Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

Energy Technology Data Exchange (ETDEWEB)

Firestone, Mary [Univ. of California, Berkeley, CA (United States)

2015-03-31

It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbon decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.

Coexistence facilitates interspecific biofilm formation in complex microbial communities

DEFF Research Database (Denmark)

Madsen, Jonas Stenløkke; Røder, Henriette Lyng; Russel, Jakob

2016-01-01

Social interactions in which bacteria respond to one another by modifying their phenotype are central determinants of microbial communities. It is known that interspecific interactions influence the biofilm phenotype of bacteria; a phenotype that is central to the fitness of bacteria. However......, the underlying role of fundamental ecological factors, specifically coexistence and phylogenetic history, in biofilm formation remains unclear. This study examines how social interactions affect biofilm formation in multi-species co-cultures from five diverse environments. We found prevalence of increased...

Formation and Stability of Microbially Derived Soil Organic Matter

Science.gov (United States)

Waldrop, M. P.; Creamer, C.; Foster, A. L.; Lawrence, C. R.; Mcfarland, J. W.; Schulz, M. S.

2017-12-01

Soil carbon is vital to soil health, food security, and climate change mitigation, but the underlying mechanisms controlling the stabilization and destabilization of soil carbon are still poorly understood. There has been a conceptual paradigm shift in how soil organic matter is formed which now emphasizes the importance of microbial activity to build stable (i.e. long-lived) and mineral-associated soil organic matter. In this conceptual model, the consumption of plant carbon by microorganisms, followed by subsequent turnover of microbial bodies closely associated with mineral particles, produces a layering of amino acid and lipid residues on the surfaces of soil minerals that remains protected from destabilization by mineral-association and aggregation processes. We tested this new model by examining how isotopically labeled plant and microbial C differ in their fundamental stabilization and destabilization processes on soil minerals through a soil profile. We used a combination of laboratory and field-based approaches to bridge multiple spatial scales, and used soil depth as well as synthetic minerals to create gradients of soil mineralogy. We used Raman microscopy as a tool to probe organic matter association with mineral surfaces, as it allows for the simultaneous quantification and identification of living microbes, carbon, minerals, and isotopes through time. As expected, we found that the type of minerals present had a strong influence on the amount of C retained, but the stabilization of new C critically depends on growth, death, and turnover of microbial cells. Additionally, the destabilization of microbial residue C on mineral surfaces was little affected by flushes of DOC relative to wet-dry cycles alone. We believe this new insight into microbial mechanisms of C stabilization in soils will eventually lead to new avenues for measuring and modeling SOM dynamics in soils, and aid in the management of soil C to mediate global challenges.

New method for characterizing electron mediators in microbial systems using a thin-layer twin-working electrode cell.

Science.gov (United States)

Hassan, Md Mahamudul; Cheng, Ka Yu; Ho, Goen; Cord-Ruwisch, Ralf

2017-01-15

Microbial biofilms are significant ecosystems where the existence of redox gradients drive electron transfer often via soluble electron mediators. This study describes the use of two interfacing working electrodes (WEs) to simulate redox gradients within close proximity (250µm) for the detection and quantification of electron mediators. By using a common counter and reference electrode, the potentials of the two WEs were independently controlled to maintain a suitable "voltage window", which enabled simultaneous oxidation and reduction of electron mediators as evidenced by the concurrent anodic and cathodic currents, respectively. To validate the method, the electrochemical properties of different mediators (hexacyanoferrate, HCF, riboflavin, RF) were characterized by stepwise shifting the "voltage window" (ranging between 25 and 200mV) within a range of potentials after steady equilibrium current of both WEs was established. The resulting differences in electrical currents between the two WEs were recorded across a defined potential spectrum (between -1V and +0.5V vs. Ag/AgCl). Results indicated that the technique enabled identification (by the distinct peak locations at the potential scale) and quantification (by the peak of current) of the mediators for individual species as well as in an aqueous mixture. It enabled a precise determination of mid-potentials of the externally added mediators (HCF, RF) and mediators produced by pyocyanin-producing Pseudomonas aeruginosa (WACC 91) culture. The twin working electrode described is particularly suitable for studying mediator-dependent microbial electron transfer processes or simulating redox gradients as they exist in microbial biofilms. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

Science.gov (United States)

Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand...

Microbially mediated mineral carbonation

Science.gov (United States)

Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

2010-12-01

Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

Acoustic and Electrical Property Changes Due to Microbial Growth and Biofilm Formation in Porous Media

Science.gov (United States)

A laboratory study was conducted to investigate the effect of microbial growth and biofilm formation on compressional waves, and complex conductivity during stimulated microbial growth. Over the 29 day duration of the experiment, compressional wave amplitudes and arrival times f...

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

Science.gov (United States)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system

Bentonite. Geotechnical barrier and source for microbial life

International Nuclear Information System (INIS)

Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea; Steglich, Jennifer

2017-01-01

Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N_2/CO_2-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.

Bentonite. Geotechnical barrier and source for microbial life

Energy Technology Data Exchange (ETDEWEB)

Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). HZDR Young Investigator Group; Steglich, Jennifer

2017-06-01

Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N{sub 2}/CO{sub 2}-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.

High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.

Science.gov (United States)

Zhou, Jizhong; He, Zhili; Yang, Yunfeng; Deng, Ye; Tringe, Susannah G; Alvarez-Cohen, Lisa

2015-01-27

Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied "open-format" and "closed-format" detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions. Copyright © 2015 Zhou et al.

[Formation of microbial biofilms in causative agents of acute and chronic pyelonephritis].

Science.gov (United States)

Lagun, L V; Atanasova, Iu V; Tapal'skiĭ, D V

2013-01-01

Study the intensity of formation of microbial biofilms by Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus strains isolated during various forms of pyelonephritis. 150 clinical isolates of microorganisms isolated from urine ofpatientswith acute and chronic pyelonephritiswere included into the study. Determination of intensity of film-formation was carried out by staining of the formed biofilms by crystal violet with consequent extraction of the dye and measurement of its concentration in washout solution. Among causative agents ofpyelonephritis P. aeruginosa isolates had the maximum film-forming ability. The intensity of biofilm formation of these isolates was 2-3 time higher than staphylococcus and enterobacteria strains. Strains isolated from patients with chronic pyelonephritis by ability to form biofilms significantly surpassed strains isolated from acute pyelonephritis patients. A higher ability to form microbial biofilms for microorganisms--causative agents of pyelonephritis progressing against the background ofurolithiasis was noted. The ability to form biofilms is determined by both causative agent species and character of the infectious process in which this microorganism participates. Intensive formation of biofilms by E. coli, P. aeruginosa, K. pneumoniae, S. aureus clinical isolates may be an important factor of chronization of urinary tract infections.

Chemotactic preferences govern competition and pattern formation in simulated two-strain microbial communities.

Science.gov (United States)

Centler, Florian; Thullner, Martin

2015-01-01

Substrate competition is a common mode of microbial interaction in natural environments. While growth properties play an important and well-studied role in competition, we here focus on the influence of motility. In a simulated two-strain community populating a homogeneous two-dimensional environment, strains competed for a common substrate and only differed in their chemotactic preference, either responding more sensitively to a chemoattractant excreted by themselves or responding more sensitively to substrate. Starting from homogeneous distributions, three possible behaviors were observed depending on the competitors' chemotactic preferences: (i) distributions remained homogeneous, (ii) patterns formed but dissolved at a later time point, resulting in a shifted community composition, and (iii) patterns emerged and led to the extinction of one strain. When patterns formed, the more aggregating strain populated the core of microbial aggregates where starving conditions prevailed, while the less aggregating strain populated the more productive zones at the fringe or outside aggregates, leading to a competitive advantage of the less aggregating strain. The presence of a competitor was found to modulate a strain's behavior, either suppressing or promoting aggregate formation. This observation provides a potential mechanism by which an aggregated lifestyle might evolve even if it is initially disadvantageous. Adverse effects can be avoided as a competitor hinders aggregate formation by a strain which has just acquired this ability. The presented results highlight both, the importance of microbial motility for competition and pattern formation, and the importance of the temporal evolution, or history, of microbial communities when trying to explain an observed distribution.

High salinity facilitates dolomite precipitation mediated by Haloferax volcanii DS52

Science.gov (United States)

Qiu, Xuan; Wang, Hongmei; Yao, Yanchen; Duan, Yong

2017-08-01

Although most modern dolomites occur in hypersaline environments, the effects of elevated salinity on the microbial mediation of dolomite precipitation have not been fully evaluated. Here we report results of dolomite precipitation in association with a batch culture of Haloferax volcanii DS52, a halophilic archaeon, under various salinities (from 120‰ to 360‰) and the impact of salinity on microbe-mediated dolomite formation. The mineral phases, morphology and atomic arrangement of the precipitates were analyzed by XRD, SEM and TEM, respectively. The amount of amino acids on the archaeal cell surface was quantified by HPLC/MS. The XRD analysis indicated that disordered dolomite formed successfully with the facilitation of cells harvested from cultures with relatively high salinities (200‰ and 280‰) but was not observed in association with cells harvested from cultures with lower salinity (120‰) or the lysates of cells harvested from extremely high salinity (360‰). The TEM analysis demonstrated that the crystals from cultures with a salinity of 200‰ closely matched that of dolomite. Importantly, we found that more carboxyl groups were presented on the cell surface under high salinity conditions to resist the high osmotic pressure, which may result in the subsequent promotion of dolomite formation. Our finding suggests a link between variations in the hydro-chemical conditions and the formation of dolomite via microbial metabolic activity and enhances our understanding about the mechanism of microbially mediated dolomite formation under high salinity conditions.

Microbially mediated barite dissolution in anoxic brines

International Nuclear Information System (INIS)

Ouyang, Bingjie; Akob, Denise M.; Dunlap, Darren; Renock, Devon

2017-01-01

Fluids injected into shale formations during hydraulic fracturing of black shale return with extraordinarily high total-dissolved-solids (TDS) and high concentrations of barium (Ba) and radium (Ra). Barite, BaSO_4, has been implicated as a possible source of Ba as well as a problematic mineral scale that forms on internal well surfaces, often in close association with radiobarite, (Ba,Ra)SO_4. The dissolution of barite by abiotic processes is well quantified. However, the identification of microbial communities in flowback and produced water necessitates the need to understand barite dissolution in the presence of bacteria. Therefore, we evaluated the rates and mechanisms of abiotic and microbially-mediated barite dissolution under anoxic and hypersaline conditions in the laboratory. Barite dissolution experiments were conducted with bacterial enrichment cultures established from produced water from Marcellus Shale wells located in northcentral Pennsylvania. These cultures were dominated by anaerobic halophilic bacteria from the genus Halanaerobium. Dissolved Ba was determined by ICP-OES and barite surfaces were investigated by SEM and AFM. Our results reveal that: 1) higher amounts of barium (up to ∼5 × ) are released from barite in the presence of Halanaerobium cultures compared to brine controls after 30 days of reaction, 2) etch pits that develop on the barite (001) surface in the presence of Halanaerobium exhibit a morphology that is distinct from those that form during control experiments without bacteria, 3) etch pits that develop in the presence of Halanaerobium exhibit a morphology that is similar to the morphology of etch pits formed in the presence of strong organic chelators, EDTA and DTPA, and 4) experiments using dialysis membranes to separate barite from bacteria suggest that direct contact between the two is not required in order to promote dissolution. These results suggest that Halanaerobium increase the rate of barite dissolution in anoxic

Microbial growth yield estimates from thermodynamics and its importance for degradation of pesticides and formation of biogenic non-extractable residues

DEFF Research Database (Denmark)

Brock, Andreas Libonati; Kästner, M.; Trapp, Stefan

2017-01-01

NER. Formation of microbial mass can be estimated from the microbial growth yield, but experimental data is rare. Instead, we suggest using prediction methods for the theoretical yield based on thermodynamics. Recently, we presented the Microbial Turnover to Biomass (MTB) method that needs a minimum...... and using the released CO2 as a measure for microbial activity, we predicted a range for the formation of biogenic NER. For the majority of the pesticides, a considerable fraction of the NER was estimated to be biogenic. This novel approach provides a theoretical foundation applicable to the evaluation...

Effect of anode polarization on biofilm formation and electron transfer in Shewanella oneidensis/graphite felt microbial fuel cells.

Science.gov (United States)

Pinto, David; Coradin, Thibaud; Laberty-Robert, Christel

2018-04-01

In microbial fuel cells, electricity generation is assumed by bacterial degradation of low-grade organics generating electrons that are transferred to an electrode. The nature and efficiency of the electron transfer from the bacteria to the electrodes are determined by several chemical, physical and biological parameters. Specifically, the application of a specific potential at the bioanode has been shown to stimulate the formation of an electro-active biofilm, but the underlying mechanisms remain poorly understood. In this study, we have investigated the effect of an applied potential on the formation and electroactivity of biofilms established by Shewanella oneidensis bacteria on graphite felt electrodes in single- and double-chamber reactor configurations in oxic conditions. Using amperometry, cyclic voltammetry, and OCP/Power/Polarization curves techniques, we showed that a potential ranging between -0.3V and +0.5V (vs. Ag/AgCl/KCl sat.) and its converse application to a couple of electrodes leads to different electrochemical behaviors, anodic currents and biofilm architectures. For example, when the bacteria were confined in the anodic compartment of a double-chamber cell, a negative applied potential (-0.3V) at the bioanode favors a mediated electron transfer correlated with the progressive formation of a biofilm that fills the felt porosity and bridges the graphite fibers. In contrast, a positive applied potential (+0.3V) at the bioanode stimulates a direct electron transfer resulting in the fast-bacterial colonization of the fibers only. These results provide significant insight for the understanding of the complex bacteria-electrode interactions in microbial fuel cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Volatile-mediated suppression of plant pathogens is related to soil properties and microbial community composition

NARCIS (Netherlands)

Van Agtmaal, M.; Straathof, A.L.; Termorshuizen, Aad J; Lievens, Bart; Hoffland, Ellis; De Boer, W.

2018-01-01

There is increasing evidence that the soil microbial community produces a suite of volatile organic compounds that suppress plant pathogens. However, it remains unknown which soil properties and management practices influence volatile-mediated pathogen suppression. The aim of this study was to

Volatile-mediated suppression of plant pathogens is related to soil properties and microbial community composition

NARCIS (Netherlands)

Agtmaal, van Maaike; Straathof, Angela L.; Termorshuizen, Aad; Lievens, Bart; Hoffland, Ellis; Boer, de Wietse

2018-01-01

There is increasing evidence that the soil microbial community produces a suite of volatile organic compounds that suppress plant pathogens. However, it remains unknown which soil properties and management practices influence volatile-mediated pathogen suppression. The aim of this study was to

Mediator structure and rearrangements required for holoenzyme formation.

Science.gov (United States)

Tsai, Kuang-Lei; Yu, Xiaodi; Gopalan, Sneha; Chao, Ti-Chun; Zhang, Ying; Florens, Laurence; Washburn, Michael P; Murakami, Kenji; Conaway, Ronald C; Conaway, Joan W; Asturias, Francisco J

2017-04-13

The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.

Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

Science.gov (United States)

Davis, C. A.; Pyrak-Nolte, L. J.; Atekwana, E. A.; Werkema, D. D.; Haugen, M. E.

2009-12-01

Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand columns. A control column (non-biostimulated) and a biostimulated column were studied in a 2D acoustic scanning apparatus, and a second set of columns were constructed with Ag-AgCl electrodes for complex conductivity measurements. At the completion of the 29-day experiment, compressional wave amplitudes and arrival times for the control column were observed to be relatively uniform over the scanned 2D region. However, the biostimulated sample exhibited a high degree of spatial variability within the column for both the amplitude and arrival times. Furthermore, portions of the sample exhibited increased attenuation (~ 80%) concurrent with an increase in the arrival times, while other portions exhibited decreased attenuation (~ 45%) and decreased arrival time. The acoustic amplitude and arrival times changed significantly in the biostimulated column between Days 5 and 7 of the experiment and are consistent with a peak in the imaginary conductivity (σ”) values. The σ” response corresponds to different stages of biofilm development. That is, we interpret the peak σ” with the maximum biofilm thickness and decreasing σ” due to cell death or detachment. Environmental scanning electron microscope (ESEM) imaging confirmed microbial cell attachment to sand surfaces in the biostimulated columns, showed apparent differences in the morphology of attached biomass between regions of increased and decreased attenuation, and indicated no mineral precipitation or biomineralization. The heterogeneity in the elastic properties arises from the differences in the morphology and structure of attached biofilms. These results suggest that combining acoustic imaging and complex conductivity techniques

Selection of methanogenic microbial by gamma irradiation on improvement of unaerobic digestion efficiency on biogas formation

International Nuclear Information System (INIS)

M Yazid; Aris Bastianudin

2011-01-01

Selection of methanogenic microbial by gamma irradiation as an effort on improvement of efficiency process on biogas formation has been done. The objectives of this research is to obtain the methanogenic microbial isolate with high specific growth constant (μ), there for will be applicable for increasing the efficiency of biogas formation process. The microbial content sludge sample was taken from the digester tank conventional biogas installation located in Marangan village, Bokoharjo, Prambanan, Sleman and the sludge was irradiated using Co-60 gamma irradiator with varied dosage dose of 0-25 KGy. Microbial culture formation is conducted in growing media with 30% liquid rumen content in un-aerobe condition by addition of 80% H2 and 20% CO_2 gas mixture. Analysis of colony growth was performed by observation using long-wave ultraviolet rays (UV rays), while the microbial growth was by spectro-photometric analysis. Determination of gas methane product was done using gas chromatographic method. The result shown that 4 isolated methanogenic microbial (RB10, RB15, RB20 and RB25) that grown on 10-25 kGy gamma irradiation. The identification result shows that isolate RB10 and RB25 are belong to Methanobacterium genus, while isolate RB15 and RB20 are belong to Methanosarcina and Methanospirillum genus respectively. The specific growth constant (μ) values of the 4 bacterial isolates are in the range between 0.022 - 0.031. On the other hand, the efficiency of methane gas production for each isolates is in the range of 53.4%. - 67.6%. It can be concluded that isolate RB25 was the isolate with the highest specific growth constant (μ) value 0.031 and its efficiency of methane gas production was 67.6%. (author)

Modeling the formation of soluble microbial products (SMP in drinking water biofiltration

Directory of Open Access Journals (Sweden)

Yu Xin

2008-09-01

Full Text Available Both a theoretical and an empirical model were developed for predicting the formation of soluble microbial products (SMP during drinking water biofiltration. Four pilot-scale biofilters with ceramsite as the medium were fed with different acetate loadings for the determination of SMP formation. Using numerically simulated and measured parameters, the theoretical model was developed according to the substrate and biomass balance. The results of this model matched the measured data better for higher SMP formation but did not fit well when SMP formation was lower. In order to better simulate the reality and overcome the difficulties of measuring the kinetic parameters, a simpler empirical model was also developed. In this model, SMP formation was expressed as a function of fed organic loadings and the depth of the medium, and a much better fit was obtained.

Formation of industrial mixed culture biofilm in chlorophenol cultivated medium of microbial fuel cell

Science.gov (United States)

Hassan, Huzairy; Jin, Bo; Dai, Sheng; Ngau, Cornelius

2016-11-01

The formation of microbial biofilm while maintaining the electricity output is a challenging topic in microbial fuel cell (MFC) studies. This MFC critical factor becomes more significant when handling with industrial wastewater which normally contains refractory and toxic compounds. This study explores the formation of industrial mixed culture biofilm in chlorophenol cultivated medium through observing and characterizing microscopically its establishment on MFC anode surface. The mixed culture was found to develop its biofilm on the anode surface in the chlorophenol environment and established its maturity and dispersal stages with concurrent electricity generation and phenolic degradation. The mixed culture biofilm engaged the electron transfer roles in MFC by generating current density of 1.4 mA/m2 and removing 53 % of 2,4-dichlorophenol. The results support further research especially on hazardous wastewater treatment using a benign and sustainable method.

Modulation of neonatal microbial recognition: TLR-mediated innate immune responses are specifically and differentially modulated by human milk.

Science.gov (United States)

LeBouder, Emmanuel; Rey-Nores, Julia E; Raby, Anne-Catherine; Affolter, Michael; Vidal, Karine; Thornton, Catherine A; Labéta, Mario O

2006-03-15

The mechanisms controlling innate microbial recognition in the neonatal gut are still to be fully understood. We have sought specific regulatory mechanisms operating in human breast milk relating to TLR-mediated microbial recognition. In this study, we report a specific and differential modulatory effect of early samples (days 1-5) of breast milk on ligand-induced cell stimulation via TLRs. Although a negative modulation was exerted on TLR2 and TLR3-mediated responses, those via TLR4 and TLR5 were enhanced. This effect was observed in human adult and fetal intestinal epithelial cell lines, monocytes, dendritic cells, and PBMC as well as neonatal blood. In the latter case, milk compensated for the low capacity of neonatal plasma to support responses to LPS. Cell stimulation via the IL-1R or TNFR was not modulated by milk. This, together with the differential effect on TLR activation, suggested that the primary effect of milk is exerted upstream of signaling proximal to TLR ligand recognition. The analysis of TLR4-mediated gene expression, used as a model system, showed that milk modulated TLR-related genes differently, including those coding for signal intermediates and regulators. A proteinaceous milk component of > or =80 kDa was found to be responsible for the effect on TLR4. Notably, infant milk formulations did not reproduce the modulatory activity of breast milk. Together, these findings reveal an unrecognized function of human milk, namely, its capacity to influence neonatal microbial recognition by modulating TLR-mediated responses specifically and differentially. This in turn suggests the existence of novel mechanisms regulating TLR activation.

The role microbial sulfate reduction in the direct mediation of sedimentary authigenic carbonate precipitation

Science.gov (United States)

Turchyn, A. V.; Walker, K.; Sun, X.

2016-12-01

The majority of modern deep marine sediments are bathed in water that is undersaturated with respect to calcium carbonate. However, within marine sediments changing chemical conditions, driven largely by the microbial oxidation of organic carbon in the absence of oxygen, lead to supersaturated conditions and drive calcium carbonate precipitation. This sedimentary calcium carbonate is often called `authigenic carbonate', and is found in the form of cements and disseminated crystals within the marine sedimentary pile. As this precipitation of this calcium carbonate is microbially mediated, identifying authigenic carbonate within the geological record and understanding what information its geochemical and/or isotopic signature may hold is key for understanding its importance and what information it may contain past life. However, the modern controls on authigenic carbonate precipitation remain enigmatic because the myriad of microbially mediated reactions occurring within sediments both directly and indirectly impact the proton balance. In this submission we present data from 25 ocean sediment cores spanning the globe where we explore the deviation from the stoichiometrically predicted relationships among alkalinity, calcium and sulfate concentrations. In theory for every mol of organic carbon reduced by sulfate, two mol of alkalinity is produced, and to precipitate subsurface calcium carbonate one mol of calcium is used to consume two mol of alkalinity. We use this data with a model to explore changes in carbonate saturation state with depth below the seafloor. Alkalinity changes in the subsurface are poorly correlated with changes in calcium concentrations, however calcium concentrations are directly and tightly coupled to changes in sulfate concentrations in all studied sites. This suggests a direct role for sulfate reducing bacteria in the precipitation of subsurface carbonate cements.

Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases.

Science.gov (United States)

Welch, David; Buonanno, Manuela; Grilj, Veljko; Shuryak, Igor; Crickmore, Connor; Bigelow, Alan W; Randers-Pehrson, Gerhard; Johnson, Gary W; Brenner, David J

2018-02-09

Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207-222 nm) efficiently inactivates bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm 2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.

Live microbial cells adsorb Mg2+ more effectively than lifeless organic matter

Science.gov (United States)

Qiu, Xuan; Yao, Yanchen; Wang, Hongmei; Duan, Yong

2018-03-01

The Mg2+ content is essential in determining different Mg-CaCO3 minerals. It has been demonstrated that both microbes and the organic matter secreted by microbes are capable of allocating Mg2+ and Ca2+ during the formation of Mg-CaCO3, yet detailed scenarios remain unclear. To investigate the mechanism that microbes and microbial organic matter potentially use to mediate the allocation of Mg2+ and Ca2+ in inoculating systems, microbial mats and four marine bacterial strains ( Synechococcus elongatus, Staphylococcus sp., Bacillus sp., and Desulfovibrio vulgaris) were incubated in artificial seawater media with Mg/Ca ratios ranging from 0.5 to 10.0. At the end of the incubation, the morphology of the microbial mats and the elements adsorbed on them were analyzed using scanning electronic microscopy (SEM) and energy diffraction spectra (EDS), respectively. The content of Mg2+ and Ca2+ adsorbed by the extracellular polysaccharide substances (EPS) and cells of the bacterial strains were analyzed with atomic adsorption spectroscopy (AAS). The functional groups on the surface of the cells and EPS of S. elongatus were estimated using automatic potentiometric titration combined with a chemical equilibrium model. The results show that live microbial mats generally adsorb larger amounts of Mg2+ than Ca2+, while this rarely is the case for autoclaved microbial mats. A similar phenomenon was also observed for the bacterial strains. The living cells adsorb more Mg2+ than Ca2+, yet a reversed trend was observed for EPS. The functional group analysis indicates that the cell surface of S. elongatus contains more basic functional groups (87.24%), while the EPS has more acidic and neutral functional groups (83.08%). These features may be responsible for the different adsorption behavior of Mg2+ and Ca2+ by microbial cells and EPS. Our work confirms the differential Mg2+ and Ca2+ mediation by microbial cells and EPS, which may provide insight into the processes that microbes use to

Microbial Adhesion and Biofilm Formation on Microfiltration Membranes: A Detailed Characterization Using Model Organisms with Increasing Complexity

Directory of Open Access Journals (Sweden)

L. Vanysacker

2013-01-01

Full Text Available Since many years, membrane biofouling has been described as the Achilles heel of membrane fouling. In the present study, an ecological assay was performed using model systems with increasing complexity: a monospecies assay using Pseudomonas aeruginosa or Escherichia coli separately, a duospecies assay using both microorganisms, and a multispecies assay using activated sludge with or without spiked P. aeruginosa. The microbial adhesion and biofilm formation were evaluated in terms of bacterial cell densities, species richness, and bacterial community composition on polyvinyldifluoride, polyethylene, and polysulfone membranes. The data show that biofouling formation was strongly influenced by the kind of microorganism, the interactions between the organisms, and the changes in environmental conditions whereas the membrane effect was less important. The findings obtained in this study suggest that more knowledge in species composition and microbial interactions is needed in order to understand the complex biofouling process. This is the first report describing the microbial interactions with a membrane during the biofouling development.

Microbial Adhesion and Biofilm Formation on Microfiltration Membranes: A Detailed Characterization Using Model Organisms with Increasing Complexity

Science.gov (United States)

Vanysacker, L.; Denis, C.; Declerck, P.; Piasecka, A.; Vankelecom, I. F. J.

