualiang

    2004-07-09

    Helicobacter pylori is a gram-negative pathogenic bacterium, which is associated with peptic ulcer disease and gastric cancer. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. In bacteria, peptide deformylase (PDF) catalyzes the removal of a formyl group from the N-termini of nascent polypeptides. Due to its essentiality and absence in mammalian cells, PDF has been considered as an attractive target for the discovery of novel antibiotics. In this work, a new PDF gene (def) from H. pylori strain SS1 was cloned, expressed, and purified in Escherichia coli system. Sequence alignment shows that H. pylori PDF (HpPDF) shares about 40% identity to E. coli PDF (EcPDF). The enzymatic properties of HpPDF demonstrate its relatively high activity toward formyl-Met-Ala-Ser, with K(cat) of 3.4s(-1), K(m) of 1.7 mM, and K(cat) / K(m) of 2000M(-1)s(-1). HpPDF enzyme appears to be fully active at pH between 8.0 and 9.0, and temperature 50 degrees C. The enzyme activity of Co(2+)-containing HpPDF is apparently higher than that of Zn(2+)-containing HpPDF. This present work thereby supplies a potential platform that facilitates the discovery of novel HpPDF inhibitors and further of possible antimicrobial agents against H. pylori.

  6. Biomimetic Synthesis of Silver Nanoparticles Using Endosymbiotic Bacterium Inhabiting Euphorbia hirta L. and Their Bactericidal Potential

    Directory of Open Access Journals (Sweden)

    Baker Syed

    2016-01-01

    Full Text Available The present investigation aims to evaluate biomimetic synthesis of silver nanoparticles using endophytic bacterium EH 419 inhabiting Euphorbia hirta L. The synthesized nanoparticles were initially confirmed with change in color from the reaction mixture to brown indicating the synthesis of nanoparticles. Further confirmation was achieved with the characteristic absorption peak at 440 nm using UV-Visible spectroscopy. The synthesized silver nanoparticles were subjected to biophysical characterization using hyphenated techniques. The possible role of biomolecules in mediating the synthesis was depicted with FTIR analysis. Further crystalline nature of synthesized nanoparticles was confirmed using X-ray diffraction (XRD with prominent diffraction peaks at 2θ which can be indexed to the (111, (200, (220, and (311 reflections of face centered cubic structure (fcc of metallic silver. Transmission electron microscopy (TEM revealed morphological characteristics of synthesized silver nanoparticles to be polydisperse in nature with size ranging from 10 to 60 nm and different morphological characteristics such as spherical, oval, hexagonal, and cubic shapes. Further silver nanoparticles exhibited bactericidal activity against panel of significant pathogenic bacteria among which Pseudomonas aeruginosa was most sensitive compared to other pathogens. To the best of our knowledge, present study forms first report of bacterial endophyte inhabiting Euphorbia hirta L. in mediating synthesizing silver nanoparticles.

  7. Interactions between the pathogenic bacterium Vibrio parahaemolyticus and red-tide dinoflagellates

    Science.gov (United States)

    Seong, Kyeong Ah; Jeong, Hae Jin

    2011-06-01

    Vibrio parahaemolyticus is a common pathogenic bacterium in marine and estuarine waters. To investigate interactions between V. parahaemolyticus and co-occurring redtide dinoflagellates, we monitored the daily abundance of 5 common red tide dinoflagellates in laboratory culture; Amphidinium carterae, Cochlodinium ploykrikoides, Gymnodinium impudicum, Prorocentrum micans, and P. minimum. Additionally, we measured the ingestion rate of each dinoflagellate on V. parahaemolyticus as a function of prey concentration. Each of the dinoflagellates responded differently to the abundance of V. parahaemolyticus. The abundances of A. carterae and P. micans were not lowered by V. parahaemolyticus, whereas that of C. polykrikodes was lowered considerably. The harmful effect depended on bacterial concentration and incubation time. Most C. polykrikoides cells died after 1 hour incubation when the V. parahaemolyticus concentration was 1.4×107 cells ml-1, while cells died within 2 days of incubation when the bacterial concentration was 1.5×106 cells ml-1. With increasing V. parahaemolyticus concentration, ingestion rates of P. micans, P. minimum, and A. carterae on the prey increased, whereas that on C. polykrikoides decreased. The maximum or highest ingestion rates of P. micans, P. minimum, and A. carterae on V. parahaemolyticus were 55, 5, and 2 cells alga-1 h-1, respectively. The results of the present study suggest that V. parahaemolyticus can be both the killer and prey for some red tide dinoflagellates.