2013-01-01

Since many years, membrane biofouling has been described as the Achilles heel of membrane fouling. In the present study, an ecological assay was performed using model systems with increasing complexity: a monospecies assay using Pseudomonas aeruginosa or Escherichia coli separately, a duospecies assay using both microorganisms, and a multispecies assay using activated sludge with or without spiked P. aeruginosa. The microbial adhesion and biofilm formation were evaluated in terms of bacterial cell densities, species richness, and bacterial community composition on polyvinyldifluoride, polyethylene, and polysulfone membranes. The data show that biofouling formation was strongly influenced by the kind of microorganism, the interactions between the organisms, and the changes in environmental conditions whereas the membrane effect was less important. The findings obtained in this study suggest that more knowledge in species composition and microbial interactions is needed in order to understand the complex biofouling process. This is the first report describing the microbial interactions with a membrane during the biofouling development. PMID:23986906

Theoretical Propositions for the Citizen Formation Mediated by Technology

Directory of Open Access Journals (Sweden)

Tania Margarita Martínez de Padrón

2018-02-01

Full Text Available The research presented emerges from the connotations concerning the formation of the citizenship by the information technology and communication. Be part of the conception of the current citizen and the influence that has emerged through the utility of the various social networks, as well as Canaima education project and the guidance provided to schoolchildren in this sense. The general objective was to generate propositions theoretical that guide the formation of citizenship mediated by ICT in the primary schools of Santa Teresa del Tuy. The methodology used was the qualitative paradigm, based on the interpretative phenomenological approach of Heidegger, which is interested in discovering and understanding the meanings, habits and practices of the human being. Castle (2000: 5. The researcher approached the field object of study to observe, describe and interpret a reality. As an instrument used the interview in depth. The information obtained was recorded in pictures which allowed to comply with the development of specific objectives through triangulation. On whose findings prevailed deviating from the use of technological tools and how these have formed the formation of citizenship in school children in their behavior and actions. At the same time, allowed know from educational technological approach, that sparing the teacher provides guidance that redirect the formation of citizenship. Also was the stated objective as it was the theoretical propositions that guide the formation of citizens ICT-mediated.

Characteristics of microbial community involved in early biofilms formation under the influence of wastewater treatment plant effluent.

Science.gov (United States)

Peng, Yuke; Li, Jie; Lu, Junling; Xiao, Lin; Yang, Liuyan

2018-04-01

Effluents from wastewater treatment plants (WWTPs) containing microorganisms and residual nutrients can influence the biofilm formation. Although the process and mechanism of bacterial biofilm formation have been well characterized, little is known about the characteristics and interaction of bacteria, archaea and eukaryotes in the early colonization, especially under the influence of WWTP effluent. The aim of this study was to characterize the important bacterial, archaeal and eukaryotic species in the early stage of biofilm formation downstream of the WWTP outlet. Water and biofilm samples were collected 24 and 48hr after the deposition of bio-cords in the stream. Illumina Miseq sequencing of the 16S and 18S rDNA showed that, among the three domains, the bacterial biofilm community had the largest alpha and beta diversity. The early bacterial colonizers appeared to be "biofilm-specific", with only a few dominant operational taxonomic units (OTUs) shared between the biofilm and the ambient water environment. Alpha-proteobacteria and Ciliophora tended to dominate the bacterial and eukaryotic communities, respectively, of the early biofilm already at 24hr, whereas archaea played only a minor role during the early stage of colonization. The network analysis showed that the three domains of microbial community connected highly during the early colonization and it might be a characteristic of the microbial communities in the biofilm formation process where co-occurrence relationships could drive coexistence and diversity maintenance within the microbial communities. Copyright © 2017. Published by Elsevier B.V.

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient

Science.gov (United States)

Chapman, Eric; Cadillo-Quiroz, Hinsby; Childers, Daniel L.; Turetsky, Merritt R.; Waldrop, Mark P.

2017-01-01

Climate change is modifying global biogeochemical cycles. Microbial communities play an integral role in soil biogeochemical cycles; knowledge about microbial composition helps provide a mechanistic understanding of these ecosystem-level phenomena. Next generation sequencing approaches were used to investigate changes in microbial functional groups during ecosystem development, in response to climate change, in northern boreal wetlands. A gradient of wetlands that developed following permafrost degradation was used to characterize changes in the soil microbial communities that mediate C cycling: a bog representing an “undisturbed” system with intact permafrost, and a younger bog and an older bog that formed following the disturbance of permafrost thaw. Reference 16S rRNA databases and several diversity indices were used to assess structural differences among these communities, to assess relationships between soil microbial community composition and various environmental variables including redox potential and pH. Rates of potential CO2 and CH4 gas production were quantified to correlate sequence data with gas flux. The abundance of organic C degraders was highest in the youngest bog, suggesting higher rates of microbial processes, including potential CH4 production. In addition, alpha diversity was also highest in the youngest bog, which seemed to be related to a more neutral pH and a lower redox potential. These results could potentially be driven by increased niche differentiation in anaerobic soils. These results suggest that ecosystem structure, which was largely driven by changes in edaphic and plant community characteristics between the “undisturbed” permafrost bog and the two bogs formed following permafrost thaw, strongly influenced microbial function.

[Formation of microbial populations on the surface of protective coatings].

Science.gov (United States)

Kopteva, Zh P; Zanina, V V; Piliashenko-Novokhatnyĭ, A I; Kopteva, A E; Kozlova, I A

2001-01-01

Formation of microbial cenosis on the surface of polyethylene-, polyurethane- and oil-bitumen-based protective coatings was studied in dynamics during 1, 3, 7, 14 and 21 days. It has been shown that the biofilm was formed on the protective materials during 14 days and consisted of ammonifying, denitrifying, hydrocarbon-oxidizing and sulphate-reducing bacteria referred to Pseudomonas, Arthrobacter, Bacillus and Kesulfovibrio genera. The bacteria which form the biofilm on coatings possess high denitrifying and sulphate-reducing activities. Corrosion inhibitors-biocydes, introduced in composition of oil-bitumen coatings suppressed growth and metabolic activity of corrosion-active bacteria.

Chitosan matrices modified with carbon nanotubes for use in mediated microbial biosensing

International Nuclear Information System (INIS)

Demirkol, D.O.; Timur, S.

2011-01-01

We describe a microbial sensor based on Pseudomonas fluorescens cells that was prepared by modifying graphite electrodes with chitosan and carbon nanotubes. Chronoamperometry was performed at +0.3 V in the presence of hexacyanoferrate as a mediator and revealed a good response to glucose which is linear in the 1.0 to 5.0 mM concentration range. Linearity was defined by the equation of y = 102.120x-13.279 (R2 = 0.998) (y shows current density as nA. cm-2 and x shows glucose concentration in mM). The effect of the CNTs on the response was compared to that of electrodes made without CNTs. (author)

Role of EPS, Dispersant and Nutrients on the Microbial Response and MOS Formation in the Subarctic Northeast Atlantic

Directory of Open Access Journals (Sweden)

Tony Gutierrez

2017-04-01

Full Text Available In this study we report the formation of marine oil snow (MOS, its associated microbial community, the factors influencing its formation, and the microbial response to crude oil in surface waters of the Faroe-Shetland Channel (FSC. The FSC is a subarctic region that is hydrodynamically complex located in the northeast Atlantic where oil extraction is currently occurring and where exploration is likely to expand into its deeper waters (>500 m. A major oil spill in this region may mirror the aftermath that ensued following the Deepwater Horizon (DWH blowout in the Gulf of Mexico, where the massive influx of Macondo crude oil triggered the formation of copious quantities of rapidly sinking MOS and successional blooms of opportunistic oil-degrading bacteria. In laboratory experiments, we simulated environmental conditions in sea surface waters of the FSC using water collected from this site during the winter of 2015. We demonstrated that the presence of dispersant triggers the formation of MOS, and that nutrient amendments magnify this. Illumina MiSeq sequencing revealed the enrichment on MOS of associated oil-degrading (Cycloclasticus, Thalassolituus, Marinobacter and EPS-producing (Halomonas, Pseudoalteromonas, Alteromonas bacteria, and included major representation by Psychrobacter and Cobetia with putative oil-degrading/EPS-producing qualities. The formation of marine snow, in the absence of crude oil and dispersant, in seawater amended with nutrients alone indicated that the de novo synthesis of bacterial EPS is a key factor in MOS formation, and the glycoprotein composition of the MOS aggregates confirmed that its amorphous biopolymeric matrix was of microbial (likely bacterial origin. The presence of dispersants and crude oil with/without nutrients resulted in distinct microbial responses marked by intermittent, and in some cases short-lived, blooms of opportunistic heterotrophs, principally obligate hydrocarbonoclastic (Alcanivorax

Vertical microbial community variability of carbonate-based cones may provide insight into ancient conical stromatolite formation

Science.gov (United States)

Bradley, James; Daille, Leslie; Trivedi, Christopher; Bojanowski, Caitlin; Nunn, Heather; Stamps, Blake; Johnson, Hope; Stevenson, Bradley; Berelson, Will; Corsetti, Frank; Spear, John

2016-04-01

Stromatolite morphogenesis is poorly understood, and the process by which microbial mats become mineralized is a primary question in microbialite formation. Ancient conical stromatolites are primarily carbonate-based whereas the few modern analogues in hot springs are either non-mineralized or mineralized by silica. A team from the 2015 International GeoBiology Course investigated carbonate-rich microbial cones from near Little Hot Creek (LHC), Long Valley Caldera, California, to investigate how conical stromatolites might form in a hot spring carbonate system. The cones rise up from a layered microbial mat on the east side of a 45° C pool with very low flow that is super-saturated with respect to CaCO3. Cone structures are 8-30 mm in height, are rigid and do not deform when removed from the pool. Morphological characterization through environmental scanning electronic microscopy revealed that the cone structure is maintained by a matrix of intertwining microbial filaments around carbonate grains. This matrix gives rise to cone-filaments that are arranged vertically or horizontally, and provides further stability to the cone. Preliminary 16S rRNA gene analysis indicated variability of community composition between different vertical levels of the cone. The cone tip had comparatively greater abundance of filamentous cyanobacteria including Leptolingbya, Phormidium and Isosphaera and fewer heterotrophs (e.g. Chloroflexi) compared to the cone bottom. This supports the hypothesis that cone formation may depend on the differential abundance of the microbial community and their potential functional roles. Metagenomic analyses of the cones revealed potential genes related to chemotaxis and motility. Specifically, a genomic bin identified as a member of the genus Isosphaera contained an hmp chemotaxis operon implicated in gliding motility in the cyanobacterium Nostoc punctiforme. Isosphaera is a Planctomycete shown to have phototactic capabilities, and may play a role in

Effects of gene-augmentation on the formation, characteristics and microbial community of 2,4-dichlorophenoxyacetic acid degrading aerobic microbial granules

International Nuclear Information System (INIS)

Quan, Xiang-chun; Ma, Jing-yun; Xiong, Wei-cong; Yang, Zhi-feng

2011-01-01

Highlights: ► The first study to cultivate aerobic granules capable of utilizing 2,4-D as the sole carbon source. ► Granules cultivated through gene-augmentation were first compared systematically with the control on granule formation, degradation kinetics, morphology, and microbial community. ► The first report on the fate of transconjugats in the granules during long term operation after bioaugmentation. ► The first study to isolate in dominant bacteria in 2,4-D degrading microbial granules. - Abstract: Development of 2,4-dichlorophenoxyacetic acid (2,4-D) degrading aerobic granular sludge was conducted in two sequencing batch reactors (SBR) with one bioaugmented with a plasmid pJP4 donor strain Pseudomonas putida SM1443 and the other as a control. Half-matured aerobic granules pre-grown on glucose were used as the starting seeds and a two-stage operation strategy was applied. Granules capable of utilizing 2,4-D (about 500 mg/L) as the sole carbon source was successfully cultivated in both reactors. Gene-augmentation resulted in the enhancement of 2,4-D degradation rates by the percentage of 65–135% for the granules on Day 18, and 6–24% for the granules on Day 105. Transconjugants receiving plasmid pJP4 were established in the granule microbial community after bioaugmentation and persisted till the end of operation. Compared with the control granules, the granules in the bioaugmented reactor demonstrated a better settling ability, larger size, more abundant microbial diversity and stronger tolerance to 2,4-D. The finally obtained granules in the bioaugmented and control reactor had a granule size of around 600 μm and 500 μm, a Shannon–Weaver diversity index (H) of 0.96 and 0.55, respectively. A shift in microbial community was found during the granulation process.

Biomarker Analysis of Samples Visually Identified as Microbial in the Eocene Green River Formation: An Analogue for Mars.

Science.gov (United States)

Olcott Marshall, Alison; Cestari, Nicholas A

2015-09-01

One of the major exploration targets for current and future Mars missions are lithofacies suggestive of biotic activity. Although such lithofacies are not confirmation of biotic activity, they provide a way to identify samples for further analyses. To test the efficacy of this approach, we identified carbonate samples from the Eocene Green River Formation as "microbial" or "non-microbial" based on the macroscale morphology of their laminations. These samples were then crushed and analyzed by gas chromatography/mass spectroscopy (GC/MS) to determine their lipid biomarker composition. GC/MS analysis revealed that carbonates visually identified as "microbial" contained a higher concentration of more diverse biomarkers than those identified as "non-microbial," suggesting that this could be a viable detection strategy for selecting samples for further analysis or caching on Mars.

Extracellular Saccharide-Mediated Reduction of Au3+ to Gold Nanoparticles: New Insights for Heavy Metals Biomineralization on Microbial Surfaces.

Science.gov (United States)

Kang, Fuxing; Qu, Xiaolei; Alvarez, Pedro J J; Zhu, Dongqiang

2017-03-07

Biomineralization is a critical process controlling the biogeochemical cycling, fate, and potential environmental impacts of heavy metals. Despite the indispensability of extracellular polymeric substances (EPS) to microbial life and their ubiquity in soil and aquatic environments, the role played by EPS in the transformation and biomineralization of heavy metals is not well understood. Here, we used gold ion (Au 3+ ) as a model heavy metal ion to quantitatively assess the role of EPS in biomineralization and discern the responsible functional groups. Integrated spectroscopic analyses showed that Au 3+ was readily reduced to zerovalent gold nanoparticles (AuNPs, 2-15 nm in size) in aqueous suspension of Escherichia coli or dissolved EPS extracted from microbes. The majority of AuNPs (95.2%) was formed outside Escherichia coli cells, and the removal of EPS attached to cells pronouncedly suppressed Au 3+ reduction, reflecting the predominance of the extracellular matrix in Au 3+ reduction. XPS, UV-vis, and FTIR analyses corroborated that Au 3+ reduction was mediated by the hemiacetal groups (aldehyde equivalents) of reducing saccharides of EPS. Consistently, the kinetics of AuNP formation obeyed pseudo-second-order reaction kinetics with respect to the concentrations of Au 3+ and the hemiacetal groups in EPS, with minimal dependency on the source of microbial EPS. Our findings indicate a previously overlooked, universally significant contribution of EPS to the reduction, mineralization, and potential detoxification of metal species with high oxidation state.

The formation of group norms in computer-mediated communication

NARCIS (Netherlands)

Postmes, T; Spears, R; Lea, M

The formation of group norms in computer-mediated communication (CMC) was examined among students who used e-mail as part of a course. A network analysis of group structures revealed that (a) content and form of communication is normative, group norms defining communication patterns within groups,

Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils

Energy Technology Data Exchange (ETDEWEB)

Jeremy Semrau; Sung-Woo Lee; Jeongdae Im; Sukhwan Yoon; Michael Barcelona

2010-09-30

The overall objective of this project, 'Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils' was to develop effective, efficient, and economic methodologies by which microbial production of nitrous oxide can be minimized while also maximizing microbial consumption of methane in landfill cover soils. A combination of laboratory and field site experiments found that the addition of nitrogen and phenylacetylene stimulated in situ methane oxidation while minimizing nitrous oxide production. Molecular analyses also indicated that methane-oxidizing bacteria may play a significant role in not only removing methane, but in nitrous oxide production as well, although the contribution of ammonia-oxidizing archaea to nitrous oxide production can not be excluded at this time. Future efforts to control both methane and nitrous oxide emissions from landfills as well as from other environments (e.g., agricultural soils) should consider these issues. Finally, a methanotrophic biofiltration system was designed and modeled for the promotion of methanotrophic activity in local methane 'hotspots' such as landfills. Model results as well as economic analyses of these biofilters indicate that the use of methanotrophic biofilters for controlling methane emissions is technically feasible, and provided either the costs of biofilter construction and operation are reduced or the value of CO{sub 2} credits is increased, can also be economically attractive.

Acid-deposition research program. Volume 2. Effects of acid-forming emissions on soil microorganisms and microbially-mediated processes

Energy Technology Data Exchange (ETDEWEB)

Visser, S.; Danielson, R.M.; Parr, J.F.

1987-02-01

The interactions of soil physical, chemical, and biological processes are ultimately expressed in a soil's fertility and its capacity for plant production. Consequently, much of the research conducted to date regarding the impact of acid-forming pollutants on soil properties has been geared towards possible effects on plant productivity. This trend continues in this paper where the effects of acidic deposition on microbial communities are reviewed in relation to potential impact on plant growth. The objectives of the review are to discuss: (1) The effects of acid-forming emissions (primarily S-containing pollutants) on microbial community structure with emphasis on qualitative and quantitative aspects; (2) The effects of acidic deposition on microbially mediated processes (i.e., community functions); (3) Acidification effects of pollutants on symbiotic and disease-causing microorganisms. The symbionts discussed include ectomycorrhizal fungi, vesicular-arbuscular mycorrhizal fungi, and N/sub 2/-fixing bacteria, particularly Rhizobium, while the disease-causing microorganisms will include those responsible for foliage, stem, and root diseases.

Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analogue

Directory of Open Access Journals (Sweden)

Stuart E Denman

2015-10-01

Full Text Available Japanese goats fed a diet of 50% Timothy grass and 50% concentrate with increasing levels of the anti-methanogenic compound, bromochloromethane (BCM were investigated with respect to the microbial shifts in the rumen. Microbial ecology methods identified many species that exhibited positive and negative responses to the increasing levels of BCM. The methane-inhibited rumen appeared to adapt to the higher H2 levels by shifting fermentation to propionate which was mediated by an increase in the population of hydrogen-consuming Prevotella and Selenomonas spp. Metagenomic analysis of propionate production pathways was dominated by genomic content from these species. Reductive acetogenic marker gene libraries and metagenomics analysis indicate that reductive acetogenic species do not play a major role in the BCM treated rumen.

Nutrient limitation and microbially mediated chemistry: studies using tuff inoculum obtained from the Exploratory Studies Facility, Yucca Mountain

International Nuclear Information System (INIS)

Chen, C. I.; Chuu, Y. J.; Meike, A.; Ringelberg, D.; Sawvel, A.

1998-01-01

Flow-through bioreactors are used to investigate the relationship between the supply (and limitation) of major nutrients required by microorganisms (C, N, P, S) and effluent chemistry to obtain data that can be useful to develop models of microbially mediated aqueous chemistry. The bioreactors were inoculated with crushed tuff from Yucca Mountain. Six of the 14 bioreactor experiments currently in operation have shown growth, which occurred in as few as 5 days and as much as a few months after initiation of the experiment. All of the bioreactors exhibiting growth contained glucose as a carbon source, but other nutritional components varied. Chemical signatures of each bioreactor were compared to each other and selected results were compared to computer simulations of the equivalent abiotic chemical reactions. At 21 C, the richest medium formulation produced a microbial community that lowered the effluent pH from 6.4 to as low as 3.9. The same medium formulation at 50 C produced no significant change in pH but caused a significant increase in Cl after a period of 200 days. Variations in concentrations of other elements, some of which appear to be periodic (Ca, Mg, etc.) also occur. Bioreactors fed with low C, N, P, S media showed growth, but had stabilized at lower cell densities. The room temperature bioreactor in this group exhibited a phospholipid fatty acid (PLFA) signature of sulfur- or iron-reducing bacteria, which produced a significant chemical signature in the effluent from that bioreactor. Growth had not been observed yet in the alkaline bioreactors, even in those containing glucose. The value of combining detailed chemical and community (e.g., ester-linked PLFA) analyses, long-duration experiments, and abiotic chemical models to distinguish chemical patterns is evident. Although all of the bioreactors contain the same initial microorganisms and mineral constituents, PLFA analysis demonstrates that both input chemistry and temperature determine the

Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of methanogenesis in production water of high-temperature oil reservoirs amended with bicarbonate

Directory of Open Access Journals (Sweden)

Guang-Chao eYang

2016-03-01

Full Text Available CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in Carbon Dioxide Capture and Storage (CDCS facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form (0~90 mM with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs.

Formation of Chromophoric Dissolved Organic Matter by Bacterial Degradation of Phytoplankton-Derived Aggregates

Directory of Open Access Journals (Sweden)

Joanna D. Kinsey

2018-01-01

Full Text Available Organic matter produced and released by phytoplankton during growth is processed by heterotrophic bacterial communities that transform dissolved organic matter into biomass and recycle inorganic nutrients, fueling microbial food web interactions. Bacterial transformation of phytoplankton-derived organic matter also plays a poorly known role in the formation of chromophoric dissolved organic matter (CDOM which is ubiquitous in the ocean. Despite the importance of organic matter cycling, growth of phytoplankton and activities of heterotrophic bacterial communities are rarely measured in concert. To investigate CDOM formation mediated by microbial processing of phytoplankton-derived aggregates, we conducted growth experiments with non-axenic monocultures of three diatoms (Skeletonema grethae, Leptocylindrus hargravesii, Coscinodiscus sp. and one haptophyte (Phaeocystis globosa. Phytoplankton biomass, carbon concentrations, CDOM and base-extracted particulate organic matter (BEPOM fluorescence, along with bacterial abundance and hydrolytic enzyme activities (α-glucosidase, β-glucosidase, leucine-aminopeptidase were measured during exponential growth and stationary phase (~3–6 weeks and following 6 weeks of degradation. Incubations were performed in rotating glass bottles to keep cells suspended, promoting cell coagulation and, thus, formation of macroscopic aggregates (marine snow, more similar to surface ocean processes. Maximum carbon concentrations, enzyme activities, and BEPOM fluorescence occurred during stationary phase. Net DOC concentrations (0.19–0.46 mg C L−1 increased on the same order as open ocean concentrations. CDOM fluorescence was dominated by protein-like signals that increased throughout growth and degradation becoming increasingly humic-like, implying the production of more complex molecules from planktonic-precursors mediated by microbial processing. Our experimental results suggest that at least a portion of open

Microbial carbon pump and its significance for carbon sequestration in soils

Science.gov (United States)

Liang, Chao

2017-04-01

Studies of the decomposition, transformation and stabilization of soil organic carbon have dramatically increased in recent years due to growing interest in studying the global carbon cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic carbon reservoir in soils depends upon microbial involvement because soil carbon dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microbe-mediated processes lead to soil carbon stabilization. Here, two pathways, ex vivo modification and in vivo turnover, were defined to jointly explain soil carbon dynamics driven by microbial catabolism and/or anabolism. Accordingly, a conceptual framework consisting of the raised concept of the soil "microbial carbon pump" (MCP) was demonstrated to describe how microbes act as an active player in soil carbon storage. The hypothesis is that the long-term microbial assimilation process may facilitate the formation of a set of organic compounds that are stabilized (whether via protection by physical interactions or a reduction in activation energy due to chemical composition), ultimately leading to the sequestration of microbial-derived carbon in soils. The need for increased efforts was proposed to seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil carbon dynamics to the responses of the terrestrial carbon cycle under global change.

The Mediating Role of Psychosocial Benefits in the Satisfaction Formation Process

NARCIS (Netherlands)

O. Prevo; P. Leunisse; H. Roest (Henk)

1999-01-01

textabstractIn this paper we investigate the mediating role of psychosocial benefits in the customer satisfaction/dissatisfaction formation process. Most research on this subject deals with the causality direction of psychosocial benefits and satisfaction, sometimes preceded by an overall functional

The importance of anabolism in microbial control over soil carbon storage

Energy Technology Data Exchange (ETDEWEB)

Liang, Chao; Schimel, Joshua P.; Jastrow, Julie D.

2017-07-25

Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolism and/or anabolism. Accordingly, we use the conceptual framework of the soil ‘microbial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.

Spatial Autocorrelation, Source Water and the Distribution of Total and Viable Microbial Abundances within a Crystalline Formation to a Depth of 800 m

Directory of Open Access Journals (Sweden)

E. D. Beaton

2017-09-01

Full Text Available Proposed radioactive waste repositories require long residence times within deep geological settings for which we have little knowledge of local or regional subsurface dynamics that could affect the transport of hazardous species over the period of radioactive decay. Given the role of microbial processes on element speciation and transport, knowledge and understanding of local microbial ecology within geological formations being considered as host formations can aid predictions for long term safety. In this relatively unexplored environment, sampling opportunities are few and opportunistic. We combined the data collected for geochemistry and microbial abundances from multiple sampling opportunities from within a proposed host formation and performed multivariate mixing and mass balance (M3 modeling, spatial analysis and generalized linear modeling to address whether recharge can explain how subsurface communities assemble within fracture water obtained from multiple saturated fractures accessed by boreholes drilled into the crystalline formation underlying the Chalk River Laboratories site (Deep River, ON, Canada. We found that three possible source waters, each of meteoric origin, explained 97% of the samples, these are: modern recharge, recharge from the period of the Laurentide ice sheet retreat (ca. ∼12000 years before present and a putative saline source assigned as Champlain Sea (also ca. 12000 years before present. The distributed microbial abundances and geochemistry provide a conceptual model of two distinct regions within the subsurface associated with bicarbonate – used as a proxy for modern recharge – and manganese; these regions occur at depths relevant to a proposed repository within the formation. At the scale of sampling, the associated spatial autocorrelation means that abundances linked with geochemistry were not unambiguously discerned, although fine scale Moran’s eigenvector map (MEM coefficients were correlated with

Information transmission in microbial and fungal communication: from classical to quantum.

Science.gov (United States)

Majumdar, Sarangam; Pal, Sukla

2018-06-01

Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.

Microbial herd protection mediated by antagonistic interaction in polymicrobial communities.

Science.gov (United States)

Wong, Megan; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian; Dong, Tao G

2016-09-16

In the host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist - despite significant antagonistic interactions between species - are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through delivery of toxic effectors. It is well established that intra-species protection is conferred by immunity proteins that neutralize effector toxicities. By contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS active antagonistic bacteria, Aeromonas hydrophila (AH) and Vibrio cholerae (VC), to demonstrate that interspecies protection is dependent on effectors. AH and VC do not share conserved immunity genes but could equally co-exist in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the other competing wild type. Time-lapse microscopy analyses show that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interaction inside each cluster and restricting it to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulate our experimental observation. These results provide mechanistic insights for the general role of microbial weapons in determining the structures of complex multispecies communities. Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in determining community structures and exchange of genetic materials

Microbial Herd Protection Mediated by Antagonistic Interaction in Polymicrobial Communities

Science.gov (United States)

Wong, Megan J. Q.; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian

2016-01-01

ABSTRACT In host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist, despite significant antagonistic interactions between species, are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through the delivery of toxic effectors. It is well established that intraspecies protection is conferred by immunity proteins that neutralize effector toxicities. In contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS-active antagonistic bacterial species, Aeromonas hydrophila and Vibrio cholerae, to demonstrate that interspecies protection is dependent on effectors. A. hydrophila and V. cholerae do not share conserved immunity genes but could coexist equally in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the competing wild-type strain. Time-lapse microscopic analyses showed that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interactions inside each cluster and restricting the interactions to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulated our experimental observations. These results provide mechanistic insights regarding the general role of microbial weapons in determining the structures of complex multispecies communities. IMPORTANCE Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in

Geochemical patterns and microbial contribution to iron plaque formation in the rice plant rhizosphere

Science.gov (United States)

Maisch, Markus; Murata, Chihiro; Unger, Julia; Kappler, Andreas; Schmidt, Caroline

2015-04-01

Rice is the major food source for more than half of the world population and 80 percent of the worldwide rice cultivation is performed on water logged paddy soils. The establishment of reducing conditions in the soil and across the soil-water interface not only stimulates the microbial production and release of the greenhouse gas methane. These settings also create optimal conditions for microbial iron(III) reduction and therefore saturate the system with reduced ferrous iron. Through the reduction and dissolution of ferric minerals that are characterized by their high surface activity, sorbed nutrients and contaminants (e.g. arsenic) will be mobilized and are thus available for uptake by plants. Rice plants have evolved a strategy to release oxygen from their roots in order to prevent iron toxification in highly ferrous environments. The release of oxygen to the reduced paddy soil causes ferric iron plaque formation on the rice roots and finally increases the sorption capacity for toxic metals. To this date the geochemical and microbiological processes that control the formation of iron plaque are not deciphered. It has been hypothesized that iron(II)-oxidizing bacteria play a potential role in the iron(III) mineral formation along the roots. However, not much is known about the actual processes, mineral products, and geochemical gradients that establish within the rhizosphere. In the present study we have developed a growth set-up that allows the co-cultivation of rice plants and iron(II)-oxidizing bacteria, as well as the visual observation and in situ measurement of geochemical parameters. Oxygen and dissolved iron(II) gradients have been measured using microelectrodes and show geochemical hot spots that offer optimal growth conditions for microaerophilic iron(II) oxidizers. First mineral identification attempts of iron plaque have been performed using Mössbauer spectroscopy and microscopy. The obtained results on mineraology and crystallinity have been

Macrophage conditioned medium induced cellular network formation in MCF-7 cells through enhanced tunneling nanotube formation and tunneling nanotube mediated release of viable cytoplasmic fragments

International Nuclear Information System (INIS)

Patheja, Pooja; Sahu, Khageswar

2017-01-01

Infiltrating macrophages in tumor microenvironment, through their secreted cytokines and growth factors, regulate several processes of cancer progression such as cancer cell survival, proliferation, invasion, metastasis and angiogenesis. Recently, intercellular cytoplasmic bridges between cancer cells referred as tunneling nanotubes (TNTs) have been recognized as novel mode of intercellular communication between cancer cells. In this study, we investigated the effect of inflammatory mediators present in conditioned medium derived from macrophages on the formation of TNTs in breast adenocarcinoma cells MCF-7. Results show that treatment with macrophage conditioned medium (MφCM) not only enhanced TNT formation between cells but also stimulated the release of independently migrating viable cytoplasmic fragments, referred to as microplasts, from MCF-7 cells. Time lapse microscopy revealed that microplasts were released from parent cancer cells in extracellular space through formation of TNT-like structures. Mitochondria, vesicles and cytoplasm could be transferred from parent cell body to microplasts through connecting TNTs. The microplasts could also be resorbed into the parent cell body by retraction of the connecting TNTs. Microplast formation inhibited in presence cell migration inhibitor, cytochalasin-B. Notably by utilizing migratory machinery within microplasts, distantly located MCF-7 cells formed several TNT based intercellular connections, leading to formation of physically connected network of cells. Together, these results demonstrate novel role of TNTs in microplast formation, novel modes of TNT formation mediated by microplasts and stimulatory effect of MφCM on cellular network formation in MCF-7 cells mediated through enhanced TNT and microplast formation.

Macrophage conditioned medium induced cellular network formation in MCF-7 cells through enhanced tunneling nanotube formation and tunneling nanotube mediated release of viable cytoplasmic fragments

Energy Technology Data Exchange (ETDEWEB)

Patheja, Pooja, E-mail: pooja.patheja8@gmail.com [Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore 452013, Madhya Pradesh (India); Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra (India); Sahu, Khageswar [Laser Biomedical Applications Section, Raja Ramanna Centre for Advanced Technology, Indore 452013, Madhya Pradesh (India)

2017-06-15

Infiltrating macrophages in tumor microenvironment, through their secreted cytokines and growth factors, regulate several processes of cancer progression such as cancer cell survival, proliferation, invasion, metastasis and angiogenesis. Recently, intercellular cytoplasmic bridges between cancer cells referred as tunneling nanotubes (TNTs) have been recognized as novel mode of intercellular communication between cancer cells. In this study, we investigated the effect of inflammatory mediators present in conditioned medium derived from macrophages on the formation of TNTs in breast adenocarcinoma cells MCF-7. Results show that treatment with macrophage conditioned medium (MφCM) not only enhanced TNT formation between cells but also stimulated the release of independently migrating viable cytoplasmic fragments, referred to as microplasts, from MCF-7 cells. Time lapse microscopy revealed that microplasts were released from parent cancer cells in extracellular space through formation of TNT-like structures. Mitochondria, vesicles and cytoplasm could be transferred from parent cell body to microplasts through connecting TNTs. The microplasts could also be resorbed into the parent cell body by retraction of the connecting TNTs. Microplast formation inhibited in presence cell migration inhibitor, cytochalasin-B. Notably by utilizing migratory machinery within microplasts, distantly located MCF-7 cells formed several TNT based intercellular connections, leading to formation of physically connected network of cells. Together, these results demonstrate novel role of TNTs in microplast formation, novel modes of TNT formation mediated by microplasts and stimulatory effect of MφCM on cellular network formation in MCF-7 cells mediated through enhanced TNT and microplast formation.

Chlorination or monochloramination: Balancing the regulated trihalomethane formation and microbial inactivation in marine aquaculture waters

KAUST Repository

Sanawar, Huma

2017-08-15

Disinfection methods like chlorination are increasingly used to sanitize the water, equipment, tools and surfaces in aquaculture facilities. This is to improve water quality, and to maintain a hygienic environment for the well-being of aquatic organisms. However, chlorination can result in formation of regulated disinfection byproducts (DBPs) that can be carcinogenic and toxic. This study aims to evaluate if an optimal balance can be achieved between minimal regulated DBP formation and effective microbial inactivation with either chlorination or monochloramination for application in the Red Sea aquaculture waters. Upon chlorination, the concentration of total trihalomethanes (THMs), primarily bromoform, exceeded the regulatory limit of 80μg/L even at the lowest tested concentration of chlorine (1mg/L) and contact time (1h). Comparatively, regulated THMs concentration was only detectable at 30μg/L level in one of the three sets of monochloraminated marine aquaculture waters. The average log reduction of antibiotic-resistant bacteria (ARB) by chlorine ranged from 2.3-log to 3.2-log with different contact time. The average log reduction of ARB by monochloramine was comparatively lower at 1.9 to 2.9-log. Although viable Staphylococcus aureus was recovered from monochloraminated samples as opposed to chlorinated samples, the abundance of S. aureus was not high enough to result in any significant microbial risks. Both chlorination and monochloramination did not provide any significant improvement in the reduction of antibiotic resistance genes (ARGs). This study demonstrates that a systematic evaluation is needed to determine the optimal disinfectant required to balance both microbial and chemical risks. Compared to chlorine, monochloramine may be a more appropriate disinfection strategy for the treatment of aquaculture effluents prior to discharge or for recirculatory use in the aquaculture facility.

Effect of advanced oxidation on N-nitrosodimethylamine (NDMA) formation and microbial ecology during pilot-scale biological activated carbon filtration.

Science.gov (United States)

Li, Dong; Stanford, Ben; Dickenson, Eric; Khunjar, Wendell O; Homme, Carissa L; Rosenfeldt, Erik J; Sharp, Jonathan O

2017-04-15

Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H 2 O 2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H 2 O 2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated. While microbial populations were highly similar in the upper reaches, deeper samples revealed a divergence within and between BAC filtration systems where EBCT was identified to be a significant environmental predictor for shifts in microbial populations. The abundance of Nitrospira in the top samples of both columns provides an explanation for the oxidation of nitrite and corresponding increases in nitrate concentrations during BAC transit and support interplay between nitrogen cycling with nitrosamine formation. The results of this study demonstrate that pretreatments using ozone versus UV/H 2 O 2 impart modest differences to the overall BAC microbial population structural and functional attributes, and further highlight the need to evaluate NDMA formation prior to full-scale implementation of BAC in potable reuse applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial bebop: creating music from complex dynamics in microbial ecology.

Science.gov (United States)

Larsen, Peter; Gilbert, Jack

2013-01-01

In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

Gold nanoparticles produced in situ mediate bioelectricity and hydrogen production in a microbial fuel cell by quantized capacitance charging.

Science.gov (United States)

Kalathil, Shafeer; Lee, Jintae; Cho, Moo Hwan

2013-02-01

Oppan quantized style: By adding a gold precursor at its cathode, a microbial fuel cell (MFC) is demonstrated to form gold nanoparticles that can be used to simultaneously produce bioelectricity and hydrogen. By exploiting the quantized capacitance charging effect, the gold nanoparticles mediate the production of hydrogen without requiring an external power supply, while the MFC produces a stable power density. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Macrophage conditioned medium induced cellular network formation in MCF-7 cells through enhanced tunneling nanotube formation and tunneling nanotube mediated release of viable cytoplasmic fragments.

Science.gov (United States)

Patheja, Pooja; Sahu, Khageswar

2017-06-15

Infiltrating macrophages in tumor microenvironment, through their secreted cytokines and growth factors, regulate several processes of cancer progression such as cancer cell survival, proliferation, invasion, metastasis and angiogenesis. Recently, intercellular cytoplasmic bridges between cancer cells referred as tunneling nanotubes (TNTs) have been recognized as novel mode of intercellular communication between cancer cells. In this study, we investigated the effect of inflammatory mediators present in conditioned medium derived from macrophages on the formation of TNTs in breast adenocarcinoma cells MCF-7. Results show that treatment with macrophage conditioned medium (MɸCM) not only enhanced TNT formation between cells but also stimulated the release of independently migrating viable cytoplasmic fragments, referred to as microplasts, from MCF-7 cells. Time lapse microscopy revealed that microplasts were released from parent cancer cells in extracellular space through formation of TNT-like structures. Mitochondria, vesicles and cytoplasm could be transferred from parent cell body to microplasts through connecting TNTs. The microplasts could also be resorbed into the parent cell body by retraction of the connecting TNTs. Microplast formation inhibited in presence cell migration inhibitor, cytochalasin-B. Notably by utilizing migratory machinery within microplasts, distantly located MCF-7 cells formed several TNT based intercellular connections, leading to formation of physically connected network of cells. Together, these results demonstrate novel role of TNTs in microplast formation, novel modes of TNT formation mediated by microplasts and stimulatory effect of MɸCM on cellular network formation in MCF-7 cells mediated through enhanced TNT and microplast formation. Copyright © 2017 Elsevier Inc. All rights reserved.

Models of microbiome evolution incorporating host and microbial selection.

Science.gov (United States)

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

Non-enzymatic palladium recovery on microbial and synthetic surfaces.

Science.gov (United States)

Rotaru, Amelia-Elena; Jiang, Wei; Finster, Kai; Skrydstrup, Troels; Meyer, Rikke Louise

2012-08-01

The use of microorganisms as support for reduction of dissolved Pd(II) to immobilized Pd(0) nanoparticles is an environmentally friendly approach for Pd recovery from waste. To better understand and engineer Pd(0) nanoparticle synthesis, one has to consider the mechanisms by which Pd(II) is reduced on microbial surfaces. Escherichia coli, Shewanella oneidensis, and Pseudomonas putida were used as model organisms in order to elucidate the role of microbial cells in Pd(II) reduction under acidic conditions. Pd(II) was reduced by formate under acidic conditions, and the process occurred substantially faster in the presence of cells as compared to cell-free controls. We found no difference between native (untreated) and autoclaved cells, and could demonstrate that even a non-enzymatic protein (bovine serum albumin) stimulated Pd(II) reduction as efficiently as bacterial cells. Amine groups readily interact with Pd(II), and to specifically test their role in surface-assisted Pd(II) reduction by formate, we replaced bacterial cells with polystyrene microparticles functionalized with amine or carboxyl groups. Amine-functionalized microparticles had the same effect on Pd(II) reduction as bacterial cells, and the effect could be hampered if the amine groups were blocked by acetylation. The interaction with amine groups was confirmed by infrared spectroscopy on whole cells and amine-functionalized microparticles. In conclusion, bio-supported Pd(II) reduction on microbial surfaces is possibly mediated by a non-enzymatic mechanism. We therefore suggest the use of amine-rich biomaterials rather than intact cells for Pd bio-recovery from waste. Copyright © 2012 Wiley Periodicals, Inc.

What do we really know about the role of microorganisms in iron sulfide mineral formation?

Science.gov (United States)

Picard, Aude A.; Gartman, Amy; Girguis, Peter R.

2016-01-01

Iron sulfide mineralization in low-temperature systems is a result of biotic and abiotic processes, though the delineation between these two modes of formation is not always straightforward. Here we review the role of microorganisms in the precipitation of extracellular iron sulfide minerals. We summarize the evidence that links sulfur-metabolizing microorganisms and sulfide minerals in nature and we present a critical overview of laboratory-based studies of the nucleation and growth of iron sulfide minerals in microbial cultures. We discuss whether biologically derived minerals are distinguishable from abiotic minerals, possessing attributes that are uniquely diagnostic of biomineralization. These inquiries have revealed the need for additional thorough, mechanistic and high-resolution studies to understand microbially mediated formation of a variety of sulfide minerals across a range of natural environments.

Contribution of eukaryotic microbial communities to the formation of Fe-rich accretions in an extreme acidic environment

Science.gov (United States)

Rodrigues, L.; Valente, T.; Correia, A.; Alves, A.; Foing, B.; Davies, G. R.

2012-04-01

In the acid mine drainage of Valdarcas, northern Portugal, Fe-rich tubular and spherical macroaccretions are directly associated with the presence of eukaryotic microorganisms. This raises the question whether they are biogenically-derived or the result of an abiotic process mediated by microeukaryotic phototrophs. The drainage water at Valdarcas is characterized by very low pH values (pHhigh metal solubility and presence of iron colloids. Mineralogical analysis (XRD and SEM) of the precipitates indicates a mixture of goethite, schwertmannite and jarosite. Euglenophyta and Chlorophyta acidophilic algal were previously identified in this site. The spatial distribution of Euglena mutabilis indicated that it has a preference to grow up on schwertmannite-rich precipitates. Field observations demonstrate the existence of oxygenated microenvironments created by algal activity suggesting that algae influence iron minerals precipitation, especially schwertmannite. The mineral-microorganism interactions are relevant to understanding this unique and extreme environment. Further investigations regarding the mineralogical and chemical characterization of these deposits, and the identification of microorganisms involved in the process could be helpful to enhance our knowledge of past Fe formations throughout Earth's primordial environment. It is expectable that this information will contribute to establish a framework for recognition of biosignatures on other planets and extraterrestrial bodies. In this study, results on the chemical and mineralogical composition of the structures are presented. The biological context is characterised based on observations made by optical microscopy complemented with molecular data on the microbial communities obtained by culture independent methods. The results are discussed within the context of two models: the studied Fe-rich stromatolites are microeukaryotic-mediated as described by previous workers from similar environments or are the

Swimming Motility Mediates the Formation of Neutrophil Extracellular Traps Induced by Flagellated Pseudomonas aeruginosa.

Directory of Open Access Journals (Sweden)

Madison Floyd

2016-11-01

Full Text Available Pseudomonas aeruginosa is an opportunistic pathogen causing severe infections often characterized by robust neutrophilic infiltration. Neutrophils provide the first line of defense against P. aeruginosa. Aside from their defense conferred by phagocytic activity, neutrophils also release neutrophil extracellular traps (NETs to immobilize bacteria. Although NET formation is an important antimicrobial process, the details of its mechanism are largely unknown. The identity of the main components of P. aeruginosa responsible for triggering NET formation is unclear. In this study, our focus was to identify the main bacterial factors mediating NET formation and to gain insight into the underlying mechanism. We found that P. aeruginosa in its exponential growth phase promoted strong NET formation in human neutrophils while its NET-inducing ability dramatically decreased at later stages of bacterial growth. We identified the flagellum as the primary component of P. aeruginosa responsible for inducing NET extrusion as flagellum-deficient bacteria remained seriously impaired in triggering NET formation. Purified P. aeruginosa flagellin, the monomeric component of the flagellum, does not stimulate NET formation in human neutrophils. P. aeruginosa-induced NET formation is independent of the flagellum-sensing receptors TLR5 and NLRC4 in both human and mouse neutrophils. Interestingly, we found that flagellar motility, not flagellum binding to neutrophils per se, mediates NET release induced by flagellated bacteria. Immotile, flagellar motor-deficient bacterial strains producing paralyzed flagella did not induce NET formation. Forced contact between immotile P. aeruginosa and neutrophils restored their NET-inducing ability. Both the motAB and motCD genetic loci encoding flagellar motor genes contribute to maximal NET release; however the motCD genes play a more important role. Phagocytosis of P. aeruginosa and superoxide production by neutrophils were also

Microbial effects on high-level waste disposal. Research review and perspective

Energy Technology Data Exchange (ETDEWEB)

Ohnuki, Toshihiko [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

2002-09-01

Various microorganisms have been observed in deep geologic formation. The effects of such microorganisms on the performance of HLW disposal are still unknown. This paper reviews the studies of microbial effects on the long-term containment of HLW disposal, and discusses the future work to be carried out. Microbial reduction and oxidation and byproducts derived from microbial activities affect performance of HLW repository and have a potential to enhance actinides migration in geologic formation (degradation of the materials of repository, complex-formation, dissolution of actinides precipitates and occurrence of nm scale colloid formation). Potential microbial perturbation of performance of the barriers may enhance confinement of actinides by biomineralization, bioadsorption, bioaccumulation and precipitation. These studies indicate that further experiments are required to elucidate microbial effects on the performance of HLW disposal. (author)

Formation and functions of aerobic microbial granula; Entstehung und Funktionen aerober mikrobieller Granula

Energy Technology Data Exchange (ETDEWEB)

Etterer, T.; Wilderer, P.A. [Technische Univ. Muenchen, Garching (Germany). Lehrstuhl und Pruefamt fuer Wasserguete- und Abfallwirtschaft

1999-07-01

The present project investigates the phenomenon of the formation of aerobic microbial granula and their properties. To generate granula, sequencing batch reactors fed in batches were used. As shown by microbiological assays, fungi played an above-average role in granula formation and build-up. In first degradation experiments, furthermore, chemical oxygen demand (COD) could be reduced by over 90 %. The determination yielded comparable values to activated sludge, standing on average at 1.044g/ml. (orig.) [German] Im Rahmen des hier vorgestellten Projekts wurde das Phaenomen der Bildung aerober mikrobieller Granula sowie deren Eigenschaften untersucht. Zur Erzeugung von Granula wurden schubweise beschickte Reaktoren, sogenannte Sequencing-Batch-Reaktoren (SBR) verwendet. Wie mikrobiologische Untersuchungen zeigten spielen Pilze bei der Entstehung und beim Aufbau eine ueberdurchschnittliche Rolle. Des weiteren konnte in ersten Abbauversuchen der chemische Sauerstoff-Bedarf (CSB) um ueber 90% gesenkt werden. Die Dichtebestimmung ergab vergleichbare Werte zu Belebtschlamm und zwar im Durchschnitt 1,044 g/ml. (orig.)

Microbial involvement in the formation of Cambrian sea-floor silica-iron oxide deposits, Australia

Science.gov (United States)

Duhig, Nathan C.; Davidson, Garry J.; Stolz, Joe

1992-06-01

The Cambrian-Ordovician Mount Windsor volcanic belt in northern Australia is host to stratiform lenses of massive ferruginous chert that are spatially associated with volcanogenic massive sulfide occurrences, in particular the Thalanga zinc-lead-copper-silver deposit. The rocks are composed principally of Fe2O3 and SiO2, with very low concentrations of alkalic elements, and lithogenous elements such as Al, Zr, and Ti; they are interpreted as nearly pure chemical sediments. Textural evidence is documented of the integral role of filamentous bacteria (and/or fungi) in depositing iron from hydrothermal fluids, and of the inorganic precipitation of silica-iron-oxyhydroxide gels that subsequently matured to subcrystalline and crystalline silica forms. At least three distinct iron-accumulating microbial forms are distinguished: networks of septate filaments, nonseptate filament networks, and extremely coarse branching filaments that do not reconnect. Values for δ34S in disseminated pyrite are up to 50‰ lighter than those of contemporaneous Cambrian seawater, suggesting postdepositional colonization of some ironstones by sulfur-reducing bacteria. The site not only preserves the textural interplay of biological and inorganic depositional processes in exhalites, but also extends the oldest known instance of microbial mediation in vent-proximal hydrothermal iron precipitation to at least 500 Ma.

Microbial bebop: creating music from complex dynamics in microbial ecology.

Directory of Open Access Journals (Sweden)

Peter Larsen

Full Text Available In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm. from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

Contaminant immobilization via microbial activity

International Nuclear Information System (INIS)

1991-11-01

The aim of this study was to search the literature to identify biological techniques that could be applied to the restoration of contaminated groundwaters near uranium milling sites. Through bioremediation it was hypothesized that the hazardous heavy metals could be immobilized in a stable, low-solubility form, thereby halting their progress in the migrating groundwater. Three basic mechanisms were examined: reduction of heavy metals by microbially produced hydrogen sulfide; direct microbial mediated reduction; and biosorption

Microbial Metabolism in Serpentinite Fluids

Science.gov (United States)

Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

2013-12-01

Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid

Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

Directory of Open Access Journals (Sweden)

Darine Trabelsi

2013-01-01

Full Text Available The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Genome-scale biological models for industrial microbial systems.

Science.gov (United States)

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality.

Science.gov (United States)

Douterelo, Isabel; Jackson, M; Solomon, C; Boxall, J

2016-04-01

Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality.

Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth.

Science.gov (United States)

Du, Wei; Jongbloets, Joeri A; van Boxtel, Coco; Pineda Hernández, Hugo; Lips, David; Oliver, Brett G; Hellingwerf, Klaas J; Branco Dos Santos, Filipe

2018-01-01

Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass. Based on well-established constraint-based analysis techniques such as OptKnock and FVA, we developed an in silico pipeline-FRUITS-that specifically 'Finds Reactions Usable in Tapping Side-products'. It analyses a metabolic network to identify compounds produced in anabolism that are suitable to be coupled to growth by deletion of their re-utilization pathway(s), and computes their respective biomass and product formation rates. When applied to Synechocystis sp. PCC6803, a model cyanobacterium explored for sustainable bioproduction, a total of nine target metabolites were identified. We tested our approach for one of these compounds, acetate, which is used in a wide range of industrial applications. The model-guided engineered strain shows an obligatory coupling between acetate production and photoautotrophic growth as predicted. Furthermore, the stability of acetate productivity in this strain was confirmed by performing prolonged turbidostat cultivations. This work demonstrates a novel approach to stabilize the production of target compounds in cyanobacteria that culminated in the first report of a photoautotrophic growth-coupled cell factory. The method developed is generic and can easily be extended to any other modeled microbial production system.

Studies on potential effects of fumaric acid on rumen microbial fermentation, methane production and microbial community.

Science.gov (United States)

Riede, Susanne; Boguhn, Jeannette; Breves, Gerhard

2013-01-01

The greenhouse gas methane (CH4) contributes substantially to global climate change. As a potential approach to decrease ruminal methanogenesis, the effects of different dosages of fumaric acid (FA) on ruminal microbial metabolism and on the microbial community (archaea, bacteria) were studied using a rumen simulation technique (RUSITEC). FA acts as alternative hydrogen acceptor diverting 2H from methanogenesis of archaea towards propionate formation of bacteria. Three identical trials were conducted with 12 fermentation vessels over a period of 14 days. In each trial, four fermentation vessels were assigned to one of the three treatment groups differing in FA dosage: low fumaric acid (LFA), high fumaric acid (HFA) and without FA (control). FA was continuously infused with the buffer. Grass silage and concentrate served as substrate. FA led to decreases in pH and to higher production rates of total short chain fatty acids (SCFA) mediated by increases in propionate for LFA of 1.69 mmol d(-1) and in propionate and acetate production for HFA of 4.49 and 1.10 mmol d(-1), respectively. Concentrations of NH3-N, microbial crude protein synthesis, their efficiency, degradation of crude nutrients and detergent fibre fraction were unchanged. Total gas and CH4 production were not affected by FA. Effects of FA on structure of microbial community by means of single strand conformation polymorphism (SSCP) analyses could not be detected. Given the observed increase in propionate production and the unaffected CH4 production it can be supposed that the availability of reduction equivalents like 2H was not limited by the addition of FA in this study. It has to be concluded from the present study that the application of FA is not an appropriate approach to decrease the ruminal CH4 production.

Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae

Directory of Open Access Journals (Sweden)

Maia Segura-Wang

2017-10-01

Full Text Available To ensure genomic integrity, living organisms have evolved diverse molecular processes for sensing and repairing damaged DNA. If improperly repaired, DNA damage can give rise to different types of mutations, an important class of which are genomic structural variants (SVs. In spite of their importance for phenotypic variation and genome evolution, potential contributors to SV formation in Saccharomyces cerevisiae (budding yeast, a highly tractable model organism, are not fully recognized. Here, we developed and applied a genome-wide assay to identify yeast gene knockout mutants associated with de novo deletion formation, in particular single-strand annealing (SSA-mediated deletion formation, in a systematic manner. In addition to genes previously linked to genome instability, our approach implicates novel genes involved in chromatin remodeling and meiosis in affecting the rate of SSA-mediated deletion formation in the presence or absence of stress conditions induced by DNA-damaging agents. We closely examined two candidate genes, the chromatin remodeling gene IOC4 and the meiosis-related gene MSH4, which when knocked-out resulted in gene expression alterations affecting genes involved in cell division and chromosome organization, as well as DNA repair and recombination, respectively. Our high-throughput approach facilitates the systematic identification of processes linked to the formation of a major class of genetic variation.

Significance, mechanisms and environmental implications of microbial bio-mineralization

International Nuclear Information System (INIS)

Benzerara, K.; Miot, J.; Morin, G.; Ona-Nguema, G.; Skouri-Panet, F.; Ferard, C.

2011-01-01

Microorganisms can mediate the formation of minerals by a process called bio-mineralization. This process offers an efficient way to sequester inorganic pollutants within relatively stable solid phases. Here we review some of the main mechanisms involved in the mediation of mineral precipitation by microorganisms. This includes supersaturation caused by metabolic activity, the triggering of nucleation by production of more or less specific organic molecules, and the impact of mineral growth. While these processes have been widely studied in the laboratory, assessment of their importance in the environment is more difficult. We illustrate this difficulty using a case study on an As-contaminated acid mine drainage located in the South of France (Carnoules, Gard). In particular, we explore the potential relationships that might exist between microbial diversity and mineral precipitation. The present review, far from being exhaustive, highlights some recent advances in the field of bio-mineralogy and provides non-specialists an introduction to some of the main approaches and some questions that remain unanswered. (authors)

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

Science.gov (United States)

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

2016-11-01

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium.

Science.gov (United States)

Zafra, German; Taylor, Todd D; Absalón, Angel E; Cortés-Espinosa, Diana V

2016-11-15

In this study, we used a taxonomic and functional metagenomic approach to analyze some of the effects (e.g. displacement, permanence, disappearance) produced between native microbiota and a previously constructed Polycyclic Aromatic Hydrocarbon (PAH)-degrading microbial consortium during the bioremediation process of a soil polluted with PAHs. Bioaugmentation with a fungal-bacterial consortium and biostimulation of native microbiota using corn stover as texturizer produced appreciable changes in the microbial diversity of polluted soils, shifting native microbial communities in favor of degrading specific populations. Functional metagenomics showed changes in gene abundance suggesting a bias towards aromatic hydrocarbon and intermediary degradation pathways, which greatly favored PAH mineralization. In contrast, pathways favoring the formation of toxic intermediates such as cytochrome P450-mediated reactions were found to be significantly reduced in bioaugmented soils. PAH biodegradation in soil using the microbial consortium was faster and reached higher degradation values (84% after 30 d) as a result of an increased co-metabolic degradation when compared with other mixed microbial consortia. The main differences between inoculated and non-inoculated soils were observed in aromatic ring-hydroxylating dioxygenases, laccase, protocatechuate, salicylate and benzoate-degrading enzyme genes. Based on our results, we propose that several concurrent metabolic pathways are taking place in soils during PAH degradation. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

Energy Technology Data Exchange (ETDEWEB)

Li, Minjing [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Qian, Wei-Jun [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Shi, Liang [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Yuanyuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nelson, William C. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nicora, Carrie D. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Resch, Charles T. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Thompson, Christopher [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Yan, Sen [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Fredrickson, James K. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Zachara, John M. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055 People' s Republic of China

2017-07-13

Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

Seasonality in ocean microbial communities.