  8. Spatio-temporal remodeling of functional membrane microdomains organizes the signaling networks of a bacterium.

    Directory of Open Access Journals (Sweden)

    Johannes Schneider

    2015-04-01

    Full Text Available Lipid rafts are membrane microdomains specialized in the regulation of numerous cellular processes related to membrane organization, as diverse as signal transduction, protein sorting, membrane trafficking or pathogen invasion. It has been proposed that this functional diversity would require a heterogeneous population of raft domains with varying compositions. However, a mechanism for such diversification is not known. We recently discovered that bacterial membranes organize their signal transduction pathways in functional membrane microdomains (FMMs that are structurally and functionally similar to the eukaryotic lipid rafts. In this report, we took advantage of the tractability of the prokaryotic model Bacillus subtilis to provide evidence for the coexistence of two distinct families of FMMs in bacterial membranes, displaying a distinctive distribution of proteins specialized in different biological processes. One family of microdomains harbors the scaffolding flotillin protein FloA that selectively tethers proteins specialized in regulating cell envelope turnover and primary metabolism. A second population of microdomains containing the two scaffolding flotillins, FloA and FloT, arises exclusively at later stages of cell growth and specializes in adaptation of cells to stationary phase. Importantly, the diversification of membrane microdomains does not occur arbitrarily. We discovered that bacterial cells control the spatio-temporal remodeling of microdomains by restricting the activation of FloT expression to stationary phase. This regulation ensures a sequential assembly of functionally specialized membrane microdomains to strategically organize signaling networks at the right time during the lifespan of a bacterium.

  9. Gamma-aminobutyric acid fermentation with date residue by a lactic acid bacterium, Lactobacillus brevis.

    Science.gov (United States)

    Hasegawa, Momoko; Yamane, Daisuke; Funato, Kouichi; Yoshida, Atsushi; Sambongi, Yoshihiro

    2018-03-01

    Dates are commercially consumed as semi-dried fruit or processed into juice and puree for further food production. However, the date residue after juice and puree production is not used, although it appears to be nutrient enriched. Here, date residue was fermented by a lactic acid bacterium, Lactobacillus brevis, which has been generally recognized as safe. Through degradation of sodium glutamate added to the residue during the fermentation, γ-aminobutyric acid (GABA), which reduces neuronal excitability, was produced at the conversion rate of 80-90% from glutamate. In order to achieve this GABA production level, pretreatment of the date residue with carbohydrate-degrading enzymes, i.e., cellulase and pectinase, was necessary. All ingredients used for this GABA fermentation were known as being edible. These results provide us with a solution for the increasing commercial demand for GABA in food industry with the use of date residue that has been often discarded. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  10. The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals.

    Science.gov (United States)

    Sneed, Jennifer M; Sharp, Koty H; Ritchie, Kimberly B; Paul, Valerie J

    2014-07-07

    Microbial biofilms induce larval settlement for some invertebrates, including corals; however, the chemical cues involved have rarely been identified. Here, we demonstrate the role of microbial biofilms in inducing larval settlement with the Caribbean coral Porites astreoides and report the first instance of a chemical cue isolated from a marine biofilm bacterium that induces complete settlement (attachment and metamorphosis) of Caribbean coral larvae. Larvae settled in response to natural biofilms, and the response was eliminated when biofilms were treated with antibiotics. A similar settlement response was elicited by monospecific biofilms of a single bacterial strain, Pseudoalteromonas sp. PS5, isolated from the surface biofilm of a crustose coralline alga. The activity of Pseudoalteromonas sp. PS5 was attributed to the production of a single compound, tetrabromopyrrole (TBP), which has been shown previously to induce metamorphosis without attachment in Pacific acroporid corals. In addition to inducing settlement of brooded larvae (P. astreoides), TBP also induced larval settlement for two broadcast-spawning species, Orbicella (formerly Montastraea) franksi and Acropora palmata, indicating that this compound may have widespread importance among Caribbean coral species. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  11. Cesiribacter roseus sp. nov., a pink-pigmented bacterium isolated from desert sand.