Science.gov (United States)

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

Methane production from formate, acetate and H2/CO2; focusing on kinetics and microbial characterization

DEFF Research Database (Denmark)

Pan, Xiaofang; Angelidaki, Irini; Alvarado-Morales, Merlin

2016-01-01

For evaluating the methanogenesis from typical methanogenic precursors (formate, acetate and H-2/CO2), CH4 production kinetics were investigated at 37 +/- 1 degrees C in batch anaerobic digestion tests and stimulated by modified Gompertz model. The results showed that maximum methanation rate from...... formate, acetate and H-2/CO2 were 19.58 +/- 0.49, 42.65 +/- 1.17 and 314.64 +/- 3.58 N mL/gVS/d in digested manure system and 6.53 +/- 0.31, 132.04 +/- 3.96 and 640.16 +/- 19.92 N mL/gVS/d in sewage sludge system during second generation incubation. Meanwhile the model could not fit well in granular...... sludge system, while the rate of formate methanation was faster than from H-2/CO2 and acetate. Considering both the kinetic results and microbial assay we could conclude that H-2/CO2 methanation was the fastest methanogenic step in digested manure and sewage sludge system with Methanomicrobiales...

Microbe and Mineral Mediated Transformation of Heavy Metals, Radionuclides, and Organic Contaminants

Science.gov (United States)

Gerlach, R.

2011-12-01

Microorganisms influence their surroundings in many ways and humans have utilized microbially catalyzed reactions for benefit for centuries. Over the past few decades, microorganisms have been used for the control of contaminant transport in subsurface environments where many microbe mineral interactions occur. This presentation will discuss microbially influenced mineral formation and transformation as well as their influence on the fate of organic contaminants such as chlorinated aliphatics & 2,4,6-trinitrotoluene (TNT), heavy metals such as chromium, and radionuclides such as uranium & strontium. Both, batch and flow experiments have been performed, which monitor the net effect of microbe mineral interactions on the fate of these contaminants. This invited presentation will place an emphasis on the relative importance of direct microbial (i.e. biotic) transformations, mineral-mediated transformations as well as other abiotic reactions influencing the fate of environmental contaminants. Experiments will be summarized and placed in context of past and future engineered applications for the control of subsurface contaminants.

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

Science.gov (United States)

Valdespino-Castillo, Patricia M.; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M.; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A.; Holman, Hoi-Ying; Falcón, Luisa I.

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations. PMID

Microbial mitigation-exacerbation continuum: a novel framework for microbiome effects on hosts in the face of stress.

Science.gov (United States)

David, Aaron S; Thapa-Magar, Khum B; Afkhami, Michelle E

2018-03-01

A key challenge to understanding microbiomes and their role in ecological processes is contextualizing their effects on host organisms, particularly when faced with environmental stress. One influential theory, the Stress Gradient Hypothesis, might predict that the frequency of positive interactions increases with stressful conditions such that microbial taxa would mitigate harmful effects on host performance. Yet, equally plausible is that microbial taxa could exacerbate these effects. Here, we introduce the Mitigation-Exacerbation Continuum as a novel framework to conceptualize microbial mediation of stress. We (1) use this continuum to quantify microbial mediation of stress for six plant species and (2) test the association between these continuum values and natural species' abundance. We factorially manipulated a common stress (allelopathy) and the presence of soil microbes to quantify microbial effects in benign and stressed environments for two critical early life-history metrics, seed germination and seedling biomass. Although we found evidence of both mitigation and exacerbation among the six species, exacerbation was more common. Across species, the degree of microbial-mediated effects on germination explained >80% of the variation of natural field abundances. Our results suggest a critical role of soil microbes in mediating plant stress responses, and a potential microbial mechanism underlying species abundance. © 2018 by the Ecological Society of America.

Microbial biofilm formation and its consequences for the CELSS program

Science.gov (United States)

Mitchell, R.

1994-01-01

A major goal of the Controlled Ecology Life Support System (CELSS) program is to provide reliable and efficient life support systems for long-duration space flights. A principal focus of the program is on the growth of higher plants in growth chambers. These crops should be grown without the risk of damage from microbial contamination. While it is unlikely that plant pathogens will pose a risk, there are serious hazards associated with microorganisms carried in the nutrient delivery systems and in the atmosphere of the growth chamber. Our experience in surface microbiology showed that colonization of surfaces with microorganisms is extremely rapid even when the inoculum is small. After initial colonization extensive biofilms accumulate on moist surfaces. These microbial films metabolize actively and slough off continuously to the air and water. During plant growth in the CELSS program, microbial biofilms have the potential to foul sensors and to plug nutrient delivery systems. In addition both metabolic products of microbial growth and degradation products of materials being considered for use as nutrient reservoirs and for delivery are likely sources of chemicals known to adversly affect plant growth.

Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

Science.gov (United States)

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.

Microbial control of the dark end of the biological pump

NARCIS (Netherlands)

Herndl, G.J.; Reinthaler, T.

2013-01-01

A fraction of the carbon captured by phytoplankton in the sunlit surface ocean sinks to depth as dead organic matter and faecal material. The microbial breakdown of this material in the subsurface ocean generates carbon dioxide. Collectively, this microbially mediated flux of carbon from the

An overview of electron acceptors in microbial fuel cells

DEFF Research Database (Denmark)

Ucar, Deniz; Zhang, Yifeng; Angelidaki, Irini

2017-01-01

Microbial fuel cells (MFC) have recently received increasing attention due to their promising potential in sustainable wastewater treatment and contaminant removal. In general, contaminants can be removed either as an electron donor via microbial catalyzed oxidization at the anode or removed at t...... acceptors (e.g., nitrate, iron, copper, perchlorate) and mediators....

Periodontitis: from microbial immune subversion to systemic inflammation

Science.gov (United States)

Hajishengallis, George

2014-01-01

Periodontitis is a dysbiotic inflammatory disease with an adverse impact on systemic health. Recent studies have provided insights into the emergence and persistence of dysbiotic oral microbial communities, which can mediate inflammatory pathology at local as well as distant sites. This Review discusses mechanisms of microbial immune subversion that tip the balance from homeostasis to disease in oral or extraoral sites. PMID:25534621

CD14 is a key mediator of both lysophosphatidic acid and lipopolysaccharide induction of foam cell formation.

Science.gov (United States)

An, Dong; Hao, Feng; Zhang, Fuqiang; Kong, Wei; Chun, Jerold; Xu, Xuemin; Cui, Mei-Zhen

2017-09-01

Macrophage uptake of oxidized low-density lipoprotein (oxLDL) plays an important role in foam cell formation and the pathogenesis of atherosclerosis. We report here that lysophosphatidic acid (LPA) enhances lipopolysaccharide (LPS)-induced oxLDL uptake in macrophages. Our data revealed that both LPA and LPS highly induce the CD14 expression at messenger RNA and protein levels in macrophages. The role of CD14, one component of the LPS receptor cluster, in LPA-induced biological functions has been unknown. We took several steps to examine the role of CD14 in LPA signaling pathways. Knockdown of CD14 expression nearly completely blocked LPA/LPS-induced oxLDL uptake in macrophages, demonstrating for the first time that CD14 is a key mediator responsible for both LPA- and LPS-induced oxLDL uptake/foam cell formation. To determine the molecular mechanism mediating CD14 function, we demonstrated that both LPA and LPS significantly induce the expression of scavenger receptor class A type I (SR-AI), which has been implicated in lipid uptake process, and depletion of CD14 levels blocked LPA/LPS-induced SR-AI expression. We further showed that the SR-AI-specific antibody, which quenches SR-AI function, blocked LPA- and LPS-induced foam cell formation. Thus, SR-AI is the downstream mediator of CD14 in regulating LPA-, LPS-, and LPA/LPS-induced foam cell formation. Taken together, our results provide the first experimental evidence that CD14 is a novel connecting molecule linking both LPA and LPS pathways and is a key mediator responsible for LPA/LPS-induced foam cell formation. The LPA/LPS-CD14-SR-AI nexus might be the new convergent pathway, contributing to the worsening of atherosclerosis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Microbially-Mediated Precipitation of Calcium Carbonate Nanoparticles.

Science.gov (United States)

Kang, Ser Ku; Roh, Yul

2016-02-01

The objective of this study was to investigate the biomineralization of carbonate minerals using microorganisms (Wu Do-1) enriched from rhodoliths. A 16S rRNA sequence analysis showed that Wu Do-1 mainly contained Proteus mirabilis. The pH decreased from 6.5 to 5.3 over the first 4 days of incubation due to microbial oxidation of organic acids, after which it increased to 7.8 over the remaining incubation period. XRD analysis showed that the precipitates were Mg-rich cal- cite (MgxCa(1-x)CO3), whereas no precipitates were formed without the addition of Wu Do-1 in D-1 medium. SEM-EDS analyses showed that the Mg-rich calcite had a rhombohedron shape and consisted of Ca, Si and Mg with an extracelluar polymeric substance (EPS). In addition, TEM-EDS analyses revealed they were hexagon in shape, 500-700 nm in size, and composed of Ca, Mg, C, and O. These results indicated that Wu Do-1 induced precipitation of Mg-rich calcite on the cell walls and EPS via the accumulation of Ca and/or Mg ions. Therefore, microbial precipitation of carbonate nanoparticles may play an important role in metal and carbon biogeochemistry, as well as in carbon sequestration in natural environments.

Microbial ecology of bacterially mediated PCB biodegradation

International Nuclear Information System (INIS)

Pettigrew, C.A. Jr.

1989-01-01

The roles of plasmid mediated and consortia mediated polychlorinated biphenyl (PCB) biodegradation by bacterial populations isolated from PCB contaminated freshwater sediments were investigated. PCB degrading bacteria were isolated by DNA:DNA colony hybridization, batch enrichments, and chemostat enrichment. Analysis of substrate removal and metabolite production were done using chlorinated biphenyl spray plates, reverse phase high pressure liquid chromatography, Cl - detection, and 14 C-labeled substrate mineralization methods. A bacterial consortium, designated LPS10, involved in a concerted metabolic attack on chlorinated biphenyls, was shown to mineralize 4-chlorobiphenyl (4CB) and 4,4'-dichlorobiphenyl (4,4' CB). The LPS10 consortium was isolated by both batch and chemostat enrichment using 4CB and biphenyl (BP) as sole carbon source and was found to have tree bacterial isolates that predominated; these included: Pseudomonas, testosteroni LPS10A which mediated the breakdown of 4CB and 4,4' CB to the putative meta-cleavage product and subsequently to 4-chlorobenzoic acid (4CBA), an isolate tentatively identified as an Arthrobacter sp. LPS10B which mediated 4CBA degradation, and Pseudomonas putida by A LPS10C whose role in the consortium has not been determined

Evidence of synsedimentary microbial activity and iron deposition in ferruginous crusts of the Late Cenomanian Utrillas Formation (Iberian Basin, central Spain)

Science.gov (United States)

García-Hidalgo, José F.; Elorza, Javier; Gil-Gil, Javier; Herrero, José M.; Segura, Manuel

2018-02-01

Ferruginous sandstones and crusts are prominent sedimentary features throughout the continental (braided)-coastal siliciclastic (estuarine-tidal) wedges of the Late Cenomanian Utrillas Formation in the Iberian Basin. Crust types recognized are: Ferruginous sandy crusts (Fsc) with oxides-oxyhydroxides (hematite and goethite) concentrated on sandstone tops presenting a fibro-radial internal structure reminding organic structures that penetrate different mineral phases, suggesting the existence of bacterial activity in crust development; Ferruginous muddy crusts (Fmc) consisting of wavy, laminated, microbial mats, being composed mainly of hematite. On the other hand, a more dispersed and broader mineralization included as Ferruginous sandstones with iron oxides and oxyhydroxides (hematite and goethite) representing a limited cement phase on these sediments. The presence of microbial remains, ferruginous minerals, Microbially-induced sedimentary structures, microbial laminites and vertebrate tracks preserved due to the presence of biofilms suggest firstly a direct evidence of syn-depositional microbial activity in these sediments; and, secondly, that iron accumulation and ferruginous crusts development occurred immediately after deposition of the host, still soft sediments. Ferruginous crusts cap sedimentary cycles and they represent the gradual development of hard substrate conditions, and the development of a discontinuity surface at the top of the parasequence sets, related to very low sedimentary rates; the overlying sediments record subsequent flooding of underlying shallower environments; crusts are, consequently, interpreted as boundaries for these higher-order cycles in the Iberian Basin.

Petrographic Evidence of Microbial Mats in the Upper Cretaceous Fish-Bearing, Organic-Rich Limestone, Agua Nueva Formation, Central Mexico

Science.gov (United States)

Blanco, A.; Maurrasse, F. J.; Hernández-Ávila, J.; Ángeles-Trigueros, S. A.; García-Cabrera, M. E.

2013-05-01

We document petrographic evidence of microbial mats in the Upper Cretaceous Agua Nueva Formation in the area of Xilitla (San Luis Potosí, Central Mexico), located in the southern part of the Tampico-Misantla basin. The sequence consists predominantly of alternating decimeter-thick beds of fossiliferous dark laminated limestone (C-org > 1.0wt%), and light gray, bioturbated limestone (C-org Duque-Botero and Maurrasse, 2005; 2008). These structures are also analogous to microbial mats in present environments, and Devonian deposits (Kremer, 2006). In addition, the laminae at Xilitla include filamentous bacterial structures, as thin and segmented red elements. In some thin sections, filaments appear to be embedded within the crinkly laminae and shreds showing the same pattern of folding, suggestive of biomorphic elements that represent the main producers of the organic matter associated with the laminae. Thus, exceptional bacterial activity characterizes sedimentation during the accumulation of the Agua Nueva Formation. Oxygen-deficient conditions related to the microbial mats were an important element in the mass mortality and preservation of the fish assemblages. Absence of bioturbation, pervasive framboidal pyrite, and the high concentration of organic matter (TOC ranges from 1.2% to 8wt%) in the dark limestones are consistent with persistent recurring dysoxic/anoxic conditions, and the light-gray bioturbated limestones represent relatively well-oxygenated episodes. Planktonic foraminifera (Rotalipora cushmani) and Inoceramu labiatus indicate a time interval from the latest Cenomanian through the earliest Turonian, thus this long interval of severe oxygen deficiency is coeval with Oceanic Anoxic Event 2 (OAE-2). [Duque-Botero and Maurrasse. 2005. Jour. Iberian Geology (31), 85-98; 2008. Cret. Res., 29, 957-964; Kremer. 2006. Acta Palaeontologica Polonica (51, 1), 143-154

Non-microbial methane emissions from soils

Science.gov (United States)

Wang, Bin; Hou, Longyu; Liu, Wei; Wang, Zhiping

2013-12-01

Traditionally, methane (CH4) is anaerobically formed by methanogenic archaea. However, non-microbial CH4 can also be produced from geologic processes, biomass burning, animals, plants, and recently identified soils. Recognition of non-microbial CH4 emissions from soils remains inadequate. To better understand this phenomenon, a series of laboratory incubations were conducted to examine effects of temperature, water, and hydrogen peroxide (H2O2) on CH4 emissions under both aerobic and anaerobic conditions using autoclaved (30 min, 121 °C) soils and aggregates (>2000 μm, A1; 2000-250 μm, A2; 250-53 μm, M1; and A2 > A1 > M2 and C-based emission an order of M2 > M1 > A1 > A2, demonstrating that both organic carbon quantity and property are responsible for CH4 emissions from soils at the scale of aggregate. Whole soil-based order of A2 > A1 > M1 > M2 suggests that non-microbial CH4 release from forest soils is majorly contributed by macro-aggregates (i.e., >250 μm). The underlying mechanism is that organic matter through thermal treatment, photolysis, or reactions with free radicals produce CH4, which, in essence, is identical with mechanisms of other non-microbial sources, indicating that non-microbial CH4 production may be a widespread phenomenon in nature. This work further elucidates the importance of non-microbial CH4 formation which should be distinguished from the well-known microbial CH4 formation in order to define both roles in the atmospheric CH4 global budget.

Neutral lipids associated with haemozoin mediate efficient and rapid β-haematin formation at physiological pH, temperature and ionic composition

Directory of Open Access Journals (Sweden)

Ambele Melvin A

2012-10-01

Full Text Available Abstract Background The malaria parasite disposes of host-derived ferrihaem (iron(IIIprotoporphyrin IX, Fe(IIIPPIX by conversion to crystalline haemozoin in close association with neutral lipids. Lipids mediate synthetic haemozoin (β-haematin formation very efficiently. However, the effect on reaction rates of concentrations of lipid, Fe(IIIPPIX and physiologically relevant ions and biomolecules are unknown. Methods Lipid emulsions containing Fe(IIIPPIX were prepared in aqueous medium (pH 4.8, 37°C to mediate β-haematin formation. The reaction was quenched at various times and free Fe(IIIPPIX measured colorimetrically as a pyridine complex and the kinetics and yields analysed. Products were also characterized by FTIR, TEM and electron diffraction. Autofluorescence was also used to monitor β-haematin formation by confocal microscopy. Results At fixed Fe(IIIPPIX concentration, β-haematin yields remained constant with decreasing lipid concentration until a cut-off ratio was reached whereupon efficiency decreased dramatically. For the haemozoin-associated neutral lipid blend (NLB and monopalmitoylglycerol (MPG, this occurred below a lipid/Fe(IIIPPIX (L/H ratio of 0.54. Rate constants were found to increase with L/H ratio above the cut-off. At 16 μM MPG, Fe(IIIPPIX concentration could be raised until the L/H ratio reached the same ratio before a sudden decline in yield was observed. MPG-mediated β-haematin formation was relatively insensitive to biologically relevant cations (Na+, K+, Mg2+, Ca2+, or anions (H2PO4−, HCO3−, ATP, 2,3-diphosphoglycerate, glutathione. Confocal microscopy demonstrated β-haematin formation occurs in association with the lipid particles. Conclusions Kinetics of β-haematin formation have shown that haemozoin-associated neutral lipids alone are capable of mediating β-haematin formation at adequate rates under physiologically realistic conditions of ion concentrations to account for haemozoin formation.

Papillae formation on trichome cell walls requires the function of the mediator complex subunit Med25.

Science.gov (United States)

Fornero, Christy; Suo, Bangxia; Zahde, Mais; Juveland, Katelyn; Kirik, Viktor

2017-11-01

Glassy Hair 1 (GLH1) gene that promotes papillae formation on trichome cell walls was identified as a subunit of the transcriptional mediator complex MED25. The MED25 gene is shown to be expressed in trichomes. The expression of the trichome development marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) is not affected in the glh1 mutant. Presented data suggest that Arabidopsis MED25 mediator component is likely involved in the transcription of genes promoting papillae deposition in trichomes. The plant cell wall plays an important role in communication, defense, organization and support. The importance of each of these functions varies by cell type. Specialized cells, such as Arabidopsis trichomes, exhibit distinct cell wall characteristics including papillae. To better understand the molecular processes important for papillae deposition on the cell wall surface, we identified the GLASSY HAIR 1 (GLH1) gene, which is necessary for papillae formation. We found that a splice-site mutation in the component of the transcriptional mediator complex MED25 gene is responsible for the near papillae-less phenotype of the glh1 mutant. The MED25 gene is expressed in trichomes. Reporters for trichome developmental marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) were not affected in the glh1 mutant. Collectively, the presented results show that MED25 is necessary for papillae formation on the cell wall surface of leaf trichomes and suggest that the Arabidopsis MED25 mediator component is likely involved in the transcription of a subset of genes that promote papillae deposition in trichomes.

Application of biocathode in microbial fuel cells: cell performance and microbial community

Energy Technology Data Exchange (ETDEWEB)

Guo-Wei, Chen [Pusan National Univ. (Korea). Dept. of Environmental Engineering; Hefei Univ. of Technology (China). School of Civil Engineering; Choi, Soo-Jung; Lee, Tae-Ho; Lee, Gil-Young; Cha, Jae-Hwan; Kim, Chang-Won [Pusan National Univ. (Korea). Dept. of Environmental Engineering

2008-06-15

Instead of the utilization of artificial redox mediators or other catalysts, a biocathode has been applied in a two-chamber microbial fuel cell in this study, and the cell performance and microbial community were analyzed. After a 2-month startup, the microorganisms of each compartment in microbial fuel cell were well developed, and the output of microbial fuel cell increased and became stable gradually, in terms of electricity generation. At 20 ml/min flow rate of the cathodic influent, the maximum power density reached 19.53 W/m{sup 3}, while the corresponding current and cell voltage were 15.36 mA and 223 mV at an external resistor of 14.9 {omega}, respectively. With the development of microorganisms in both compartments, the internal resistance decreased from initial 40.2 to 14.0 {omega}, too. Microbial community analysis demonstrated that five major groups of the clones were categorized among those 26 clone types derived from the cathode microorganisms. Betaproteobacteria was the most abundant division with 50.0% (37 of 74) of the sequenced clones in the cathode compartment, followed by 21.6% (16 of 74) Bacteroidetes, 9.5% (7 of 74) Alphaproteobacteria, 8.1% (6 of 74) Chlorobi, 4.1% (3 of 74) Deltaproteobacteria, 4.1% (3 of 74) Actinobacteria, and 2.6% (2 of 74) Gammaproteobacteria. (orig.)

The response of soil carbon storage and microbially mediated carbon turnover to simulated climatic disturbance in a northern peatland forest. Revisiting the concept of soil organic matter recalcitrance

Energy Technology Data Exchange (ETDEWEB)

Kostka, Joel [Georgia Inst. of Technology, Atlanta, GA (United States)

2015-09-14

closely paralleled the chemical evolution of peat, with large shifts in microbial populations occurring in the biogeochemical hotspot, the mesotelm, where the highest rates of decomposition were detected. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens dominated in the deeper catotelm. Evidence pointed to the availability of phosphorus as well as nitrogen limiting the microbially-mediated turnover of organic carbon at MEF. Prior to initiation of the experimental treatments, our study provided key baseline data for the SPRUCE site on the vertical stratification of peat decomposition, key enzymatic pathways, and microbial taxa containing these pathways. The sensitivity of soil carbon turnover to climate change is strongly linked to recalcitrant carbon stocks and the temperature sensitivity of decomposition is thought to increase with increasing molecular complexity of carbon substrates. This project delivered results on how climate change perturbations impact the microbially-mediated turnover of recalcitrant organic matter in peatland forest soils, both under controlled conditions in the laboratory and at the ecosystem-scale in the field. This project revisited the concept of “recalcitrance” in the regulation of soil carbon turnover using a combination of natural abundance radiocarbon and optical spectroscopic measurements on bulk DOM, and high resolution molecular characterization of DOM. The project elucidated how organic matter reactivity and decomposition will respond to climate change in a both a qualitative (organic matter lability) and quantitiative (increased rates) manner. An Aromaticity Index was developed to represent a more direct and accurate parameter for modeling of DOM reactivity in peatlands. The abundance and community

Microbial biofilm growth on irradiated, spent nuclear fuel cladding

International Nuclear Information System (INIS)

Bruhn, D.F.; Frank, S.M.; Roberto, F.F.; Pinhero, P.J.; Johnson, S.G.

2009-01-01

A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 x 10 3 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments

Formation of higher plant component microbial community in closed ecological system

Science.gov (United States)

Tirranen, L. S.

2001-07-01

Closed ecological systems (CES) place at the disposal of a researcher unique possibilities to study the role of microbial communities in individual components and of the entire system. The microbial community of the higher plant component has been found to form depending on specific conditions of the closed ecosystem: length of time the solution is reused, introduction of intrasystem waste water into the nutrient medium, effect of other component of the system, and system closure in terms of gas exchange. The higher plant component formed its own microbial complex different from that formed prior to closure. The microbial complex of vegetable polyculture is more diverse and stable than the monoculture of wheat. The composition of the components' microflora changed, species diversity decreased, individual species of bacteria and fungi whose numbers were not so great before the closure prevailed. Special attention should be paid to phytopathogenic and conditionally pathogenic species of microorganisms potentially hazardous to man or plants and the least controlled in CES. This situation can endanger creation of CES and make conjectural existence of preplanned components, man, specifically, and consequently, of CES as it is.

Free radical mediated formation of 3-monochloropropanediol (3-MCPD) fatty acid diesters.

Science.gov (United States)

Zhang, Xiaowei; Gao, Boyan; Qin, Fang; Shi, Haiming; Jiang, Yuangrong; Xu, Xuebing; Yu, Liangli Lucy

2013-03-13

The present study was conducted to test the hypothesis that a free radical was formed and mediated the formation of 3-monochloropropanediol (3-MCPD) fatty acid diesters, a group of food contaminants, from diacylglycerols at high temperature under a low-moisture condition for the first time. The presence of free radicals in a vegetable oil kept at 120 °C for 20 min was demonstrated using an electron spin resonance (ESR) spectroscopy examination with 5,5-dimethylpyrroline-N-oxide (DMPO) as the spin trap agent. ESR investigation also showed an association between thermal treatment degree and the concentration of free radicals. A Fourier transform infrared spectroscopy (FT-IR) analysis of sn-1,2-stearoylglycerol (DSG) at 25 and 120 °C suggested the possible involvement of an ester carbonyl group in forming 3-MCPD diesters. On the basis of these results, a novel free radical mediated chemical mechanism was proposed for 3-MCPD diester formation. Furthermore, a quadrupole-time of flight (Q-TOF) MS/MS investigation was performed and detected the DMPO adducts with the cyclic acyloxonium free radical (CAFR) and its product MS ions, proving the presence of CAFR. Furthermore, the free radical mechanism was validated by the formation of 3-MCPD diesters through reacting DSG with a number of organic and inorganic chlorine sources including chlorine gas at 120 and 240 °C. The findings of this study might lead to the improvement of oil and food processing conditions to reduce the level of 3-MCPD diesters in foods and enhance food safety.

Microbial-caddisfly bioherm association from the Lower Cretaceous Shinekhudag Formation, Mongolia: Earliest record of plant armoring in fossil caddisfly cases.

Directory of Open Access Journals (Sweden)

Tsolmon Adiya

Full Text Available Caddisfly larvae construct underwater protective cases using surrounding materials, thus providing information on environmental conditions in both modern and ancient systems. Microbial bioherms associated with caddisfly cases are found in the Berriassian-Hauterivian (~140-130 Ma Shinekhudag Formation of Mongolia, and yield new insights into aspects of lacustrine paleoecosystems and paleoenvironments. This formation contains the earliest record of plant-armored caddisfly cases and a rare occurrence of microbial-caddisfly association from the Mesozoic. The bioherms are investigated within the context of stratigraphic correlations, depositional environment interpretations, and basin-evolution models of the sedimentary fill. The bioherms form 0.5-2.0 m diameter mound-shaped bodies and are concentrated within a single, oil shale-bound stratigraphic interval. Each bioherm is composed of up to 40% caddisfly cases along with stromatolites of millimeter-scale, micritic laminations. Petrographic analyses reveal these bioherms are composed of non-systematic associations of columnar and oncoidal microbialites, constructed around colonies of caddisfly cases. The cases are straight to curved, slightly tapered, and tube-shaped, with a progressively increasing length and width trend (7-21 mm by 1.5-2.5 mm. Despite these variations, the case architectures reveal similar construction materials; the particles used for cases are dominated by plant fragments, ostracod valves, carbonate rocks, and rare mica and feldspar grains. Allochems within the bioherms include ooids, ostracods, plant fragments, rare gastropods, feldspar grains bound in micritic matrices, and are consolidated by carbonate dominated cements. The combination of microbial-caddisfly association, plant fragment case particles, and ooids/oncoids are indicative of a shallow, littoral lake setting. Stratigraphic juxtaposition of nearshore bioherms and the bounding distal oil-shale facies suggests that

The formation of illite from nontronite by mesophilic and thermophilic bacterial reaction

Science.gov (United States)

Jaisi, Deb P.; Eberl, Dennis D.; Dong, Hailiang; Kim, Jinwook

2011-01-01

The formation of illite through the smectite-to-illite (S-I) reaction is considered to be one of the most important mineral reactions occurring during diagenesis. In biologically catalyzed systems, however, this transformation has been suggested to be rapid and to bypass the high temperature and long time requirements. To understand the factors that promote the S-I reaction, the present study focused on the effects of pH, temperature, solution chemistry, and aging on the S-I reaction in microbially mediated systems. Fe(III)-reduction experiments were performed in both growth and non-growth media with two types of bacteria: mesophilic (Shewanella putrefaciens CN32) and thermophilic (Thermus scotoductus SA-01). Reductive dissolution of NAu-2 was observed and the formation of illite in treatment with thermophilic SA-01 was indicated by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). A basic pH (8.4) and high temperature (65°C) were the most favorable conditions for the formation of illite. A long incubation time was also found to enhance the formation of illite. K-nontronite (non-permanent fixation of K) was also detected and differentiated from the discrete illite in the XRD profiles. These results collectively suggested that the formation of illite associated with the biologically catalyzed smectite-to-illite reaction pathway may bypass the prolonged time and high temperature required for the S-I reaction in the absence of microbial activity.

Investigating the impact of microbial interactions with geologic media on geophysical properties

Science.gov (United States)

Davis, Caroline Ann

The goals of this study were to investigate the effect of: (1) microbial metabolic byproducts, microbial growth, and biofilm formation on the low frequency electrical properties of porous media, (2) biofilm formation on acoustic wave properties, and (3) the natural electrical (self-potential) signatures associated with an in-situ biological permeable reactive barrier (PRB). The results suggest: (1) increases in electrolytic conductivity are consistent with increased concentrations of organic acids and biosurfactants; (2) mineral weathering promoted by organic acids causes increases in electrolytic conductivity, concomitant with increases in major cation concentrations; (3) interfacial conductivity generally parallels microbial cell concentrations and biofilm formation; (4) variations in microbial growth and biofilms causes spatiotemporal heterogeneity in the elastic properties of porous media; (5) SP signatures associated with the injection of groundwater into an in-situ biological PRB are dominated by diffusion potentials induced by the injections. The results suggest that electrolytic conductivity may be useful as an indicator of metabolism, while interfacial conductivity may be used as proxy indicator for microbial growth and biofilm formation in porous media. In addition, acoustic measurements may provide diagnostic spatiotemporal data for the validation of bioclogging models/simulations. Collectively, this study provides further evidence that geophysical measurements are sensitive to microbial-induced changes to geologic media, and may be useful for the detection and monitoring of subsurface microbial growth, activity, and distribution such as in microbial enhanced oil recovery, assessing biofilm barriers used for contaminant remediation, or as sealants for reservoirs in CO2 sequestration studies.

Recent advances in engineering topography mediated antibacterial surfaces

Science.gov (United States)

Hasan, Jafar; Chatterjee, Kaushik

2015-09-01

The tendency of bacterial cells to adhere and colonize a material surface leading to biofilm formation is a fundamental challenge underlying many different applications including microbial infections associated with biomedical devices and products. Although, bacterial attachment to surfaces has been extensively studied in the past, the effect of surface topography on bacteria-material interactions has received little attention until more recently. We review the recent progress in surface topography based approaches for engineering antibacterial surfaces. Biomimicry of antibacterial surfaces in nature is a popular strategy. Whereas earlier endeavors in the field aimed at minimizing cell attachment, more recent efforts have focused on developing bactericidal surfaces. However, not all such topography mediated bactericidal surfaces are necessarily cytocompatible thus underscoring the need for continued efforts for research in this area for developing antibacterial and yet cytocompatible surfaces for use in implantable biomedical applications. This mini-review provides a brief overview of the current strategies and challenges in the emerging field of topography mediated antibacterial surfaces.

Biofilm formation and microbial community analysis of the simulated river bioreactor for contaminated source water remediation.

Science.gov (United States)

Xu, Xiang-Yang; Feng, Li-Juan; Zhu, Liang; Xu, Jing; Ding, Wei; Qi, Han-Ying

2012-06-01

The start-up pattern of biofilm remediation system affects the biofilm characteristics and operating performances. The objective of this study was to evaluate the performances of the contaminated source water remediation systems with different start-up patterns in view of the pollutants removal performances and microbial community succession. The operating performances of four lab-scale simulated river biofilm reactors were examined which employed different start-up methods (natural enrichment and artificial enhancement via discharging sediment with influent velocity gradient increase) and different bio-fillers (Elastic filler and AquaMats® ecobase). At the same time, the microbial communities of the bioreactors in different phases were analyzed by polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing. The pollutants removal performances became stable in the four reactors after 2 months' operation, with ammonia nitrogen and permanganate index (COD(Mn)) removal efficiencies of 84.41-94.21% and 69.66-76.60%, respectively. The biomass of mature biofilm was higher in the bioreactors by artificial enhancement than that by natural enrichment. Microbial community analysis indicated that elastic filler could enrich mature biofilm faster than AquaMats®. The heterotrophic bacteria diversity of biofilm decreased by artificial enhancement, which favored the ammonia-oxidizing bacteria (AOB) developing on the bio-fillers. Furthermore, Nitrosomonas- and Nitrosospira-like AOB coexisted in the biofilm, and Pseudomonas sp., Sphaerotilus sp., Janthinobacterium sp., Corynebacterium aurimucosum were dominant in the oligotrophic niche. Artificial enhancement via the combination of sediment discharging and influent velocity gradient increasing could enhance the biofilm formation and autotrophic AOB enrichment in oligotrophic niche.

Stable, geochemically mediated biospheres in the Deep Mine Microbial Observatory, SD, USA

Science.gov (United States)

Osburn, M. R.; Casar, C. P.; Kruger, B.; Flynn, T. M.

2017-12-01

The terrestrial subsurface is a vast reservoir of life, hosting diverse microbial ecosystems with varying levels of connectivity to surface inputs. Understanding long term ecosystem dynamics within the subsurface biosphere is very challenging due to limitations in accessibility, sample availability, and slow microbial growth rates. The establishment of the Deep Mine Microbial Observatory (DeMMO) at the Sanford Underground Research Facility, SD, USA has allowed for bimonthly sampling for nearly two years at six sites spanning 250 to 1500 m below the surface. Here we present a time-resolved analysis of the geomicrobiology of the six DeMMO sites, which have been created from legacy mine boreholes modified to allow for controlled sampling. Our interdisciplinary approach includes analysis of passively draining fracture fluid for aqueous and gas geochemistry, DNA sequencing, microscopy, and isotopic measurements of organic and inorganic substrates. Fluid geochemistry varies significantly between sites, but is relatively stable over time for a given site, even through significant external perturbations such as drilling and installation of permanent sampling devices into the boreholes. The fluid-hosted microbial diversity follows these trends, with consistent populations present at each site through time, even through drilling events. For instance, the shallowest site (DeMMO 1) consistently hosts >30% uncharacterized phyla and >25% Omnitrophica whereas the deepest site (DeMMO 6) is dominated by Firmicutes and Bacterioidetes. Microbial diversity appears to respond to the availability of energy sources such as organic carbon, sulfate, sulfide, hydrogen, and iron. Carbon isotopic measurements reveal closed system behavior with significant recycling of organic carbon into the DIC pool. Together these observations suggest DeMMO hosts isolated subsurface microbial populations adapted to local geochemistry that are stable on yearlong timescales.

Response of humic acid formation to elevated nitrate during chicken manure composting.

Science.gov (United States)

Shi, Mingzi; Wei, Zimin; Wang, Liqin; Wu, Junqiu; Zhang, Duoying; Wei, Dan; Tang, Yu; Zhao, Yue

2018-06-01

Nitrate can stimulate microbes to degrade aromatic compounds, whereas humic acid (HA) as a high molecular weight aromatic compound, its formation may be affected by elevated nitrate during composting. Therefore, this study is conducted to determine the effect of elevated nitrate on HA formation. Five tests were executed by adding different nitrate concentrations to chicken manure composting. Results demonstrate that the concentration of HA in treatment group is significantly decreased compared with control group (p < 0.05), especially in the highest nitrate concentration group. RDA indicates that the microbes associated with HA and environmental parameters are influenced by elevated nitrate. Furthermore, structural equation model reveals that elevated nitrate reduces HA formation by mediating microbes directly, or by affecting ammonia and pH as the indirect drivers to regulate microbial community structure. Copyright © 2018 Elsevier Ltd. All rights reserved.

Investigation of microbial-mineral interactions by Moessbauer spectroscopy

International Nuclear Information System (INIS)

Sawicki, J.A.; Brown, D.A.

1998-01-01

Moessbauer spectroscopy was used to investigate the reactions of microbes with iron minerals in aqueous solutions and as components of rocks in banded iron formations and granite. A microbial biofilm that formed on a wall of an excavated granite vault in a deep underground laboratory initiated this research. At the aerobic face of the biofilm, iron was found in a form of ferrihydrite; in the anaerobic face against the rock, iron was found as very small siderite particles. Laboratory incubations of the biofilm microbial consortium showed different mineral species could be formed. When the microbial consortium from the biofilm was incubated with magnetite grains, up to about 10% of the iron was altered in three weeks to hematite. The ability of the consortium to precipitate iron both as Fe 2+ and Fe 3+ in close proximity may have a bearing on the deposition of banded iron formations. These reactions could also be important in microbially induced corrosion

Nitric oxide mediates strigolactone signaling in auxin and ethylene-sensitive lateral root formation in sunflower seedlings

OpenAIRE

Bharti, Niharika; Bhatla, Satish C

2015-01-01

Strigolactones (SLs) play significant role in shaping root architecture whereby auxin-SL crosstalk has been observed in SL-mediated responses of primary root elongation, lateral root formation and adventitious root (AR) initiation. Whereas GR24 (a synthetic strigolactone) inhibits LR and AR formation, the effect of SL biosynthesis inhibitor (fluridone) is just the opposite (root proliferation). Naphthylphthalamic acid (NPA) leads to LR proliferation but completely inhibits AR development. The...

EVALUATION OF MICROBIAL SURVIVAL IN EXTRATERRESTRIAL ENVIRONMENTS

Directory of Open Access Journals (Sweden)

Betül BULUÇ

2012-08-01

Full Text Available In this paper, the space environments where microbial terrestrial life could form and evolve in, were evaluted with the base of the physical and chemical properties. In addition, Earthial microbial life formation conditions in the interstellar medium and the other planets are investigated and the survival of microorganisms in the space environments are questioned. As a result, considering the aspects of terrestrial microbial life, we suggest that the space environment and other planets could not be a habitat for Earthial microorganisms.

Strain- and Substrate-Dependent Redox Mediator and Electricity Production by Pseudomonas aeruginosa.

Science.gov (United States)

Bosire, Erick M; Blank, Lars M; Rosenbaum, Miriam A

2016-08-15

Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm(-2) with ∼150 μg ml(-1) phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial

Biologically mediated dissolution of volcanic glass in seawater

NARCIS (Netherlands)

Staudigel, H; Yayanos, A; Chastain, R; Davies, G.T.; Verdurmen, E.A Th; Schiffmann, P; Bourcier, R; de Baar, H.J.W.

1998-01-01

We studied the effects of biological mediation on the dissolution of basaltic glass in seawater. Experiments with typical seawater microbial populations were contrasted with a sterile control, and reactions were monitored chemically and isotopically. Biologically mediated experiments produce twice

Contact in Adoption and Adoptive Identity Formation: The Mediating Role of Family Conversation

Science.gov (United States)

Korff, Lynn Von; Grotevant, Harold D.

2012-01-01

The present study examined adoption-related family conversation as a mediator of the association between adoptive parents’ facilitation of contact with birth relatives and adolescent adoptive identity formation. The sample consisted of 184 adoptive families. Data were collected in two waves from adoptive mothers and fathers, and adoptees (M = 15.68 years at adolescence; M = 24.95 years at emerging adulthood) using semistructured interviews and questionnaires. Structural equation models showed a good fit to sample data, and analyses supported the hypothesized mediation model. Contact with birth relatives is associated with more frequent adoption-related family conversation, which in turn is associated with the development of adoptive identity. These results highlight the importance of supporting activities such as contact that lead to adoption-related family conversation. PMID:21517175

Menadione induces the formation of reactive oxygen species and depletion of GSH-mediated apoptosis and inhibits the FAK-mediated cell invasion.

Science.gov (United States)

Kim, Yun Jeong; Shin, Yong Kyoo; Sohn, Dong Suep; Lee, Chung Soo

2014-09-01

Menadione induces apoptosis in tumor cells. However, the mechanism of apoptosis in ovarian cancer cells exposed to menadione is not clear. In addition, it is unclear whether menadione-induced apoptosis is mediated by the depletion of glutathione (GSH) contents that is associated with the formation of reactive oxygen species. Furthermore, the effect of menadione on the invasion and migration of human epithelial ovarian cancer cells has not been studied. Therefore, we investigated the effects of menadione exposure on apoptosis, cell adhesion, and cell migration using the human epithelial ovarian carcinoma cell lines OVCAR-3 and SK-OV-3. The results suggest that menadione may induce apoptotic cell death in ovarian carcinoma cell lines by activating the mitochondrial pathway and the caspase-8- and Bid-dependent pathways. The apoptotic effect of menadione appears to be mediated by the formation of reactive oxygen species and the depletion of GSH. Menadione inhibited fetal-bovine-serum-induced cell adhesion and migration of OVCAR-3 cells, possibly through the suppression the focal adhesion kinase (FAK)-dependent activation of cytoskeletal-associated components. Therefore, menadione might be beneficial in the treatment of epithelial ovarian adenocarcinoma and combination therapy.

Mechanism of acetaldehyde-induced deactivation of microbial lipases

Directory of Open Access Journals (Sweden)

Jaeger Karl E

2011-02-01

Full Text Available Abstract Background Microbial lipases represent the most important class of biocatalysts used for a wealth of applications in organic synthesis. An often applied reaction is the lipase-catalyzed transesterification of vinyl esters and alcohols resulting in the formation of acetaldehyde which is known to deactivate microbial lipases, presumably by structural changes caused by initial Schiff-base formation at solvent accessible lysine residues. Previous studies showed that several lipases were sensitive toward acetaldehyde deactivation whereas others were insensitive; however, a general explanation of the acetaldehyde-induced inactivation mechanism is missing. Results Based on five microbial lipases from Candida rugosa, Rhizopus oryzae, Pseudomonas fluorescens and Bacillus subtilis we demonstrate that the protonation state of lysine ε-amino groups is decisive for their sensitivity toward acetaldehyde. Analysis of the diverse modification products of Bacillus subtilis lipases in the presence of acetaldehyde revealed several stable products such as α,β-unsaturated polyenals, which result from base and/or amino acid catalyzed aldol condensation of acetaldehyde. Our studies indicate that these products induce the formation of stable Michael-adducts at solvent-accessible amino acids and thus lead to enzyme deactivation. Further, our results indicate Schiff-base formation with acetaldehyde to be involved in crosslinking of lipase molecules. Conclusions Differences in stability observed with various commercially available microbial lipases most probably result from different purification procedures carried out by the respective manufacturers. We observed that the pH of the buffer used prior to lyophilization of the enzyme sample is of utmost importance. The mechanism of acetaldehyde-induced deactivation of microbial lipases involves the generation of α,β-unsaturated polyenals from acetaldehyde which subsequently form stable Michael-adducts with the

Non-enzymatic palladium recovery on microbial and synthetic surfaces

DEFF Research Database (Denmark)

Rotaru, Amelia-Elena; Jiang, Wei; Finster, Kai

2012-01-01

in the presence of cells as compared to cell-free controls. We found no difference between native (untreated) and autoclaved cells, and could demonstrate that even a non-enzymatic protein (bovine serum albumin) stimulated Pd(II) reduction as efficiently as bacterial cells. Amine groups readily interact with Pd......(II), and to specifically test their role in surface-assisted Pd(II) reduction by formate, we replaced bacterial cells with polystyrene microparticles functionalized with amine or carboxyl groups. Amine-functionalized microparticles had the same effect on Pd(II) reduction as bacterial cells, and the effect could...... be hampered if the amine groups were blocked by acetylation. The interaction with amine groups was confirmed by infrared spectroscopy on whole cells and amine-functionalized microparticles. In conclusion, bio-supported Pd(II) reduction on microbial surfaces is possibly mediated by a non-enzymatic mechanism...

Early microbial contact, the breast milk microbiome and child health.

Science.gov (United States)

Rautava, S

2016-02-01

The significance of contact with microbes in early life for subsequent health has been the subject of intense research during the last 2 decades. Disturbances in the establishment of the indigenous intestinal microbiome caused by cesarean section delivery or antibiotic exposure in early life have been linked to the risk of immune-mediated and inflammatory conditions such as atopic disorders, inflammatory bowel disease and obesity later in life. Distinct microbial populations have recently been discovered at maternal sites including the amniotic cavity and breast milk, as well as meconium, which have previously been thought to be sterile. Our understanding of the impact of fetal microbial contact on health outcomes is still rudimentary. Breast milk is known to modulate immune and metabolic programming. The breast milk microbiome is hypothesized to guide infant gut colonization and is affected by maternal health status and mode of delivery. Immunomodulatory factors in breast milk interact with the maternal and infant gut microbiome and may mediate some of the health benefits associated with breastfeeding. The intimate connection between the mother and the fetus or the infant is a potential target for microbial therapeutic interventions aiming to support healthy microbial contact and protect against disease.

Contact in Adoption and Adoptive Identity Formation: The Mediating Role of Family Conversation

OpenAIRE

Korff, Lynn Von; Grotevant, Harold D.

2011-01-01

The present study examined adoption-related family conversation as a mediator of the association between adoptive parents’ facilitation of contact with birth relatives and adolescent adoptive identity formation. The sample consisted of 184 adoptive families. Data were collected in two waves from adoptive mothers and fathers, and adoptees (M = 15.68 years at adolescence; M = 24.95 years at emerging adulthood) using semistructured interviews and questionnaires. Structural equation models showed...

Biogeochemical signals from deep microbial life in terrestrial crust.

Directory of Open Access Journals (Sweden)

Yohey Suzuki

Full Text Available In contrast to the deep subseafloor biosphere, a volumetrically vast and stable habitat for microbial life in the terrestrial crust remains poorly explored. For the long-term sustainability of a crustal biome, high-energy fluxes derived from hydrothermal circulation and water radiolysis in uranium-enriched rocks are seemingly essential. However, the crustal habitability depending on a low supply of energy is unknown. We present multi-isotopic evidence of microbially mediated sulfate reduction in a granitic aquifer, a representative of the terrestrial crust habitat. Deep meteoric groundwater was collected from underground boreholes drilled into Cretaceous Toki granite (central Japan. A large sulfur isotopic fractionation of 20-60‰ diagnostic to microbial sulfate reduction is associated with the investigated groundwater containing sulfate below 0.2 mM. In contrast, a small carbon isotopic fractionation (<30‰ is not indicative of methanogenesis. Except for 2011, the concentrations of H2 ranged mostly from 1 to 5 nM, which is also consistent with an aquifer where a terminal electron accepting process is dominantly controlled by ongoing sulfate reduction. High isotopic ratios of mantle-derived 3He relative to radiogenic 4He in groundwater and the flux of H2 along adjacent faults suggest that, in addition to low concentrations of organic matter (<70 µM, H2 from deeper sources might partly fuel metabolic activities. Our results demonstrate that the deep biosphere in the terrestrial crust is metabolically active and playing a crucial role in the formation of reducing groundwater even under low-energy fluxes.

Microbial xanthophylls.

Science.gov (United States)

Bhosale, Prakash; Bernstein, Paul S

2005-09-01

Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

Evaluation of Kefir as a New Anodic Biocatalyst Consortium for Microbial Fuel Cell.

Science.gov (United States)

Silveira, Gustavo; Schneedorf, José Maurício

2018-02-21

Kefir, a combined consortium of bacteria and yeast encapsulated by a polymeric matrix of exopolysaccharides, was used as anodic biocatalyst in a two-chamber microbial fuel cell (MFC). Fermentation was followed during 72 h and polarization curves were obtained from linear sweep voltammetry. The effect of methylene blue as charge-transfer mediator in the kefir metabolism was evaluated. UV/Vis spectrophotometry and cyclic voltammetry were applied to evaluate the redox state of the mediator and to characterize the electrochemical activity, whereas current interruption was used for internal resistance determination. Aiming to establish a relationship between the microbial development inside the anodic chamber with the generated power in the MFC, total titratable acidity, pH, viscosity, carbohydrate assimilation, and microbial counting were assayed. The kefir-based MFC demonstrated a maximum power density of 54 mW m -2 after 24 h fermentation, revealing the potential use of kefir as a biocatalyst for microbial fuel cells.

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

Science.gov (United States)

Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Contact in adoption and adoptive identity formation: the mediating role of family conversation.

Science.gov (United States)

Von Korff, Lynn; Grotevant, Harold D

2011-06-01

The present study examined adoption-related family conversation as a mediator of the association between adoptive parents' facilitation of contact with birth relatives and adolescent adoptive identity formation. The sample consisted of 184 adoptive families. Data were collected in two waves from adoptive mothers and fathers, and adoptees (M = 15.68 years at adolescence; M = 24.95 years at emerging adulthood) using semistructured interviews and questionnaires. Structural equation models showed a good fit to sample data, and analyses supported the hypothesized mediation model. Contact with birth relatives is associated with more frequent adoption-related family conversation, which in turn is associated with the development of adoptive identity. These results highlight the importance of supporting activities such as contact that lead to adoption-related family conversation. 2011 APA, all rights reserved

Anthraquinone-2-sulfonate immobilized to conductive polypyrrole hydrogel as a bioanode to enhance power production in microbial fuel cell.

Science.gov (United States)

Tang, Xinhua; Ng, How Yong

2017-11-01

In this study, anthraquinone-2-sulfonate (AQS), a redox mediator, was covalently bound to conductive polypyrrole hydrogel (CPH) via electrochemical reduction of the in-situ-generated AQS diazonium salts. The porous structure and hydrophilic surface of this CPH/AQS anode enhanced biofilm formation while the AQS bound on the CPH/AQS anode worked as a redox mediator. The CPH/AQS bioanode reduced the charge transfer resistance from 28.3Ω to 4.1Ω while increased the maximum power density from 762±37mW/m 2 to 1919±69mW/m 2 , compared with the bare anode. These results demonstrated that the facile synthesis of the CPH/AQS anode provided an efficient route to enhance the power production of microbial fuel cell (MFC). Copyright © 2017 Elsevier Ltd. All rights reserved.

Abiogenic and Microbial Controls on Volatile Fatty Acids in Precambrian Crustal Fracture Waters

Science.gov (United States)

McDermott, J. M.; Heuer, V.; Tille, S.; Moran, J.; Slater, G.; Sutcliffe, C. N.; Glein, C. R.; Hinrichs, K. U.; Sherwood Lollar, B.

2015-12-01

Saline fracture waters within the Precambrian Shield rocks of Canada and South Africa have been sequestered underground over geologic timescales up to 1.1-1.8 Ga [1, 2]. These fluids are rich in H2 derived from radiolysis and hydration of mafic and ultramafic rocks [1, 2, 3] and host a low-biomass, low-diversity microbial ecosystem at some sites [2]. The abiogenic or biogenic nature of geochemical processes has important implications for bioavailable carbon sources and the role played by abiotic organic synthesis in sustaining a chemosynthetic deep biosphere. Volatile fatty acids (VFAs) are simple carboxylic acids that may support microbial communities in such environments, such as those found in terrestrial [4] and deep-sea [5] hot springs. We present abundance and δ13C analysis for VFAs in a spectrum of Canadian Shield fluids characterized by varying dissolved H2, CH4, and C2+ n-alkane compositions. Isotope mass balance indicates that microbially mediated fermentation of carbon-rich graphitic sulfides may produce the elevated levels of acetate (39-273 μM) found in Birchtree and Thompson mine. In contrast, thermodynamic considerations and isotopic signatures of the notably higher acetate (1.2-1.9 mM), as well as formate and propionate abundances (371-816 μM and 20-38 μM, respectively) found at Kidd Creek mine suggest a role for abiogenic production via reduction of dissolved inorganic carbon with H2 for formate, and oxidation of C2+ n-alkanes for acetate and propionate, along with possible microbial cycling. VFAs comprise the bulk of dissolved and total organic carbon in the mines surveyed, and as such represent a potential key substrate for life. [1] Holland et al. (2013) Nature 497: 367-360. [2] Lin et al. (2006) Science 314: 479-482. [3] Sherwood Lollar et al. (2014) Nature 516: 379-382. [4] Windman et al. (2007) Astrobiology 7(6): 873-890. [5] Lang et al. (2010) Geochim. Cosmochim. Acta 92: 82-99.

Microbial-Induced Heterogeneity in the Acoustic Properties of Porous Media

Science.gov (United States)

Acoustic wave data were acquired over a two-dimensional region of a microbial-stimulated sand column and an unstimulated sand column to assess the spatiotemporal changes in a porous medium caused by microbial growth and biofilm formation. The acoustic signals from the unstimulate...

Fast microbial reduction of ferrihydrite colloids from a soil effluent

Science.gov (United States)

Fritzsche, Andreas; Bosch, Julian; Rennert, Thilo; Heister, Katja; Braunschweig, Juliane; Meckenstock, Rainer U.; Totsche, Kai U.

2012-01-01

Recent studies on the microbial reduction of synthetic iron oxide colloids showed their superior electron accepting property in comparison to bulk iron oxides. However, natural colloidal iron oxides differ in composition from their synthetic counterparts. Besides a potential effect of colloid size, microbial iron reduction may be accelerated by electron-shuttling dissolved organic matter (DOM) as well as slowed down by inhibitors such as arsenic. We examined the microbial reduction of OM- and arsenic-containing ferrihydrite colloids. Four effluent fractions were collected from a soil column experiment run under water-saturated conditions. Ferrihydrite colloids precipitated from the soil effluent and exhibited stable hydrodynamic diameters ranging from 281 (±146) nm in the effluent fraction that was collected first and 100 (±43) nm in a subsequently obtained effluent fraction. Aliquots of these oxic effluent fractions were added to anoxic low salt medium containing diluted suspensions of Geobacter sulfurreducens. Independent of the initial colloid size, the soil effluent ferrihydrite colloids were quickly and completely reduced. The rates of Fe2+ formation ranged between 1.9 and 3.3 fmol h-1 cell-1, and are in the range of or slightly exceeding previously reported rates of synthetic ferrihydrite colloids (1.3 fmol h-1 cell-1), but greatly exceeding previously known rates of macroaggregate-ferrihydrite reduction (0.07 fmol h-1 cell-1). The inhibition of microbial Fe(III) reduction by arsenic is unlikely or overridden by the concurrent enhancement induced by soil effluent DOM. These organic species may have increased the already high intrinsic reducibility of colloidal ferrihydrite owing to quinone-mediated electron shuttling. Additionally, OM, which is structurally associated with the soil effluent ferrihydrite colloids, may also contribute to the higher reactivity due to increasing solubility and specific surface area of ferrihydrite. In conclusion, ferrihydrite

Biogenic amine formation and microbial spoilage in chilled garfish ( Belone belone belone ) - effect of modified atmosphere packaging and previous frozen storage

DEFF Research Database (Denmark)

Dalgaard, Paw; Madsen, H.L.; Samieian, N.

2006-01-01

Abstract Aims: To evaluate biogenic amine formation and microbial spoilage in fresh and thawed chilled garfish. Methods and Results: Storage trials were carried out with fresh and thawed garfish fillets at 0 or 5oC in air or in modified atmosphere packaging (MAP: 40% CO2 and 60% N2). During storage...... 1000 ppm of histamine was formed in garfish; thus even when it is chilled this product represents a histamine fish-poisoning risk....