    Science.gov (United States)

    Liu, Ming; Qi, Huan; Luo, Xuesong; Dai, Jun; Peng, Fang; Fang, Chengxiang

    2012-01-01

    A pink-pigmented, Gram-negative, rod-shaped, motile, strictly aerobic bacterium, designated strain 311(T), was isolated from desert sand in Xinjiang, China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 311(T) was related closely to Cesiribacter andamanensis AMV16(T) (94.6% similarity). The DNA G+C content of strain 311(T) was 47.1 mol% and the major respiratory quinone was menaquinone 7 (MK-7). The main cellular fatty acids were C(16:1)ω5c (29.9%), iso-C(15:0) (21.9%), iso-C(17:0) 3-OH (13.3%) and summed feature 4 (iso-C(17:1) I and/or anteiso-C(17:1) B; 13.0%). Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 311(T) is considered to represent a novel species of the genus Cesiribacter, for which the name Cesiribacter roseus sp. nov. is proposed. The type strain is 311(T) (=CCTCC AB 207142(T) =KACC 15456(T)).

  12. Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment.

    Science.gov (United States)

    Wu, Wen-Jie; Liu, Qian-Qian; Chen, Guan-Jun; Du, Zong-Jun

    2015-07-01

    A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08(T), was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5-8.0 and with 2-3% (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88-90% sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08(T) ( = KCTC 42261(T) = CICC 10901(T)).

  13. Partial characterization of an extracellular polysaccharide produced by the moderately halophilic bacterium Halomonas xianhensis SUR308.

    Science.gov (United States)

    Biswas, Jhuma; Ganguly, J; Paul, A K

    2015-01-01

    A moderately halophilic bacterium, Halomonas xianhensis SUR308 (Genbank Accession No. KJ933394) was isolated from a multi-pond solar saltern at Surala, Ganjam district, Odisha, India. The isolate produced a significant amount (7.87 g l(-1)) of extracellular polysaccharides (EPS) when grown in malt extract-yeast extract medium supplemented with 2.5% NaCl, 0.5% casein hydrolysate and 3% glucose. The EPS was isolated and purified following the conventional method of precipitation and dialysis. Chromatographic analysis (paper, GC and GC-MS) of the hydrolyzed EPS confirmed its heteropolymeric nature and showed that it is composed mainly of glucose (45.74 mol%), galactose (33.67 mol %) and mannose (17.83 mol%). Fourier-transform infrared spectroscopy indicated the presence of methylene and carboxyl groups as characteristic functional groups. In addition, its proton nuclear magnetic resonance spectrum revealed functional groups specific for extracellular polysaccharides. X-ray diffraction analysis revealed the amorphous nature (CIxrd, 0.56) of the EPS. It was thermostable up to 250 °C and displayed pseudoplastic rheology and remarkable stability against pH and salts. These unique properties of the EPS produced by H. xianhensis indicate its potential to act as an agent for detoxification, emulsification and diverse biological activities.

  14. Isolation of Aureimonas altamirensis, a Brucella canis-like bacterium, from an edematous canine testicle.

    Science.gov (United States)

    Reilly, Thomas J; Calcutt, Michael J; Wennerdahl, Laura A; Williams, Fred; Evans, Tim J; Ganjam, Irene K; Bowman, Jesse W; Fales, William H

    2014-11-01

    Microbiological and histological analysis of a sample from a swollen testicle of a 2-year-old Border Collie dog revealed a mixed infection of the fungus Blastomyces dermatitidis and the Gram-negative bacterium Aureimonas altamirensis. When subjected to an automated microbial identification system, the latter isolate was provisionally identified as Psychrobacter phenylpyruvicus, but the organism shared several biochemical features with Brucella canis and exhibited agglutination, albeit weakly, with anti-B. canis antiserum. Unequivocal identification of the organism was only achieved by 16S ribosomal RNA gene sequencing, ultimately establishing the identity as A. altamirensis. Since its first description in 2006, this organism has been isolated infrequently from human clinical samples, but, to the authors' knowledge, has not been reported from a veterinary clinical sample. While of unknown clinical significance with respect to the pathology observed for the polymicrobial infection described herein, it highlights the critical importance to unambiguously identify the microbe for diagnostic, epidemiological, infection control, and public health purposes. © 2014 The Author(s).