Coastal microbial mats: the physiology of a small-scale ecosystem

NARCIS (Netherlands)

Stal, L.J.

2001-01-01

Coastal inter-tidal sandy sediments, salt marshes and mangrove forests often support the development of microbial mats. Microbial mats are complex associations of one or several functional groups of microorganisms and their formation usually starts with the growth of a cyanobacterial population on a

Flow-through Column Experiments and Modeling of Microbially Mediated Cr(VI) Reduction at Hanford 100H

Science.gov (United States)

Yang, L.; Molins, S.; Beller, H. R.; Brodie, E. L.; Steefel, C.; Nico, P. S.; Han, R.

2010-12-01

Microbially mediated Cr(VI) reduction at the Hanford 100H area was investigated by flow-through column experiments. Three separate experiments were conducted to promote microbial activities associated with denitrification, iron and sulfate reduction, respectively. Replicate columns packed with natural sediments from the site under anaerobic environment were injected with 5mM Lactate as the electron donor and 5 μM Cr(VI) in all experiments. Sulfate and nitrate solutions were added to act as the main electron acceptors in the respective experiments, while iron columns relied on the indigenous sediment iron (and manganese) oxides as electron acceptors. Column effluent solutions were analyzed by IC and ICP-MS to monitor the microbial consumption/conversion of lactate and the associated Cr(VI) reduction. Biogeochemical reactive transport modeling was performed to gain further insights into the reaction mechanisms and Cr(VI) bioreduction rates. All experimental columns showed a reduction of the injected Cr(VI). Columns under denitrifying conditions showed the least Cr(VI) reduction at early stages (simulations indicated that biomass growth completely depleted influent ammonium, and called for an additional source of N to account for the measured reduction rates. Iron columns were the least active with undetectable consumption of the injected lactate, slowest cell growth, and the smallest change in Cr(VI) concentrations during the course of the experiment. In contrast, columns under sulfate-reducing/fermentative conditions exhibited the greatest Cr(VI) reduction capacity. Two sulfate columns evolved to complete lactate fermentation with acetate and propionate produced in the column effluent after 40 days of experiments. These fermenting columns showed a complete removal of injected Cr(VI), visible precipitation of sulfide minerals, and a significant increase in effluent Fe and Mn concentrations. Reactive transport simulations suggested that direct reduction of Cr(VI) by

Fate of Cd during microbial Fe(III) mineral reduction by a novel and Cd-tolerant Geobacter species.

Science.gov (United States)

Muehe, E Marie; Obst, Martin; Hitchcock, Adam; Tyliszczak, Tolek; Behrens, Sebastian; Schröder, Christian; Byrne, James M; Michel, F Marc; Krämer, Ute; Kappler, Andreas

2013-12-17

Fe(III) (oxyhydr)oxides affect the mobility of contaminants in the environment by providing reactive surfaces for sorption. This includes the toxic metal cadmium (Cd), which prevails in agricultural soils and is taken up by crops. Fe(III)-reducing bacteria can mobilize such contaminants by Fe(III) mineral dissolution or immobilize them by sorption to or coprecipitation with secondary Fe minerals. To date, not much is known about the fate of Fe(III) mineral-associated Cd during microbial Fe(III) reduction. Here, we describe the isolation of a new Geobacter sp. strain Cd1 from a Cd-contaminated field site, where the strain accounts for 10(4) cells g(-1) dry soil. Strain Cd1 reduces the poorly crystalline Fe(III) oxyhydroxide ferrihydrite in the presence of at least up to 112 mg Cd L(-1). During initial microbial reduction of Cd-loaded ferrihydrite, sorbed Cd was mobilized. However, during continuous microbial Fe(III) reduction, Cd was immobilized by sorption to and/or coprecipitation within newly formed secondary minerals that contained Ca, Fe, and carbonate, implying the formation of an otavite-siderite-calcite (CdCO3-FeCO3-CaCO3) mixed mineral phase. Our data shows that microbially mediated turnover of Fe minerals affects the mobility of Cd in soils, potentially altering the dynamics of Cd uptake into food or phyto-remediating plants.

Gut microbiota induce IGF-1 and promote bone formation and growth

Science.gov (United States)

Yan, Jing; Herzog, Jeremy W.; Tsang, Kelly; Brennan, Caitlin A.; Bower, Maureen A.; Garrett, Wendy S.; Sartor, Balfour R.; Charles, Julia F.

2016-01-01

Appreciation of the role of the gut microbiome in regulating vertebrate metabolism has exploded recently. However, the effects of gut microbiota on skeletal growth and homeostasis have only recently begun to be explored. Here, we report that colonization of sexually mature germ-free (GF) mice with conventional specific pathogen-free (SPF) gut microbiota increases both bone formation and resorption, with the net effect of colonization varying with the duration of colonization. Although colonization of adult mice acutely reduces bone mass, in long-term colonized mice, an increase in bone formation and growth plate activity predominates, resulting in equalization of bone mass and increased longitudinal and radial bone growth. Serum levels of insulin-like growth factor 1 (IGF-1), a hormone with known actions on skeletal growth, are substantially increased in response to microbial colonization, with significant increases in liver and adipose tissue IGF-1 production. Antibiotic treatment of conventional mice, in contrast, decreases serum IGF-1 and inhibits bone formation. Supplementation of antibiotic-treated mice with short-chain fatty acids (SCFAs), products of microbial metabolism, restores IGF-1 and bone mass to levels seen in nonantibiotic-treated mice. Thus, SCFA production may be one mechanism by which microbiota increase serum IGF-1. Our study demonstrates that gut microbiota provide a net anabolic stimulus to the skeleton, which is likely mediated by IGF-1. Manipulation of the microbiome or its metabolites may afford opportunities to optimize bone health and growth. PMID:27821775

Unique ζ-chain motifs mediate a direct TCR-actin linkage critical for immunological synapse formation and T-cell activation.

Science.gov (United States)

Klieger, Yair; Almogi-Hazan, Osnat; Ish-Shalom, Eliran; Pato, Aviad; Pauker, Maor H; Barda-Saad, Mira; Wang, Lynn; Baniyash, Michal

2014-01-01

TCR-mediated activation induces receptor microclusters that evolve to a defined immune synapse (IS). Many studies showed that actin polymerization and remodeling, which create a scaffold critical to IS formation and stabilization, are TCR mediated. However, the mechanisms controlling simultaneous TCR and actin dynamic rearrangement in the IS are yet not fully understood. Herein, we identify two novel TCR ζ-chain motifs, mediating the TCR's direct interaction with actin and inducing actin bundling. While T cells expressing the ζ-chain mutated in these motifs lack cytoskeleton (actin) associated (cska)-TCRs, they express normal levels of non-cska and surface TCRs as cells expressing wild-type ζ-chain. However, such mutant cells are unable to display activation-dependent TCR clustering, IS formation, expression of CD25/CD69 activation markers, or produce/secrete cytokine, effects also seen in the corresponding APCs. We are the first to show a direct TCR-actin linkage, providing the missing gap linking between TCR-mediated Ag recognition, specific cytoskeleton orientation toward the T-cell-APC interacting pole and long-lived IS maintenance. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Empirical evidence that soil carbon formation from plant inputs is positively related to microbial growth

Science.gov (United States)

Mark A. Bradford; Ashley D. Keiser; Christian A. Davies; Calley A. Mersmann; Michael S. Strickland

2012-01-01

Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant...

Matrix metalloproteinase-14 mediates formation of bile ducts and hepatic maturation of fetal hepatic progenitor cells

Energy Technology Data Exchange (ETDEWEB)

Otani, Satoshi [Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo (Japan); Kakinuma, Sei, E-mail: skakinuma.gast@tmd.ac.jp [Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo (Japan); Department for Liver Disease Control, Tokyo Medical and Dental University, Tokyo (Japan); Kamiya, Akihide [Institute of Innovative Science and Technology, Tokai University, Isehara (Japan); Goto, Fumio; Kaneko, Shun; Miyoshi, Masato; Tsunoda, Tomoyuki; Asano, Yu; Kawai-Kitahata, Fukiko; Nitta, Sayuri; Nakata, Toru; Okamoto, Ryuichi; Itsui, Yasuhiro; Nakagawa, Mina; Azuma, Seishin [Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo (Japan); Asahina, Yasuhiro [Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo (Japan); Department for Liver Disease Control, Tokyo Medical and Dental University, Tokyo (Japan); Yamaguchi, Tomoyuki [Division of Stem Cell Therapy, Institute of Medical Science, The University of Tokyo, Tokyo (Japan); Koshikawa, Naohiko [Division of Cancer Cell Research, Institute of Medical Science, The University of Tokyo, Tokyo (Japan); Seiki, Motoharu [Medical School, Kanazawa University, Kanazawa (Japan); Nakauchi, Hiromitsu [Division of Stem Cell Therapy, Institute of Medical Science, The University of Tokyo, Tokyo (Japan); and others

2016-01-22

Fetal hepatic stem/progenitor cells, called hepatoblasts, play central roles in liver development; however, the molecular mechanisms regulating the phenotype of these cells have not been completely elucidated. Matrix metalloproteinase (MMP)-14 is a type I transmembrane proteinase regulating pericellular proteolysis of the extracellular matrix and is essential for the activation of several MMPs and cytokines. However, the physiological functions of MMP-14 in liver development are unknown. Here we describe a functional role for MMP-14 in hepatic and biliary differentiation of mouse hepatoblasts. MMP-14 was upregulated in cells around the portal vein in perinatal stage liver. Formation of bile duct-like structures in MMP-14–deficient livers was significantly delayed compared with wild-type livers in vivo. In vitro biliary differentiation assays showed that formation of cholangiocytic cysts derived from MMP-14–deficient hepatoblasts was completely impaired, and that overexpression of MMP-14 in hepatoblasts promoted the formation of bile duct-like cysts. In contrast, the expression of molecules associated with metabolic functions in hepatocytes, including hepatic nuclear factor 4α and tryptophan 2,3-dioxygenase, were significantly increased in MMP-14–deficient livers. Expression of the epidermal growth factor receptor and phosphorylation of mitogen-activated protein kinases were significantly upregulated in MMP-14–deficient livers. We demonstrate that MMP-14–mediated signaling in fetal hepatic progenitor cells promotes biliary luminal formation around the portal vein and negatively controls the maturation of hepatocytes. - Highlights: • Loss of MMP-14 delayed formation of bile duct-like structures in perinatal liver. • Overexpression of MMP-14 in hepatobalsts promoted the biliary formation in vitro. • Loss of MMP-14 promoted hepatocyte maturation of hepatoblasts in vivo. • MMP-14–mediated signaling regulates terminal differentiation of

Microbial and Chemical Enhancement of In-Situ Carbon Mineralization in Geological Formation

Energy Technology Data Exchange (ETDEWEB)

Matter, J.; Chandran, K.

2013-05-31

Predictions of global energy usage suggest a continued increase in carbon emissions and rising concentrations of CO{sub 2} in the atmosphere unless major changes are made to the way energy is produced and used. Various carbon capture and storage (CCS) technologies are currently being developed, but unfortunately little is known regarding the fundamental characteristics of CO{sub 2}-mineral reactions to allow a viable in-situ carbon mineralization that would provide the most permanent and safe storage of geologically-injected CO{sub 2}. The ultimate goal of this research project was to develop a microbial and chemical enhancement scheme for in-situ carbon mineralization in geologic formations in order to achieve long-term stability of injected CO{sub 2}. Thermodynamic and kinetic studies of CO{sub 2}-mineral-brine systems were systematically performed to develop the in-situ mineral carbonation process that utilizes organic acids produced by a microbial reactor. The major participants in the project are three faculty members and their graduate and undergraduate students at the School of Engineering and Applied Science and at the Lamont-Doherty Earth Observatory at Columbia University: Alissa Park in Earth and Environmental Engineering & Chemical Engineering (PI), Juerg Matter in Earth and Environmental Science (Co-PI), and Kartik Chandran in Earth and Environmental Engineering (Co-PI). Two graduate students, Huangjing Zhao and Edris Taher, were trained as a part of this project as well as a number of graduate students and undergraduate students who participated part-time. Edris Taher received his MS degree in 2012 and Huangjing Zhao will defend his PhD on Jan. 15th, 2014. The interdisciplinary training provided by this project was valuable to those students who are entering into the workforce in the United States. Furthermore, the findings from this study were and will be published in referred journals to disseminate the results. The list of the papers is given at

Eicosanoid-mediated immunity in insects

Science.gov (United States)

Eicosanoid is a collective term for oxygenated metabolites of C20 polyunsaturated fatty acids. As seen in mammals, eicosanoids play crucial roles in mediating various physiological processes, including immune responses, in insects. Upon microbial pathogen infection, non-self recognition signals are ...

Microbial mat structures in profile: The Neoproterozoic Sonia Sandstone, Rajasthan, India

Science.gov (United States)

Samanta, Pradip; Mukhopadhyay, Soumik; Mondal, Anudeb; Sarkar, Subir

2011-01-01

Ubiquitous microorganisms, especially cyanobacteria preferably grow on the sediment surface thereby producing microbial mats. In the absence of grazers and bioturbators, microbial mat is a unique feature of the Proterozoic. Most of the papers so far published described a wide variety of bed surface microbial mat structures with rare illustrations from sections perpendicular to bedding. Nonetheless, bed surface exposures are relatively rare in rock records. This limitation of bed surface exposures in rock records suggest that a study of microbial mats in bed-across sections is needed. The 60 m thick coastal marine interval of the Sonia Sandstone Formation is bounded between two terrestrial intervals, a transgressive lag at the base and an unconformity at the top, and has been chosen for exploration of microbial mat structures in bed-across sections. A wide variety of microbial mat-induced structures in bed-across sections are preserved within the coastal interval of the Sonia Sandstone. Though many of these structures are similar in some aspects with bed surface structures, some of those presented here are new. The palaeogeographic range of these microbial structures extends from supralittoral to neritic. Diagenetic alterations of microbial mats produce pyrite and those zones are suitable for the preservation of microbial remains. SEM and EDAX analyses show fossil preservation of filamentous microbial remains that confirm the presence of microbial mats within the coastal interval of the Sonia Sandstone. Effects of proliferation of microbial mats in the siliciclastic depositional setting are numerous. The mat-cover on sediment surfaces hinders reworking and/or erosion of the sediments thereby increases the net sedimentation rate. Successive deposition and preservation of thick microbial mat layer under reducing environments should have a great potential for hydrocarbon production and preservation and therefore these Proterozoic formations could be a target for

An overview of field specific designs of microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Robertson, E.P.; Bala, G.A.; Fox, S.L.; Jackson, J.D.; Thomas, C.P.

1995-12-01

The selection and design of a microbial enhanced oil recovery (MEOR) process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (biogenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. The objective of this paper is to discuss the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR technology. Reservoir characteristics and laboratory results indicated that MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery process for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated and field isolates were characterized.

In situ formation of graphene layers on graphite surfaces for efficient anodes of microbial fuel cells.

Science.gov (United States)

Tang, Jiahuan; Chen, Shanshan; Yuan, Yong; Cai, Xixi; Zhou, Shungui

2015-09-15

Graphene can be used to improve the performance of the anode in a microbial fuel cell (MFC) due to its good biocompatibility, high electrical conductivity and large surface area. However, the chemical production and modification of the graphene on the anode are environmentally hazardous because of the use of various harmful chemicals. This study reports a novel method based on the electrochemical exfoliation of a graphite plate (GP) for the in situ formation of graphene layers on the surface of a graphite electrode. When the resultant graphene-layer-based graphite plate electrode (GL/GP) was used as an anode in an MFC, a maximum power density of 0.67 ± 0.034 W/m(2) was achieved. This value corresponds to 1.72-, 1.56- and 1.26-times the maximum power densities of the original GP, exfoliated-graphene-modified GP (EG/GP) and chemically-reduced-graphene-modified GP (rGO/GP) anodes, respectively. Electrochemical measurements revealed that the high performance of the GL/GP anode was attributable to its macroporous structure, improved electron transfer and high electrochemical capacitance. The results demonstrated that the proposed method is a facile and environmentally friendly synthesis technique for the fabrication of high-performance graphene-based electrodes for use in microbial energy harvesting. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial ecology of hot desert edaphic systems.

Science.gov (United States)

Makhalanyane, Thulani P; Valverde, Angel; Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Cowan, Don A

2015-03-01

A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Fate of Eight Different Polymers under Uncontrolled Composting Conditions: Relationships Between Deterioration, Biofilm Formation, and the Material Surface Properties.

Science.gov (United States)

Mercier, Anne; Gravouil, Kevin; Aucher, Willy; Brosset-Vincent, Sandra; Kadri, Linette; Colas, Jenny; Bouchon, Didier; Ferreira, Thierry

2017-02-21

With the ever-increasing volume of polymer wastes and their associated detrimental impacts on the environment, the plastic life cycle has drawn increasing attention. Here, eight commercial polymers selected from biodegradable to environmentally persistent materials, all formulated under a credit card format, were incubated in an outdoor compost to evaluate their fate over time and to profile the microbial communities colonizing their surfaces. After 450 days in compost, the samples were all colonized by multispecies biofilms, these latest displaying different amounts of adhered microbial biomass and significantly distinct bacterial and fungal community compositions depending on the substrate. Interestingly, colonization experiments on the eight polymers revealed a large core of shared microbial taxa, predominantly composed of microorganisms previously reported from environments contaminated with petroleum hydrocarbons or plastics debris. These observations suggest that biofilms may contribute to the alteration process of all the polymers studied. Actually, four substrates, independently of their assignment to a polymer group, displayed a significant deterioration, which might be attributed to biologically mediated mechanisms. Relevantly, the deterioration appears strongly associated with the formation of a high-cell density biofilm onto the polymer surfaces. The analysis of various surface properties revealed that roughness and hydrophilicity are likely prominent parameters for driving the biological interactions with the polymers.

Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

Science.gov (United States)

Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

2015-12-01

Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

Strain-Mediated Interfacial Dynamics during Au–PbS Core–Shell Nanostructure Formation

KAUST Repository

Niu, Kai-Yang; Liu, Miao; Persson, Kristin A.; Han, Yu; Zheng, Haimei

2016-01-01

An understanding of the hierarchical nanostructure formation is of significant importance for the design of advanced functional materials. Here, we report the in situ study of lead sulfide (PbS) growth on gold (Au) nanorod seeds using liquid cell transmission electron microscopy (TEM). By tracking the formation dynamics of Au-PbS core-shell nanoparticles, we found the preferential heterogeneous nucleation of PbS on the ends of a Au nanorod prior to the development of a complete PdS shell. During PbS shell growth, drastic sulfidation of Au nanorod was observed, leading to large volume shrinkage (up to 50%) of the initial Au nanorod seed. We also captured intriguing wavy interfacial behavior, which can be explained by our DFT calculation results that the local strain gradient at the core-shell interface facilitates the mass transport and mediates reversible phase transitions of Au ↔ Au2S during the PbS shell growth. © 2016 American Chemical Society.

Strain-Mediated Interfacial Dynamics during Au–PbS Core–Shell Nanostructure Formation

KAUST Repository

Niu, Kai-Yang

2016-05-23

An understanding of the hierarchical nanostructure formation is of significant importance for the design of advanced functional materials. Here, we report the in situ study of lead sulfide (PbS) growth on gold (Au) nanorod seeds using liquid cell transmission electron microscopy (TEM). By tracking the formation dynamics of Au-PbS core-shell nanoparticles, we found the preferential heterogeneous nucleation of PbS on the ends of a Au nanorod prior to the development of a complete PdS shell. During PbS shell growth, drastic sulfidation of Au nanorod was observed, leading to large volume shrinkage (up to 50%) of the initial Au nanorod seed. We also captured intriguing wavy interfacial behavior, which can be explained by our DFT calculation results that the local strain gradient at the core-shell interface facilitates the mass transport and mediates reversible phase transitions of Au ↔ Au2S during the PbS shell growth. © 2016 American Chemical Society.

Incorporating the soil environment and microbial community into plant competition theory.

Science.gov (United States)

Ke, Po-Ju; Miki, Takeshi

2015-01-01

Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF). PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach.

Incorporating the soil environment and microbial community into plant competition theory

Science.gov (United States)

Ke, Po-Ju; Miki, Takeshi

2015-01-01

Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF). PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach. PMID:26500621

Incorporating the soil environment and microbial community into plant competition theory

Directory of Open Access Journals (Sweden)

Po-Ju eKe

2015-10-01

Full Text Available Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF. PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach.

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

OpenAIRE

BoonFei eTan; Charmaine Marie Ng; Jean Pierre Nshimyimana; Jean Pierre Nshimyimana; Lay-Leng eLoh; Lay-Leng eLoh; Karina Yew-Hoong Gin; Janelle Renee Thompson; Janelle Renee Thompson

2015-01-01

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable reg...

Role of Sphingosine Kinase 1 and S1P Transporter Spns2 in HGF-mediated Lamellipodia Formation in Lung Endothelium.

Science.gov (United States)

Fu, Panfeng; Ebenezer, David L; Berdyshev, Evgeny V; Bronova, Irina A; Shaaya, Mark; Harijith, Anantha; Natarajan, Viswanathan

2016-12-30

Hepatocyte growth factor (HGF) signaling via c-Met is known to promote endothelial cell motility and angiogenesis. We have previously reported that HGF stimulates lamellipodia formation and motility of human lung microvascular endothelial cells (HLMVECs) via PI3K/Akt signal transduction and reactive oxygen species generation. Here, we report a role for HGF-induced intracellular sphingosine-1-phosphate (S1P) generation catalyzed by sphingosine kinase 1 (SphK1), S1P transporter, spinster homolog 2 (Spns2), and S1P receptor, S1P 1 , in lamellipodia formation and perhaps motility of HLMVECs. HGF stimulated SphK1 phosphorylation and enhanced intracellular S1P levels in HLMVECs, which was blocked by inhibition of SphK1. HGF enhanced co-localization of SphK1/p-SphK1 with actin/cortactin in lamellipodia and down-regulation or inhibition of SphK1 attenuated HGF-induced lamellipodia formation in HLMVECs. In addition, down-regulation of Spns2 also suppressed HGF-induced lamellipodia formation, suggesting a key role for inside-out S1P signaling. The HGF-mediated phosphorylation of SphK1 and its localization in lamellipodia was dependent on c-Met and ERK1/2 signaling, but not the PI3K/Akt pathway; however, blocking PI3K/Akt signaling attenuated HGF-mediated phosphorylation of Spns2. Down-regulation of S1P 1 , but not S1P 2 or S1P 3 , with specific siRNA attenuated HGF-induced lamellipodia formation. Further, HGF enhanced association of Spns2 with S1P 1 that was blocked by inhibiting SphK1 activity with PF-543. Moreover, HGF-induced migration of HLMVECs was attenuated by down-regulation of Spns2 . Taken together, these results suggest that HGF/c-Met-mediated lamellipodia formation, and perhaps motility is dependent on intracellular generation of S1P via activation and localization of SphK1 to cell periphery and Spns2-mediated extracellular transportation of S1P and its inside-out signaling via S1P 1 . © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Microbial effects

International Nuclear Information System (INIS)

Sharpe, V.J.

1985-10-01

The long term safety and integrity of radioactive waste disposal sites proposed for use by Ontario Hydro may be affected by the release of radioactive gases. Microbes mediate the primary pathways of waste degradation and hence an assessment of their potential to produce gaseous end products from the breakdown of low level waste was performed. Due to a number of unknown variables, assumptions were made regarding environmental and waste conditions that controlled microbial activity; however, it was concluded that 14 C and 3 H would be produced, albeit over a long time scale of about 1500 years for 14 C in the worst case situation

Microfluidics expanding the frontiers of microbial ecology.

Science.gov (United States)

Rusconi, Roberto; Garren, Melissa; Stocker, Roman

2014-01-01

Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.

Microbial diversity in restored wetlands of San Francisco Bay

Energy Technology Data Exchange (ETDEWEB)

Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2013-12-09

Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils, we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.

The Role of Lactate-Mediated Metabolic Coupling between Astrocytes and Neurons in Long-Term Memory Formation

Science.gov (United States)

Steinman, Michael Q.; Gao, Virginia; Alberini, Cristina M.

2016-01-01

Long-term memory formation, the ability to retain information over time about an experience, is a complex function that affects multiple behaviors, and is an integral part of an individual’s identity. In the last 50 years many scientists have focused their work on understanding the biological mechanisms underlying memory formation and processing. Molecular studies over the last three decades have mostly investigated, or given attention to, neuronal mechanisms. However, the brain is composed of different cell types that, by concerted actions, cooperate to mediate brain functions. Here, we consider some new insights that emerged from recent studies implicating astrocytic glycogen and glucose metabolisms, and particularly their coupling to neuronal functions via lactate, as an essential mechanism for long-term memory formation. PMID:26973477

The role of lactate-mediated metabolic coupling between astrocytes and neurons in long-term memory formation

Directory of Open Access Journals (Sweden)

Michael eSteinman

2016-03-01

Full Text Available Long-term memory formation, the ability to retain information over time about an experience, is a complex function that affects multiple behaviors, and is an integral part of an individual’s identity. In the last 50 years many scientists have focused their work on understanding the biological mechanisms underlying memory formation and processing. Molecular studies over the last three decades have mostly investigated, or given attention to, neuronal mechanisms. However, the brain is composed of different cell types that, by concerted actions, cooperate to mediate brain functions. Here we consider some new insights that emerged from recent studies implicating astrocytic glycogen and glucose metabolisms, and particularly their coupling to neuronal functions via lactate, as an essential mechanism for long-term memory formation.

An overview of field-specific designs of microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Robertson, E.P.; Bala, G.A.; Fox, S.L.; Jackson, J.D.; Thomas, C.P. [Idaho National Engineering Lab., Idaho Falls, ID (United States)

1995-12-31

The selection and design of an MEOR process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (bigenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. This paper discusses the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery process for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated, and field isolates were characterized.

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

International Nuclear Information System (INIS)

Wang, Yifeng; Papenguth, Hans W.

2000-01-01

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

Energy Technology Data Exchange (ETDEWEB)

WANG,YIFENG; PAPENGUTH,HANS W.

2000-05-04

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

Extracellular Electron Uptake: Among Autotrophs and Mediated by Surfaces

DEFF Research Database (Denmark)

Tremblay, Pier-Luc; Angenent, Largus T.; Zhang, Tian

2017-01-01

Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO2. Extracellular electron-transfer mechan......Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO2. Extracellular electron......; or (iii) mediator-generating enzymes detached from cells. This review explores the interactions of autotrophs with solid electron donors and their importance in nature and for biosustainable technologies....

Factors Affecting Microbial Contamination of Market Eggs: A Review

Directory of Open Access Journals (Sweden)

Svobodová J.

2015-01-01

Full Text Available The aim of the review was to analyze the ways of microbial contamination, the protective mechanism of egg, and factors that affect the quantity of contamination and microbial penetration. Eggs can be contaminated during their formation in the infected reproductive organs of hens or after laying, when eggs are exposed to contaminated environment. The eggs are equipped against microbial contamination by several protective mechanisms comprising the presence of cuticle, eggshell, eggshell membranes, occurrence of some antibacterial proteins, and high pH value of albumen. There are several factors that affect the quantity of microbial contamination and penetration such as species of bacteria, the amount of microorganisms, storage conditions, quality of eggshell or number of pores.

Evaluating the influence of process parameters on soluble microbial products formation using response surface methodology coupled with grey relational analysis.

Science.gov (United States)

Xu, Juan; Sheng, Guo-Ping; Luo, Hong-Wei; Fang, Fang; Li, Wen-Wei; Zeng, Raymond J; Tong, Zhong-Hua; Yu, Han-Qing

2011-01-01

Soluble microbial products (SMPs) present a major part of residual chemical oxygen demand (COD) in the effluents from biological wastewater treatment systems, and the SMP formation is greatly influenced by a variety of process parameters. In this study, response surface methodology (RSM) coupled with grey relational analysis (GRA) method was used to evaluate the effects of substrate concentration, temperature, NH(4)(+)-N concentration and aeration rate on the SMP production in batch activated sludge reactors. Carbohydrates were found to be the major component of SMP, and the influential priorities of these factors were: temperature>substrate concentration > aeration rate > NH(4)(+)-N concentration. On the basis of the RSM results, the interactive effects of these factors on the SMP formation were evaluated, and the optimal operating conditions for a minimum SMP production in such a batch activated sludge system also were identified. These results provide useful information about how to control the SMP formation of activated sludge and ensure the bioreactor high-quality effluent. Copyright © 2010 Elsevier Ltd. All rights reserved.

Reaction kinetic model of the surface-mediated formation of PCDD/F from pyrolysis of 2-chlorophenol on a CuP/Silica suface

Energy Technology Data Exchange (ETDEWEB)

Lomnicki, S.; Khachatryan, L.; Dellinger, B. [Louisiana State Univ., Baton Rouge (United States). Dept. of Chemistry

2004-09-15

One of the major challenges in developing predictive models of the surface mediated pollutant formation and fuel combustion is the construction of reliable reaction kinetic mechanisms and models. While the homogeneous, gas-phase chemistry of various light fuels such as hydrogen and methane is relatively well-known large uncertainties exist in the reaction paths of surface mediated reaction mechanisms for even these very simple species. To date, no detailed kinetic consideration of the surface mechanisms of formation of complex organics such as PCDD/F have been developed. In addition to the complexity of the mechanism, a major difficulty is the lack of reaction kinetic parameters (pre-exponential factor and activation energy) of surface reactions, Consequently, numerical studies of the surface-mediated formation of PCDD/F have often been incorporated only a few reactions. We report the development of a numerical multiple-step surface model based on experimental data of surface mediated (5% CuO/SiO2) conversion of 2-monochlorphenol (2-MCP) to PCDD/F under pyrolytic or oxidative conditions. A reaction kinetic model of the catalytic conversion of 2-MCP on the copper oxide catalyst under pyrolytic conditions was developed based on a detailed multistep surface reaction mechanism developed in our laboratory. The performance of the chemical model is assessed by comparing the numerical predictions with experimental measurements. SURFACE CHEMKIN (version 3.7.1) software was used for modeling. Our results confirm the validity of previously published mechanism of the reaction and provides new insight concerning the formation of PCDD/F formation in combustion processes. This model successfully explains the high yields of PCDD/F at low temperatures that cannot be explained using a purely gas-phase mode.

Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

Directory of Open Access Journals (Sweden)

Huhe

Full Text Available In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively. The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

Nanocoatings for Chronic Wound Repair—Modulation of Microbial Colonization and Biofilm Formation

Directory of Open Access Journals (Sweden)

Mara Mădălina Mihai

2018-04-01

Full Text Available Wound healing involves a complex interaction between immunity and other natural host processes, and to succeed it requires a well-defined cascade of events. Chronic wound infections can be mono- or polymicrobial but their major characteristic is their ability to develop a biofilm. A biofilm reduces the effectiveness of treatment and increases resistance. A biofilm is an ecosystem on its own, enabling the bacteria and the host to establish different social interactions, such as competition or cooperation. With an increasing incidence of chronic wounds and, implicitly, of chronic biofilm infections, there is a need for alternative therapeutic agents. Nanotechnology shows promising openings, either by the intrinsic antimicrobial properties of nanoparticles or their function as drug carriers. Nanoparticles and nanostructured coatings can be active at low concentrations toward a large variety of infectious agents; thus, they are unlikely to elicit emergence of resistance. Nanoparticles might contribute to the modulation of microbial colonization and biofilm formation in wounds. This comprehensive review comprises the pathogenesis of chronic wounds, the role of chronic wound colonization and infection in the healing process, the conventional and alternative topical therapeutic approaches designed to combat infection and stimulate healing, as well as revolutionizing therapies such as nanotechnology-based wound healing approaches.

Microbial Enhanced Oil Recovery and Wettability Research Program. Annual report, FY 1991

Energy Technology Data Exchange (ETDEWEB)

Bala, G.A.; Barrett, K.B.; Eastman, S.L.; Herd, M.D.; Jackson, J.D.; Robertson, E.P.; Thomas, C.P.

1993-09-01

This report covers research results for fiscal year 1991 for the Microbial Enhanced Oil Recovery (MEOR) and Wettability Research Program conducted by EG&G Idaho, Inc. at the Idaho National Engineering Laboratory ONEL) for the US Department of Energy Idaho Field Office (DOE-ID). The program is funded by the Assistant Secretary of Fossil Energy, and managed by DOE-ID and the Bartlesville Project Office (BPO). The objectives of this multi-year program are to develop MEOR systems for application to reservoirs containing medium to heavy crude oils and to design and implement an industry cost-shared field demonstration project of the developed technology. An understanding of the controlling mechanisms will first be developed through the use of laboratory scale testing to determine the ability of microbially mediated processes to recover oil under reservoir conditions and to develop the design criteria for scale-up to the field. Concurrently with this work, the isolation and characterization of microbial species collected from various locations including target oil field environments is underway to develop more effective oil recovery systems for specific applications. Research focus includes the study of biogenic product and formation souring processes including mitigation and prevention. Souring research performed in FY 1991 also included the development of microsensor probe technology for the detection of total sulfide in collaboration with the Montana State University Center for Interfacial Microbial Process Engineering (CIMPE). Wettability research is a multi-year collaborative effort with the New Mexico Petroleum Recovery Research Center (NMPRRC) at the New Mexico institute of Mining and Technology, Socorro, NM to evaluate reservoir wettability and its effects on oil recovery. Results from the wettability research will be applied to determine if alteration of wettability is a significant contributing mechanism for MEOR systems.

Novel approaches to microbial enhancement of oil recovery.

Science.gov (United States)

Kryachko, Yuriy

2018-01-20

Microbially enhanced oil recovery (MEOR) was shown to be feasible in a number of laboratory experiments and field trials. However, it has not been widely used in the oil industry because necessary conditions cannot always be easily established in an oil reservoir. Novel approaches to MEOR, which are based on newly discovered biosurfactant-mediated MEOR-mechanisms, are discussed in this review. Particularly, the possibility of combining MEOR with chemical enhancement of oil recovery in heterogeneous oil reservoirs, which involves rock surface wettability shifts and emulsion inversions, is discussed. In wider (centimeter/millimeter-scale) rock pores, the activity of (bio)surfactants and microbial cells attached to oil may allow releasing trapped oil blobs through oil-in-water emulsification. After no more oil can be emulsified, the addition of alkali or surfactants, which turn rock surface oil-wet, may help release oil droplets trapped in narrow (micrometer-scale) pores through coalescence of the droplets and water-in-oil emulsification. Experiments demonstrating the possibility of (bio)surfactant-mediated enhancement of immiscible gas-driven oil recovery are also reviewed. Interestingly, very low (bio)surfactant concentrations were shown to be needed for enhancement of immiscible gas-driven oil recovery. Some possible side effects of MEOR, such as unintended bioplugging and microbially influenced corrosion (MIC), are discussed as well. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

In vitro antibiofilm efficacy of Piper betle against quorum sensing mediated biofilm formation of luminescent Vibrio harveyi.

Science.gov (United States)

Srinivasan, Ramanathan; Santhakumari, Sivasubramanian; Ravi, Arumugam Veera

2017-09-01

Vibrio harveyi is a potent biofilm former, which confers resistance to multiple antimicrobials, disinfectants, chemicals and biocides. The prevalence of biofilm mediated antibiotic resistance among aquatic bacterial pathogens stresses the search for novel alternative approach to treat vibriosis in aquaculture. Exploring suitable therapeutics from natural resources could be a novel area of research. Therefore, this work was executed to evaluate the inhibitory effect of Piper betle ethyl acetate extract (PBE) on bioluminescence production and biofilm formation of V. harveyi. Minimal inhibitory concentration (MIC) of PBE against planktonic V. harveyi was found to be 1600 μg ml -1 ; furthermore, PBE inhibited the quorum sensing (QS) mediated bioluminescence production and biofilm formation in V. harveyi upto 98 and 74% respectively, at its sub-MIC concentration of 400 μg ml -1 without affecting their cell viability. Similar results were obtained for exopolysaccharides production and swimming motility related to biofilm formation of V. harveyi, where PBE reduced EPS production upto 64%. Light and confocal laser scanning microscopic analyses further confirmed that the PBE effectively prevented the initial attachment as well as microcolonies formation of V. harveyi biofilm, when compared to their untreated controls. This study demonstrates the promising antibiofilm activity of PBE and confirms the ethnopharmacological potential of this plant against V. harveyi infections. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial bioenergetics of coral-algal interactions

Directory of Open Access Journals (Sweden)

Ty N.F. Roach

2017-06-01

Full Text Available Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify

Tracing the long-term microbial production of recalcitrant fluorescent dissolved organic matter in seawater

DEFF Research Database (Denmark)

Jørgensen, Linda; Stedmon, Colin A.; Granskog, Mats A.

2014-01-01

The majority of dissolved organic matter (DOM) in the ocean is resistant to microbial degradation, yet its formation remains poorly understood. The fluorescent fraction of DOM can be used to trace the formation of recalcitrant DOM (RDOM). A long-term (> 1 year) experiment revealed 27–52% removal...... of dissolved organic carbon and a nonlinear increase in RDOM fluorescence associated with microbial turnover of semilabile DOM. This fluorescence was also produced using glucose as the only initial carbon source, suggesting that degradation of prokaryote remnants contributes to RDOM. Our results indicate...... that the formation of a fluorescent RDOM component depends on the bioavailability of the substrate: the less labile, the larger the production of fluorescent RDOM relative to organic carbon remineralized. The anticipated increase in microbial carbon demand due to ocean warming can potentially forcemicrobes...

Porosity and Organic Carbon Controls on Naturally Reduced Zone (NRZ) Formation Creating Microbial ';Hotspots' for Fe, S, and U Cycling in Subsurface Sediments

Science.gov (United States)

Jones, M. E.; Janot, N.; Bargar, J.; Fendorf, S. E.

2013-12-01

Previous studies have illustrated the importance of Naturally Reduced Zones (NRZs) within saturated sediments for the cycling of metals and redox sensitive contaminants. NRZs can provide a source of reducing equivalents such as reduced organic compounds or hydrogen to stimulate subsurface microbial communities. These NRZ's are typically characterized by low permeability and elevated concentrations of organic carbon and trace metals. However, both the formation of NRZs and their importance to the overall aquifer carbon remineralization is not fully understood. Within NRZs the hydrolysis of particulate organic carbon (POC) and subsequent fermentation of dissolved organic carbon (DOC) to form low molecular weight dissolved organic carbon (LMW-DOC) provides electron donors necessary for the respiration of Fe, S, and in the case of the Rifle aquifer, U. Rates of POC hydrolysis and subsequent fermentation have been poorly constrained and rates in excess and deficit to the rates of subsurface anaerobic respiratory processes have been suggested. In this study, we simulate the development of NRZ sediments in diffusion-limited aggregates to investigate the physical and chemical conditions required for NRZ formation. Effects of sediment porosity and POC loading on Fe, S, and U cycling on molecular and nanoscale are investigated with synchrotron-based Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS). Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and Fourier Transform Infrared spectroscopy (FTIR) are used to characterize the transformations in POC and DOC. Sediment aggregates are inoculated with the natural microbial biota from the Rifle aquifer and population dynamics are monitored by 16S RNA analysis. Overall, establishment of low permeability NRZs within the aquifer stimulate microbial respiration beyond the diffusion-limited zones and can limit the transport of U through a contaminated aquifer. However, the long-term stability of

Changes in optical characteristics of surface microlayers in the Peruvian upwelling region hint to photochemically and microbially-mediated DOM turnover

Science.gov (United States)

Engel, A.; Galgani, L.

2016-02-01

The coastal upwelling system off Peru is characterized by high biological activity and associated subsurface oxygen minimum zone, leading to an enhanced emission of atmospheric trace gases. High biological productivity in the water column may promote the establishment of enriched organic surface films, key environments for processes regulating gas fluxes across the water-air interface. During M91 cruise to the Peruvian upwelling, we focused our attention on the composition of the sea-surface microlayer (SML), the oceanic uppermost boundary directly subject to high solar radiation, often enriched in specific organic compounds of biological origin like Chromophoric Dissolved Organic Matter (CDOM) and marine gels. In the SML, the continuous photochemical and microbial recycling of organic matter may strongly influence gas exchange between marine systems and the atmosphere. In order to understand organic matter cycling in surface films, we analyzed SML and underlying water samples in 38 stations determining DOC concentrations, amino acids composition, marine gels, CDOM and bacterial abundance as indicators of photochemical and microbial alteration processes. CDOM composition was characterized by spectral slopes (S) values and Excitation-Emission Matrix fluorescence (EEMs), which allow to track changes in molecular weight (MW) of DOM, and to determine potential DOM sources. Profound changes in spectral slope properties were observed suggesting smaller MW CDOM in the SML compared to underlying water. Microbial and photochemical degradation are likely the main drivers for organic matter cycling in the top layer of the ocean. Consequences on the formation of inorganic and organic species highly relevant for air-sea gas exchange and for climate dynamics will be discussed.

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

Science.gov (United States)

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

Directory of Open Access Journals (Sweden)

Kai Ziervogel

Full Text Available The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase, as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Performance evaluation of nanoclay enriched anti-microbial hydrogels for biomedical applications

Directory of Open Access Journals (Sweden)

Sonali Karnik

2016-02-01

Full Text Available A major factor contributing to the failure of orthopedic and orthodontic implants is post-surgical infection. Coating metallic implant surfaces with anti-microbial agents has shown promise but does not always prevent the formation of bacterial biofilms. Furthermore, breakdown of these coatings within the human body can cause release of the anti-microbial drugs in an uncontrolled or unpredictable fashion. In this study, we used a calcium alginate and calcium phosphate cement (CPC hydrogel composite as the base material and enriched these hydrogels with the anti-microbial drug, gentamicin sulfate, loaded within a halloysite nanotubes (HNTs. Our results demonstrate a sustained and extended release of gentamicin from hydrogels enriched with the gentamicin-loaded HNTs. When tested against the gram-negative bacteria, the hydrogel/nanoclay composites showed a pronounced zone of inhibition suggesting that anti-microbial doped nanoclay enriched hydrogels can prevent the growth of bacteria. The release of gentamicin sulfate for a period of five days from the nanoclay-enriched hydrogels would supply anti-microbial agents in a sustained and controlled manner and assist in preventing microbial growth and biofilm formation on the titanium implant surface. A pilot study, using mouse osteoblasts, confirmed that the nanoclay enriched surfaces are also cell supportive as osteoblasts readily, proliferated and produced a type I collagen and proteoglycan matrix.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Energy Technology Data Exchange (ETDEWEB)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Science.gov (United States)

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Agriculturally important microbial biofilms: Present status and future prospects.

Science.gov (United States)

Velmourougane, Kulandaivelu; Prasanna, Radha; Saxena, Anil Kumar

2017-07-01

Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geochemical and iron isotopic insights into hydrothermal iron oxyhydroxide deposit formation at Loihi Seamount

Science.gov (United States)

Rouxel, Olivier; Toner, Brandy; Germain, Yoan; Glazer, Brian

2018-01-01

Low-temperature hydrothermal vents, such as those encountered at Loihi Seamount, harbor abundant microbial communities and provide ideal systems to test hypotheses on biotic versus abiotic formation of hydrous ferric oxide (FeOx) deposits at the seafloor. Hydrothermal activity at Loihi Seamount produces abundant microbial mats associated with rust-colored FeOx deposits and variably encrusted with Mn-oxyhydroxides. Here, we applied Fe isotope systematics together with major and trace element geochemistry to study the formation mechanisms and preservation of such mineralized microbial mats. Iron isotope composition of warm (oxidation of Fe(II) during mixing of the hydrothermal fluid with seawater. By comparing the results with experimentally determined Fe isotope fractionation factors, we determined that less than 20% of Fe(II) is oxidized within active microbial mats, although this number may reach 80% in aged or less active deposits. These results are consistent with Fe(II) oxidation mediated by microbial processes considering the expected slow kinetics of abiotic Fe oxidation in low oxygen bottom water at Loihi Seamount. In contrast, FeOx deposits recovered at extinct sites have distinctly negative Fe-isotope values down to -1.77‰ together with significant enrichment in Mn and occurrence of negative Ce anomalies. These results are best explained by the near-complete oxidation of an isotopically light Fe(II) source produced during the waning stage of hydrothermal activity under more oxidizing conditions. Light Fe isotope values of FeOx are therefore generated by subsurface precipitation of isotopically heavy Fe-oxides rather than by the activity of dissimilatory Fe reduction in the subsurface. Overall, Fe-isotope compositions of microbial mats at Loihi Seamount display a remarkable range between -1.2‰ and +1.6‰ which indicate that Fe isotope compositions of hydrothermal Fe-oxide precipitates are particularly sensitive to local environmental conditions where

Modification of the surfaces of medical devices to prevent microbial adhesion and biofilm formation.

Science.gov (United States)

Desrousseaux, C; Sautou, V; Descamps, S; Traoré, O

2013-10-01

The development of devices with surfaces that have an effect against microbial adhesion or viability is a promising approach to the prevention of device-related infections. To review the strategies used to design devices with surfaces able to limit microbial adhesion and/or growth. A PubMed search of the published literature. One strategy is to design medical devices with a biocidal agent. Biocides can be incorporated into the materials or coated or covalently bonded, resulting either in release of the biocide or in contact killing without release of the biocide. The use of biocides in medical devices is debated because of the risk of bacterial resistance and potential toxicity. Another strategy is to modify the chemical or physical surface properties of the materials to prevent microbial adhesion, a complex phenomenon that also depends directly on microbial biological structure and the environment. Anti-adhesive chemical surface modifications mostly target the hydrophobicity features of the materials. Topographical modifications are focused on roughness and nanostructures, whose size and spatial organization are controlled. The most effective physical parameters to reduce bacterial adhesion remain to be determined and could depend on shape and other bacterial characteristics. A prevention strategy based on reducing microbial attachment rather than on releasing a biocide is promising. Evidence of the clinical efficacy of these surface-modified devices is lacking. Additional studies are needed to determine which physical features have the greatest potential for reducing adhesion and to assess the usefulness of antimicrobial coatings other than antibiotics. Copyright © 2013 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

RGM regulates BMP-mediated secondary axis formation in the sea anemone Nematostella vectensis.

Science.gov (United States)

Leclère, Lucas; Rentzsch, Fabian

2014-12-11

Patterning of the metazoan dorsoventral axis is mediated by a complex interplay of BMP signaling regulators. Repulsive guidance molecule (RGM) is a conserved BMP coreceptor that has not been implicated in axis specification. We show that NvRGM is a key positive regulator of BMP signaling during secondary axis establishment in the cnidarian Nematostella vectensis. NvRGM regulates first the generation and later the shape of a BMP-dependent Smad1/5/8 gradient with peak activity on the side opposite the NvBMP/NvRGM/NvChordin expression domain. Full knockdown of Smad1/5/8 signaling blocks the formation of endodermal structures, the mesenteries, and the establishment of bilateral symmetry, while altering the gradient through partial NvRGM or NvBMP knockdown shifts the boundaries of asymmetric gene expression and the positioning of the mesenteries along the secondary axis. These findings provide insight into the diversification of axis specification mechanisms and identify a previously unrecognized role for RGM in BMP-mediated axial patterning. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Mediator-dependent Nuclear Receptor Functions

Science.gov (United States)

Chen, Wei; Roeder, Robert

2011-01-01

As gene-specific transcription factors, nuclear hormone receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss (i) our current understanding of pathways that nuclear receptors and other interacting cofactors employ to recruit Mediator to target gene enhancers and promoters, including conditional requirements for the strong NR-Mediator interactions mediated by the NR AF2 domain and the MED1 LXXLLL motifs and (ii) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. PMID:21854863

Microbial enzyme activities of peatland soils in south central Alaska lowlands

Science.gov (United States)

Microbial enzyme activities related to carbon and nutrient acquisition were measured on Alaskan peatland soils as indicators of nutrient limitation and biochemical sustainability. Peat decomposition is mediated by microorganisms and enzymes that in turn are limited by various ph...

Microbial community dynamics and transformation of vascular plant detritus in two wetland ecosystems

International Nuclear Information System (INIS)

Moran, M.A.

1987-01-01

The microbial ecology of two wetland ecosystems in southeastern Georgia, USA, was studied with respect to microbial community dynamics and microbially-mediated transformations of vascular plant detritus. In the Okefenokee Swamp, biomass of microorganisms in the water column and sediments was generally lower in winter months and higher during spring and summer. Biomass and activity (measured as 14 C-lignocellulose mineralization) differed significantly among five habitats within the Okefenokee, and also among locations within each habitat. Significant heterogeneity in the structure of Okefenokee microbial communities was found at scales from 30 cm to 150 m. In field and laboratory studies of vascular plant decomposition in the Okefenokee and a salt marsh on Sapelo Island, the mathematical model which best describes decomposition kinetics is the decaying coefficient model

Quantifying electron fluxes in methanogenic microbial communities

NARCIS (Netherlands)

Junicke, H.

2015-01-01

Anaerobic digestion is a widely applied process in which close interactions between different microbial groups result in the formation of renewable energy in the form of biogas. Nevertheless, the regulatory mechanisms of the electron transfer between acetogenic bacteria and methanogenic archaea in

Microbial Formation of Ethane in Anoxic Estuarine Sediments

OpenAIRE

Oremland, Ronald S.

1981-01-01

Estuarine sediment slurries produced methane and traces of ethane when incubated under hydrogen. Formation of methane occurred over a broad temperature range with an optimum above 65°C. Ethane formation had a temperature optimum at 40°C. Formation of these two gases was inhibited by air, autoclaving, incubation at 4 and 80°C, and by the methanogenic inhibitor, 2-bromoethanesulfonic acid. Ethane production was stimulated by addition of ethylthioethanesulfonic acid, and production from ethylthi...

Biodiversity of the microbial mat of the Garga hot spring.

Science.gov (United States)

Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

2017-12-28

Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that

Microbial granulation for lactic acid production

DEFF Research Database (Denmark)

Kim, Dong-Hoon; Lee, Mo-Kwon; Hwang, Yuhoon

2016-01-01

This work investigated the formation of microbial granules to boost the productivity of lactic acid (LA). The flocculated form of LA-producing microbial consortium, dominated by Lactobacillus sp. (91.5% of total sequence), was initially obtained in a continuous stirred-tank reactor (CSTR), which...... increased, reaching 67 g L-fermenter−1h−1 at HRT 0.17 h. The size of LA-producing granules and hydrophobicity gradually increased with decrease in HRT, reaching 6.0 mm and 60%, respectively. These biogranules were also found to have high settling velocities and low porosities, ranging 2.69-4.73 cm s−1 and 0...

Ant-mediated effects on spruce litter decomposition, solution chemistry, and microbial activity

DEFF Research Database (Denmark)

Stadler, B.; Schramm, Andreas; Kalbitz, K.

2006-01-01

the effects of ants and aphid honeydew on litter solution of Norway spruce, microbial enzyme activities, and needle decomposition in a field and greenhouse experiment during summer 2003. In the field, low ant densities had relatively little effects on litter solution 30 cm away from a tree trunk...... and %N were not affected by ants or honeydew. Our results suggest that ants have a distinct and immediate effect on solution composition and microbial activity in the litter layer indicating accelerated litter decay whereas the effect of honeydew was insignificant. Keywords: Ants; Decomposition; Formica......Forest management practices often generate clear-cut patches, which may be colonized by ants not present in the same densities in mature forests. In addition to the associated changes in abiotic conditions ants can initiate processes, which do not occur in old-growth stands. Here, we analyse...

Microbial community composition affects soil fungistasis.

Science.gov (United States)

de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

2003-02-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery.

Science.gov (United States)

Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie; Lantz, Anna Eliasson

2015-06-01

Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil-brine system after addition of a complex carbon source, molasses, with or without nitrate to boost microbial growth. Growth of the indigenous microbes was stimulated by addition of molasses. Pyrosequencing showed that specifically Anaerobaculum, Petrotoga, and Methanothermococcus were enriched. Addition of nitrate favored the growth of Petrotoga over Anaerobaculum. The microbial growth caused changes in the crude oil-brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil-brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.

Microbial electrolysis cells turning to be versatile technology: recent advances and future challenges

DEFF Research Database (Denmark)

Zhang, Yifeng; Angelidaki, Irini

2014-01-01

and achieve high-yield hydrogen production from wide range of organic matters at relatively mild conditions. This approach greatly reduces the electric energy cost for hydrogen production in contrast to direct water electrolysis. In addition to hydrogen production, MECs may also support several energetically......Microbial electrolysis cells (MECs) are an electricity-mediated microbial bioelectrochemical technology, which is originally developed for high-efficiency biological hydrogen production from waste streams. Compared to traditional biological technologies, MECs can overcome thermodynamic limitations...

The biofilm ecology of microbial biofouling, biocide resistance and corrosion

Energy Technology Data Exchange (ETDEWEB)

White, D.C. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Oak Ridge National Lab., TN (United States). Environmental Science Div.; Kirkegaard, R.D.; Palmer, R.J. Jr.; Flemming, C.A.; Chen, G.; Leung, K.T.; Phiefer, C.B. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Arrage, A.A. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Microbial Insights, Inc., Rockford, TN (United States)

1997-06-01

In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. Heterogeneous distribution of microbes and/or their metabolic activity can promote microbially influenced corrosion (MIC) which is a multibillion dollar problem. Consequently, it is important that biofilm microbial ecology be understood so it can be manipulated rationally. It is usually simple to select organisms that form biofilms by flowing a considerably dilute media over a substratum, and propagating the organisms that attach. To examine the biofilm most expeditiously, the biomass accumulation, desquamation, and metabolic activities need to be monitored on-line and non-destructively. This on-line monitoring becomes even more valuable if the activities can be locally mapped in time and space within the biofilm. Herein the authors describe quantitative measures of microbial biofouling, the ecology of pathogens in drinking water distributions systems, and localization of microbial biofilms and activities with localized MIC.

Feedbacks Between Soil Structure and Microbial Activities in Soil

Science.gov (United States)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate

Genetic interaction of two abscisic acid signaling regulators, HY5 and FIERY1, in mediating lateral root formation

KAUST Repository

Chen, Hao

2011-01-01

Root architecture is continuously shaped in a manner that helps plants to better adapt to the environment. Gene regulation at the transcriptional or post-transcriptional levels largely controls this environmental response. Recently, RNA silencing has emerged as an important player in gene regulation and is involved in many aspects of plant development, including lateral root formation. In a recent study, we found that FIERY1, a bifunctional abiotic stress and abscisic acid (ABA) signaling regulator and an endogenous RNA silencing suppressor, mediates auxin response during lateral root formation in Arabidopsis. We proposed that FRY1 regulates lateral root development through its activity on adenosine 3,5-bisphosphate (PAP), a strong inhibitor of exoribonucleases (XRNs). Interestingly, some of the phenotypes of fry1, such as enhanced response to light in repressing hypocotyl elongation and hypersensitivity to ABA in lateral root growth, are opposite to those of another light- and ABA-signaling mutant, hy5. Here we analyzed the hy5 fry1 double mutant for root and hypocotyl growth. We found that the hy5 mutation can suppress the enhanced light sensitivity in fry1 hypocotyl elongation and restore the lateral root formation. The genetic interaction between HY5 and FRY1 indicates that HY5 and FRY1 may act in overlapping pathways that mediate light signaling and lateral root development. © 2011 Landes Bioscience.