  15. Purification and characterization of an endoglucanase from a newly isolated thermophilic anaerobic bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Creuzet, N; Frixon, C [Laboratoire de Chimie Bacterienne, C.N.R.S., 13 - Marseille (France)

    1983-02-01

    An endoglucanase (1,4-..beta..-D-glucan glucanohydrolase, EC 3.2.1.4) from a new cellulotytic thermophilic bacterium was purified to apparent homogeneity after being separated from a xylanase. Little carbohydrate was associated with the endoglucanase. A molecular weight of 91,000 and 99,000 was determined by SDS-polyacrylamide gel electrophoresis and by gel filtration of the native enzyme on Ultrogel ACA 34. The optimal pH was approximately 6.4 and the enzyme was isoelectric at pH 3.85. The enzyme was found highly thermostable: it retained 50% of its activity after 1 hour at 85/sup 0/C. Hydrolysis of CMC took place with a rapid decrease in viscosity but a slow liberation of reducing sugars, indicating to hydrolyze highly ordered cellulose. Cellobiose inhibited the activity of the endoglucanase. None of the metal ions tested stimulated the activity. The enzyme was completely inactivated by 1 mM Hg/sup 2 +/ and was inhibited by thiol reagents.

  16. The Lipid A from the Haloalkaliphilic Bacterium Salinivibrio sharmensis Strain BAGT

    Directory of Open Access Journals (Sweden)

    Maria Michela Corsaro

    2013-01-01

    Full Text Available Lipid A is a major constituent of the lipopolysaccharides (or endotoxins, which are complex amphiphilic macromolecules anchored in the outer membrane of Gram-negative bacteria. The glycolipid lipid A is known to possess the minimal chemical structure for LPSs endotoxic activity, able to cause septic shock. Lipid A isolated from extremophiles is interesting, since very few cases of pathogenic bacteria have been found among these microorganisms. In some cases their lipid A has shown to have an antagonist activity, i.e., it is able to interact with the immune system of the host without triggering a proinflammatory response by blocking binding of substances that could elicit such a response. However, the relationship between the structure and the activity of these molecules is far from being completely clear. A deeper knowledge of the lipid A chemical structure can help the understanding of these mechanisms. In this manuscript, we present our work on the complete structural characterization of the lipid A obtained from the lipopolysaccharides (LPS of the haloalkaliphilic bacterium Salinivibrio sharmensis. Lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different number of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of electrospray ionization Fourier transform ion cyclotron (ESI FT-ICR mass spectrometry and chemical analysis.

  17. Identification of an entomopathogenic bacterium, Serratia sp. ANU101, and its hemolytic activity.

    Science.gov (United States)

    Kim, Yonggyun; Kim, Keunseob; Seo, Jiae; Shrestha, Sony; Kim, Hosanna H; Nalini, Madanagopal; Yi, Youngkeun

    2009-03-01

    Four different bacterial colonies were isolated from an old stock of an entomopathogenic nematode, Steinernema monticolum. They all showed entomopathogenicity to final instar larvae of beet armyworm, Spodoptera exigua, by hemocoelic injection. However, they varied in colony form, susceptibility to antibiotics, and postmortem change of the infected host insects. Biolog microbial identification and 16S rDNA sequence analyses indicate that these are four different species classified into different bacterial genera. owing to high entomopathogenicity and a cadaver color of infected insect host, Serratia sp. was selected as a main symbiotic bacterial species and analyzed for its pathogenicity. Although no virulence of Serratia sp. was detected at oral administration, the bacteria gave significant synergistic pathogenicity to fifth instar S. exigua when it was treated along with a spore-forming entomopathogenic bacterium, Bacillus thuringiensis. The synergistic effect was explained by an immunosuppressive effect of Serratia sp. by its high cytotoxic effect on hemocytes of S. exigua, because Serratia sp. caused septicemia of S. exigua when the bacterial cells were injected into S. exigua hemocoel. The cytotoxic factor(s) was present in the culture medium because the sterilized culture broth possessed high potency in the cytotoxicity, which was specific to granular cells and plasmatocytes, two main immune-associated hemocytes in insects.

  18. Degradative capacities and bioaugmentation potential of an anaerobic benzene-degrading bacterium strain DN11

    Energy Technology Data Exchange (ETDEWEB)

    Yuki Kasai; Yumiko Kodama; Yoh Takahata; Toshihiro Hoaki; Kazuya Watanabe [Marine Biotechnology Institute, Kamaishi (Japan)

    2007-09-15

    Azoarcus sp. strain DN11 is a denitrifying bacterium capable of benzene degradation under anaerobic conditions. The present study evaluated strain DN11 for its application to bioaugmentation of benzene-contaminated underground aquifers. Strain DN11 could grow on benzene, toluene, m-xylene, and benzoate as the sole carbon and energy sources under nitrate-reducing conditions, although o- and p-xylenes were transformed in the presence of toluene. Phenol was not utilized under anaerobic conditions. Kinetic analysis of anaerobic benzene degradation estimated its apparent affinity and inhibition constants to be 0.82 and 11 {mu}M, respectively. Benzene-contaminated groundwater taken from a former coal-distillation plant site in Aichi, Japan was anaerobically incubated in laboratory bottles and supplemented with either inorganic nutrients (nitrogen, phosphorus, and nitrate) alone, or the nutrients plus strain DN11, showing that benzene was significantly degraded only when DN11 was introduced. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments, and quantitative PCR revealed that DN11 decreased after benzene was degraded. Following the decrease in DN11 16S rRNA gene fragments corresponding to bacteria related to Owenweeksia hongkongensis and Pelotomaculum isophthalicum, appeared as strong bands, suggesting possible metabolic interactions in anaerobic benzene degradation. Results suggest that DN11 is potentially useful for degrading benzene that contaminates underground aquifers at relatively low concentrations. 50 refs., 6 figs., 1 tab.

  19. Augmenting Iron Accumulation in Cassava by the Beneficial Soil Bacterium Bacillus subtilis (GBO3

    Directory of Open Access Journals (Sweden)

    Monica A Freitas

    2015-08-01

    Full Text Available Cassava (Manihot esculenta, a major staple food in the developing world, provides a basic carbohydrate diet for over half a billion people living in the tropics. Despite the iron abundance in most soils, cassava provides insufficient iron for humans as the edible roots contain 3-12 times less iron than other traditional food crops such as wheat, maize, and rice. With the recent identification that the beneficial soil bacterium Bacillus subtilis (strain GB03 activates iron acquisition machinery to increase metal ion assimilation in Arabidopsis, the question arises as to whether this plant-growth promoting rhizobacterium (PGPR also augments iron assimilation to increase endogenous iron levels in cassava. Biochemical analyses reveal that shoot-propagated cassava with GB03-inoculation exhibit elevated iron accumulation after 140 days of plant growth as determined by X-ray microanalysis and total foliar iron analysis. Growth promotion and increased photosynthetic efficiency were also observed for greenhouse-grown plants with GB03-exposure. These results demonstrate the potential of microbes to increase iron accumulation in an important agricultural crop and is consistent with idea that microbial signaling can regulate plant photosynthesis.

  20. Electricity Generation in Microbial Fuel Cell (MFC) by Bacterium Isolated from Rice Paddy Field Soil

    Science.gov (United States)

    Fakhirruddin, Fakhriah; Amid, Azura; Salim, Wan Wardatul Amani Wan; Suhaida Azmi, Azlin

    2018-03-01

    Microbial fuel cell (MFC) is an alternative approach in generating renewable energy by utilising bacteria that will oxidize organic or inorganic substrates, producing electrons yielded as electrical energy. Different species of exoelectrogenic bacteria capable of generating significant amount of electricity in MFC has been identified, using various organic compounds for fuel. Soil sample taken from rice paddy field is proven to contain exoelectrogenic bacteria, thus electricity generation using mixed culture originally found in the soil, and pure culture isolated from the soil is studied. This research will isolate the exoelectrogenic bacterial species in the rice paddy field soil responsible for energy generation. Growth of bacteria isolated from the MFC is observed by measuring the optical density (OD), cell density weight (CDW) and viable cell count. Mixed bacterial species found in paddy field soil generates maximum power of 77.62 μW and 0.70 mA of current. In addition, the research also shows that the pure bacterium in rice paddy field soil can produce maximum power and current at 51.32 μW and 0.28 mA respectively.