Bacterially mediated mineralisation processes lead to biodeterioration of artworks in Maltese catacombs

International Nuclear Information System (INIS)

Zammit, Gabrielle; Sanchez-Moral, Sergio; Albertano, Patrizia

2011-01-01

Mineral structures formed by bacterial and microalgal biofilms growing on the archaeological surface in Maltese hypogea were studied using Energy Dispersive X-Ray Spectroscopy (EDS) coupled to Environmental Scanning Electron Microscopy (ESEM), X-ray micro-diffraction (XRD) and X-ray fluorescence (XRF). These techniques have shown that mineral structures having different morphologies and chemical composition were associated with the microorganisms in the subaerophytic biofilm. Salt efflorescences and mineral deposits on the archaeological surface were often formed from gypsum (CaSO 4 · 2H 2 O), halite (NaCl) and calcite (CaCO 3 ). Biogenic carbonates produced by microbial activities were a common occurrence. These assumed different forms, such as the production of mineral coats around cyanobacterial sheaths and the occurrence of calcite fibres with different morphologies on the surface of the biofilms. Moreover, vaterite (CaCO 3 ) spherulites which appeared hollow in cross-section were observed. The presence of struvite was recorded from one catacomb site. These investigations have facilitated the study of the neoformation of metastable minerals by microbially mediated processes, which potentially contribute to a better understanding of the biodeterioration of artworks in Maltese palaeo-Christian catacombs. - Research highlights: → Mineral structures formed by subaerial biofilms growing in hypogea were examined. → Efflorescences and mineral deposits were often formed from gypsum, halite, and calcite. → Biogenic carbonates assumed different forms e.g. vaterite spherulite, calcite fibres. → The formation of rare minerals e.g. struvite was mediated by bacteria. → Understanding biomineralisation processes facilitates the conservation of artworks.

Bacterially mediated mineralisation processes lead to biodeterioration of artworks in Maltese catacombs

Energy Technology Data Exchange (ETDEWEB)

Zammit, Gabrielle, E-mail: gabrielle.zammit@gmail.com [Dept. of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta (Malta); Sanchez-Moral, Sergio [Dept. de Geologia, Museo Nacional de Ciencias Naturales, CSIC, Madrid (Spain); Albertano, Patrizia [Dept. of Biology, Faculty of Science, University of Rome ' Tor Vergata' , Rome (Italy)

2011-06-15

Mineral structures formed by bacterial and microalgal biofilms growing on the archaeological surface in Maltese hypogea were studied using Energy Dispersive X-Ray Spectroscopy (EDS) coupled to Environmental Scanning Electron Microscopy (ESEM), X-ray micro-diffraction (XRD) and X-ray fluorescence (XRF). These techniques have shown that mineral structures having different morphologies and chemical composition were associated with the microorganisms in the subaerophytic biofilm. Salt efflorescences and mineral deposits on the archaeological surface were often formed from gypsum (CaSO{sub 4}{center_dot} 2H{sub 2}O), halite (NaCl) and calcite (CaCO{sub 3}). Biogenic carbonates produced by microbial activities were a common occurrence. These assumed different forms, such as the production of mineral coats around cyanobacterial sheaths and the occurrence of calcite fibres with different morphologies on the surface of the biofilms. Moreover, vaterite (CaCO{sub 3}) spherulites which appeared hollow in cross-section were observed. The presence of struvite was recorded from one catacomb site. These investigations have facilitated the study of the neoformation of metastable minerals by microbially mediated processes, which potentially contribute to a better understanding of the biodeterioration of artworks in Maltese palaeo-Christian catacombs. - Research highlights: {yields} Mineral structures formed by subaerial biofilms growing in hypogea were examined. {yields} Efflorescences and mineral deposits were often formed from gypsum, halite, and calcite. {yields} Biogenic carbonates assumed different forms e.g. vaterite spherulite, calcite fibres. {yields} The formation of rare minerals e.g. struvite was mediated by bacteria. {yields} Understanding biomineralisation processes facilitates the conservation of artworks.

Bacterial Extracellular Polysaccharides Involved in Biofilm Formation

Directory of Open Access Journals (Sweden)

Elena P. Ivanova

2009-07-01

Full Text Available Extracellular polymeric substances (EPS produced by microorganisms are a complex mixture of biopolymers primarily consisting of polysaccharides, as well as proteins, nucleic acids, lipids and humic substances. EPS make up the intercellular space of microbial aggregates and form the structure and architecture of the biofilm matrix. The key functions of EPS comprise the mediation of the initial attachment of cells to different substrata and protection against environmental stress and dehydration. The aim of this review is to present a summary of the current status of the research into the role of EPS in bacterial attachment followed by biofilm formation. The latter has a profound impact on an array of biomedical, biotechnology and industrial fields including pharmaceutical and surgical applications, food engineering, bioremediation and biohydrometallurgy. The diverse structural variations of EPS produced by bacteria of different taxonomic lineages, together with examples of biotechnological applications, are discussed. Finally, a range of novel techniques that can be used in studies involving biofilm-specific polysaccharides is discussed.

Antimicrobial properties of Kalanchoe blossfeldiana: a focus on drug resistance with particular reference to quorum sensing-mediated bacterial biofilm formation.

Science.gov (United States)

Sarkar, Ratul; Mondal, Chaitali; Bera, Rammohan; Chakraborty, Sumon; Barik, Rajib; Roy, Paramita; Kumar, Alekh; Yadav, Kirendra K; Choudhury, Jayanta; Chaudhary, Sushil K; Samanta, Samir K; Karmakar, Sanmoy; Das, Satadal; Mukherjee, Pulok K; Mukherjee, Joydeep; Sen, Tuhinadri

2015-07-01

This study attempts to investigate the antimicrobial properties of Kalanchoe blossfeldiana with a particular reference to quorum sensing (QS)-mediated biofilm formation. The methanol extract of K. blossfeldiana leaves (MEKB) was evaluated for antimicrobial properties including QS-controlled production of biofilm (including virulence factor, motility and lactone formation) in Pseudomonas aeruginosa. Methanol extract of K. blossfeldiana was also evaluated for anti-cytokine (tumour necrosis factor-alpha, interleukin-6 and interleukin-1 beta) properties in peripheral blood mononuclear cells (PBMC). Methanol extract of K. blossfeldiana exhibited antimicrobial effect on clinical isolates, as well as standard reference strains. Pseudomonas aeruginosa exposed to MEKB (subminimum inhibitory concentration (MIC)) displayed reduced biofilm formation, whereas supra-MIC produced destruction of preformed biofilms. Methanol extract of K. blossfeldiana reduced the secretion of virulence factors (protease and pyoverdin) along with generation of acyl homoserine lactone (AHL). Confocal laser scanning microscopy images indicate reduction of biofilm thickness. The extract also reduced cytokine formation in lipopolysaccharide-stimulated PBMC. Kalanchoe blossfeldiana was found to interfere with AHL production, which in turn may be responsible for downregulating QS-mediated production of biofilm and virulence. This first report on the antibiofilm and anticytokine properties of this plant may open up new vistas for future exploration of this plant for combating biofilm-related resistant infections. © 2015 Royal Pharmaceutical Society.

Electron Emission by Doppler-Mediated Formation of Doubly Excited H -** in Grazing Incidence of Protons on Clean Al(111)

Czech Academy of Sciences Publication Activity Database

Lörinčík, Jan; Šroubek, Zdeněk; Aumayr, H.; Winter, H. P.

2001-01-01

Roč. 54, č. 5 (2001), s. 633-639 ISSN 0295-5075 R&D Projects: GA AV ČR IAA1067801 Institutional research plan: CEZ:AV0Z4040901 Keywords : ion scattering from surfaces * Doppler-mediated formation * Al(111) Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.304, year: 2001

Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery

DEFF Research Database (Denmark)

Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie

2015-01-01

Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil–brine system after addition of a complex carbon source, molasses, with or with...... of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.......Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil–brine system after addition of a complex carbon source, molasses....... The microbial growth caused changes in the crude oil–brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil–brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition...

Preserved filamentous microbial biosignatures in the Brick Flat gossan, Iron Mountain, California

Science.gov (United States)

Williams, Amy J.; Sumner, Dawn Y.; Alpers, Charles N.; Karunatillake, Suniti; Hofmann, Beda A

2015-01-01

A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous

Selenite reduction by anaerobic microbial aggregates: Microbial community structure, and proteins associated to the produced selenium spheres.

Directory of Open Access Journals (Sweden)

Graciela eGonzalez-Gil

2016-04-01

Full Text Available Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0, insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20 % and Pseudomonadaceae (c.a.10 % were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (~200 m of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Selenite Reduction by Anaerobic Microbial Aggregates: Microbial Community Structure, and Proteins Associated to the Produced Selenium Spheres

KAUST Repository

Gonzalez-Gil, Graciela

2016-04-26

Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0), insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20%) and Pseudomonadaceae (c.a.10%) were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (∼200 μm) of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano)spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS) analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Unsaturated glycerophospholipids mediate heme crystallization: biological implications for hemozoin formation in the kissing bug Rhodnius prolixus.

Directory of Open Access Journals (Sweden)

Renata Stiebler

Full Text Available Hemozoin (Hz is a heme crystal produced by some blood-feeding organisms, as an efficient way to detoxify heme derived from hemoglobin digestion. In the triatomine insect Rhodnius prolixus, Hz is essentially produced by midgut extracellular phospholipid membranes known as perimicrovillar membranes (PMVM. Here, we investigated the role of commercial glycerophospholipids containing serine, choline and ethanolamine as headgroups and R. prolixus midgut lipids (RML in heme crystallization. All commercial unsaturated forms of phospholipids, as well as RML, mediated fast and efficient β-hematin formation by means of two kinetically distinct mechanisms: an early and fast component, followed by a late and slow one. The fastest reactions observed were induced by unsaturated forms of phosphatidylethanolamine (uPE and phosphatidylcholine (uPC, with half-lives of 0.04 and 0.7 minutes, respectively. β-hematin crystal morphologies were strikingly distinct among groups, with uPE producing homogeneous regular brick-shaped crystals. Interestingly, uPC-mediated reactions resulted in two morphologically distinct crystal populations: one less representative group of regular crystals, resembling those induced by uPE, and the other largely represented by crystals with numerous sharp edges and tapered ends. Heme crystallization reactions induced by RML were efficient, with a heme to β-hematin conversion rate higher than 70%, but clearly slower (t1/2 of 9.9-17.7 minutes than those induced by uPC and uPE. Interestingly, crystals produced by RML were homogeneous in shape and quite similar to those mediated by uPE. Thus, β-hematin formation can be rapidly and efficiently induced by unsaturated glycerophospholipids, particularly uPE and uPC, and may play a role on biological heme crystallization in R. prolixus midgut.

The effect of salinity, redox mediators and temperature on anaerobic biodegradation of petroleum hydrocarbons in microbial fuel cells

Energy Technology Data Exchange (ETDEWEB)

Adelaja, Oluwaseun, E-mail: o.adelaja@my.westminster.ac.uk; Keshavarz, Tajalli, E-mail: t.keshavarz@westminster.ac.uk; Kyazze, Godfrey, E-mail: g.kyazze@westminster.ac.uk

2015-02-11

Highlights: • Effective degradation of petroleum hydrocarbon mixtures was achieved using MFC. • Adapted anaerobic microbial consortium was used as inoculum. • Bio-electricity generation was enhanced by 30-fold when riboflavin, was added. • Optimum MFC performance was obtained at mesophilic and moderately saline conditions. • Stable MFC performance was obtained during prolonged fed-batch MFC operation. - Abstract: Microbial fuel cells (MFCs) need to be robust if they are to be applied in the field for bioremediation. This study investigated the effect of temperature (20–50 °C), salinity (0.5–2.5% (w/v) as sodium chloride), the use of redox mediators (riboflavin and anthraquinone-2-sulphonate, AQS) and prolonged fed-batch operation (60 days) on biodegradation of a petroleum hydrocarbon mix (i.e. phenanthrene and benzene) in MFCs. The performance criteria were degradation efficiency, % COD removal and electrochemical performance. Good electrochemical and degradation performance were maintained up to a salinity of 1.5% (w/v) but deteriorated by 35-fold and 4-fold respectively as salinity was raised to 2.5%w/v. Degradation rates and maximum power density were both improved by approximately 2-fold at 40 °C compared to MFC performance at 30 °C but decreased sharply by 4-fold when operating temperature was raised to 50 °C. The optimum reactor performance obtained at 40 °C was 1.15 mW/m{sup 2} maximum power density, 89.1% COD removal and a degradation efficiency of 97.10%; at moderately saline (1% w/v) conditions the maximum power density was 1.06 mW/m{sup 2}, 79.1% COD removal and 91.6% degradation efficiency. This work suggests the possible application of MFC technology in the effective treatment of petroleum hydrocarbons contaminated site and refinery effluents.

The effect of salinity, redox mediators and temperature on anaerobic biodegradation of petroleum hydrocarbons in microbial fuel cells

International Nuclear Information System (INIS)

Adelaja, Oluwaseun; Keshavarz, Tajalli; Kyazze, Godfrey

2015-01-01

Highlights: • Effective degradation of petroleum hydrocarbon mixtures was achieved using MFC. • Adapted anaerobic microbial consortium was used as inoculum. • Bio-electricity generation was enhanced by 30-fold when riboflavin, was added. • Optimum MFC performance was obtained at mesophilic and moderately saline conditions. • Stable MFC performance was obtained during prolonged fed-batch MFC operation. - Abstract: Microbial fuel cells (MFCs) need to be robust if they are to be applied in the field for bioremediation. This study investigated the effect of temperature (20–50 °C), salinity (0.5–2.5% (w/v) as sodium chloride), the use of redox mediators (riboflavin and anthraquinone-2-sulphonate, AQS) and prolonged fed-batch operation (60 days) on biodegradation of a petroleum hydrocarbon mix (i.e. phenanthrene and benzene) in MFCs. The performance criteria were degradation efficiency, % COD removal and electrochemical performance. Good electrochemical and degradation performance were maintained up to a salinity of 1.5% (w/v) but deteriorated by 35-fold and 4-fold respectively as salinity was raised to 2.5%w/v. Degradation rates and maximum power density were both improved by approximately 2-fold at 40 °C compared to MFC performance at 30 °C but decreased sharply by 4-fold when operating temperature was raised to 50 °C. The optimum reactor performance obtained at 40 °C was 1.15 mW/m 2 maximum power density, 89.1% COD removal and a degradation efficiency of 97.10%; at moderately saline (1% w/v) conditions the maximum power density was 1.06 mW/m 2 , 79.1% COD removal and 91.6% degradation efficiency. This work suggests the possible application of MFC technology in the effective treatment of petroleum hydrocarbons contaminated site and refinery effluents

Assessment of Soil Health in Urban Agriculture: Soil Enzymes and Microbial Properties

Directory of Open Access Journals (Sweden)

Avanthi Deshani Igalavithana

2017-02-01

Full Text Available Urban agriculture has been recently highlighted with the increased importance for recreation in modern society; however, soil quality and public health may not be guaranteed because of continuous exposure to various pollutants. The objective of this study was to evaluate the soil quality of urban agriculture by soil microbial assessments. Two independent variables, organic and inorganic fertilizers, were considered. The activities of soil enzymes including dehydrogenase, β-glucosidase, arylsulfatase, urease, alkaline and acid phosphatases were used as indicators of important microbial mediated functions and the soil chemical properties were measured in the soils applied with organic or inorganic fertilizer for 10 years. Fatty acid methyl ester analysis was applied to determine the soil microbial community composition. Relatively higher microbial community richness and enzyme activities were found in the organic fertilizers applied soils as compared to the inorganic fertilizers applied soils. Principal component analysis explained the positive influence of organic fertilizers on the microbial community. The application of organic fertilizers can be a better alternative compared to inorganic fertilizers for the long-term health and security of urban agriculture.

Superficial Dsg2 Expression Limits Epidermal Blister Formation Mediated by Pemphigus Foliaceus Antibodies and Exfoliative Toxins

Directory of Open Access Journals (Sweden)

Donna Brennan

2010-01-01

Full Text Available Cell-cell adhesion mediated by desmosomes is crucial for maintaining proper epidermal structure and function, as evidenced by several severe and potentially fatal skin disorders involving impairment of desmosomal proteins. Pemphigus foliaceus (PF and staphylococcal scalded skin syndrome (SSSS are subcorneal blistering diseases resulting from loss of function of the desmosomal cadherin, desmoglein 1 (Dsg1. To further study the pathomechanism of these diseases and to assess the adhesive properties of Dsg2, we employed a recently established transgenic (Tg mouse model expressing Dsg2 in the superficial epidermis. Neonatal Tg and wild type (WT mice were injected with purified ETA or PF Ig. We showed that ectopic expression of Dsg2 reduced the extent of blister formation in response to both ETA and PF Ig. In response to PF Ig, we observed either a dramatic loss or a reorganization of Dsg1-α, Dsg1-β, and, to a lesser extent, Dsg1-γ, in WT mice. The Inv-Dsg2 Tg mice showed enhanced retention of Dsg1 at the cell-cell border. Collectively, our data support the role for Dsg2 in cell adhesion and suggest that ectopic superficial expression of Dsg2 can increase membrane preservation of Dsg1 and limit epidermal blister formation mediated by PF antibodies and exfoliative toxins.

The development of stromatolitic features from laminated microbial mats in the coastal sabkha of Abu Dhabi (UAE)

Science.gov (United States)

Paul, Andreas; Lessa Andrade, Luiza; Dutton, Kirsten E.; Sherry, Angela; Court, Wesley M.; Van der Land, Cees; Lokier, Stephen W.; Head, Ian M.

2017-04-01

Stromatolitic features are documented from both marine and terrestrial environments worldwide. These features form through a combination of trapping and binding of allochthonous grains, and through microbially mediated and/or controlled precipitation of carbonate minerals. The combined effects of these processes result in the continuous vertical and lateral growth of stromatolites. While the Abu Dhabi coastal sabkha is well known for a vast microbial mat belt that is dominated by continuous polygonal and internally-laminated microbial mats, no stromatolitic features have been reported from this area so far. In this study, we report evidence for stromatolitic features from the coastal sabkha of Abu Dhabi, based on observations in an intertidal but permanently submerged pool. This pool lies embedded within the laminated microbial mat zone, and is marked by the development of true laminated stromatolite at its margins and microbial build-ups at its centre. In order to characterise processes that lead to the formation of these stromatolitic features, and to develop a conceptual model that describes their development in the context of variations in sea level, tidal energy and other environmental factors, we employ a multitude of environmental, sedimentological, mineralogical and geochemical methods. These methods include the analysis of water data in terms of temporal variations in temperature, salinity, dissolved oxygen and water level, the analysis of petrographic thin sections of both lithified and unlithified features as well as an analysis of the stromatolites' mineralogical composition, and the amounts of incorporated organic carbon and calcium carbonate. Initial results suggest that the development of the observed stromatolitic features in the coastal sabkha of Abu Dhabi is the result of a complex interplay between simultaneous erosion of laminated microbial mat, and biotic/abiotic lithification processes. Initially, the location of this pool was characterised by

Formation of a new crystalline form of anhydrous β-maltose by ethanol-mediated crystal transformation.

Science.gov (United States)

Verhoeven, Nicolas; Neoh, Tze Loon; Ohashi, Tetsuya; Furuta, Takeshi; Kurozumi, Sayaka; Yoshii, Hidefumi

2012-04-01

β-Maltose monohydrate was transformed into an anhydrous form by ethanol-mediated method under several temperatures with agitation. A new stable anhydrous form of β-maltose (Mβ(s)) was obtained, as substantiated by the X-ray diffraction patterns. Mβ(s) obtained by this method presented a fine porous structure, resulting in greater specific surface area compared to those of β-maltose monohydrate and anhydrous β-maltose obtained by vacuum drying (Mβ(h)). The crystal transformation presumably consisted of two steps: dehydration reaction from the hydrous to amorphous forms and crystal formation from the amorphous forms to the noble anhydrous form. The kinetics of these reactions were determined by thermal analysis using Jander's equation and Arrhenius plots. The overall activation energies of the dehydration reaction and the formation of anhydrous maltose were evaluated to be 100 and 90 kJ/mol, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Protein Adsorption and Layer Formation at the Stainless Steel-Solution Interface Mediates Shear-Induced Particle Formation for an IgG1 Monoclonal Antibody.

Science.gov (United States)

Kalonia, Cavan K; Heinrich, Frank; Curtis, Joseph E; Raman, Sid; Miller, Maria A; Hudson, Steven D

2018-03-05

Passage of specific protein solutions through certain pumps, tubing, and/or filling nozzles can result in the production of unwanted subvisible protein particles (SVPs). In this work, surface-mediated SVP formation was investigated. Specifically, the effects of different solid interface materials, interfacial shear rates, and protein concentrations on SVP formation were measured for the National Institute of Standards and Technology monoclonal antibody (NISTmAb), a reference IgG1 monoclonal antibody (mAb). A stainless steel rotary piston pump was used to identify formulation and process parameters that affect aggregation, and a flow cell (alumina or stainless steel interface) was used to further investigate the effect of different interface materials and/or interfacial shear rates. SVP particles produced were monitored using flow microscopy or flow cytometry. Neutron reflectometry and a quartz crystal microbalance with dissipation monitoring were used to characterize adsorption and properties of NISTmAb at the stainless steel interface. Pump/shear cell experiments showed that the NISTmAb concentration and interface material had a significant effect on SVP formation, while the effects of interfacial shear rate and passage number were less important. At the higher NISTmAb concentrations, the adsorbed protein became structurally altered at the stainless steel interface. The primary adsorbed layer remained largely undisturbed during flow, suggesting that SVP formation at high NISTmAb concentration was caused by the disruption of patches and/or secondary interactions.

An approach to mitigating soil CO2 emission by biochemically inhibiting cellulolytic microbial populations through mediation via the medicinal herb Isatis indigotica

Science.gov (United States)

Wu, Hong-Sheng; Chen, Su-Yun; Li, Ji; Liu, Dong-Yang; Zhou, Ji; Xu, Ya; Shang, Xiao-Xia; Wei, Dong-yang; Yu, Lu-ji; Fang, Xiao-hang; Li, Shun-yi; Wang, Ke-ke

2017-06-01

Greenhouse gases (GHGs, particularly carbon dioxide (CO2)) emissions from soil under wheat production are a significant source of agricultural carbon emissions that have not been mitigated effectively. A field experiment and a static incubation study in a lab were conducted to stimulate wheat growth and investigate its potential to reduce CO2 emissions from soil through intercropping with a traditional Chinese medicinal herb called Isatis indigotica. This work was conducted by adding I. indigotica root exudates based on the quantitative real-time PCR (qPCR) analysis of the DNA copy number of the rhizosphere or bulk soil microbial populations. This addition was performed in relation to the CO2 formation by cellulolytic microorganisms (Penicillium oxalicum, fungi and Ruminococcus albus) to elucidate the microbial ecological basis for the molecular mechanism that decreases CO2 emissions from wheat fields using I. indigotica. The results showed that the panicle weight and full grains per panicle measured through intercropping with I. indigotica (NPKWR) increased by 39% and 28.6%, respectively, compared to that of the CK (NPKW). Intercropping with I. indigotica significantly decreased the CO2 emissions from soil under wheat cultivation. Compared with CK, the total CO2 emission flux during the wheat growth period in the I. indigotica (NPKWR) intercropping treatment decreased by 29.26%. The intensity of CO2 emissions per kg of harvested wheat grain declined from 7.53 kg CO2/kg grain in the NPKW (CK) treatment to 5.55 kg CO2/kg grain in the NPKWR treatment. The qPCR analysis showed that the DNA copy number of the microbial populations of cellulolytic microorganisms (P. oxalicum, fungi and R. albus) in the field rhizosphere around I. indigotica or in the bulk soil under laboratory incubation was significantly lower than that of CK. This finding indicated that root exudates from I. indigotica inhibited the activity and number of cellulolytic microbial populations, which led

Microbial Surface Colonization and Biofilm Development in Marine Environments

Science.gov (United States)

2015-01-01

SUMMARY Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. PMID:26700108

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach.

Directory of Open Access Journals (Sweden)

Véronique Gourmelon

Full Text Available Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi, mostly in non-rainforest formations, and Planctomycetes phylum (bacteria in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from

Exocellular electron transfer in anaerobic microbial communities.

Science.gov (United States)

Stams, Alfons J M; de Bok, Frank A M; Plugge, Caroline M; van Eekert, Miriam H A; Dolfing, Jan; Schraa, Gosse

2006-03-01

Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.

Microbial drivers of spatial heterogeneity of nitrous oxide pulse dynamics following drought in an experimental tropical rainforest

Science.gov (United States)

Young, J. C.; Sengupta, A.; U'Ren, J.; Van Haren, J. L. M.; Meredith, L. K.

2017-12-01

resolve N cycling across the forest. Understanding how N2O formation is mediated by soil microbes in response to drought in tropical rainforests is challenging given the great diversity of microbial communities and metabolisms involved, but is critical for understanding the source of global increases in atmospheric N2O.

ATP measurements for monitoring microbial drinking water quality

DEFF Research Database (Denmark)

Vang, Óluva Karin

Current standard methods for surveillance of microbial drinking water quality are culture based, which are laborious and time-consuming, where results not are available before one to three days after sampling. This means that the water may have been consumed before results on deteriorated water....... The overall aim of this PhD study was to investigate various methodological features of the ATP assay for a potential implementation on a sensor platform as a real-time parameter for continuous on-line monitoring of microbial drinking water quality. Commercial reagents are commonly used to determine ATP......, microbial quality in distributed water, detection of aftergrowth, biofilm formation etc. This PhD project demonstrated that ATP levels are relatively low and fairly stable in drinking water without chlorine residual despite different sampling locations, different drinking water systems and time of year...

Microbial degradation processes in radioactive waste repository and in nuclear fuel storage areas

International Nuclear Information System (INIS)

Wolfram, J.H.; Rogers, R.D.; Gazso, L.G.

1997-01-01

The intent of the workshop organizers was to convene experts in the fields of corrosion and spent nuclear fuels. The major points which evolved from the interaction of microbiologists, material scientists, and fuel storage experts are as follows: Corrosion of basin components as well as fuel containers or cladding is occurring; Water chemistry monitoring, if done in the storage facility does not take into account the microbial component; Microbial influenced corrosion is an area that many have not considered to be an important contributor in the aging of metallurgical materials especially those exposed to a radiation field; Many observations indicate that there is a microbial or biological presence in the storage facilities but these observations have not been correlated with any deterioration or aging phenomena taking place in the storage facility; The sessions on the fundamentals of microbial influenced corrosion and biofilm pointed out that these phenomena are real, occurring on similar materials in other industries and probably are occurring in the wet storage of spent fuel; All agreed that more monitoring, testing, and education in the field of biological mediate processes be performed and financially supported; Loosing the integrity of fuel assemblies can only cause problems, relating to the future disposition of the fuel, safety concerns, and environmental issues; In other rad waste scenarios, biological processes may be playing a role, for instance in the mobility of radionuclides in soil, decomposition of organic materials of the rad waste, gas production, etc. The fundamental scientific presentations discussed the full gamut of microbial processes that relate to biological mediated effects on metallic and non-metallic materials used in the storage and containment of radioactive materials

Reprint of Design of synthetic microbial communities for biotechnological production processes.

Science.gov (United States)

Jagmann, Nina; Philipp, Bodo

2014-12-20

In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes. Copyright © 2014 Elsevier B.V. All rights reserved.

New Zealand Coals - A Potential Feedstock for Deep Microbial Life

DEFF Research Database (Denmark)

Glombitza, Clemens

2010-01-01

into the surrounding. Previous studies showed that especially oxygen containing compounds are lost from the macromolecular matrix during diagenesis and early catagenesis. Oxygen containing low molecular weight organic acids (LMWOAs) such as formate, acetate and oxalate represent important substrates for microbial...... reactions. Formate, acetate and oxalate were found to decrease continously from early diagenesis to early catagenesis. This suggests a constant release of these compounds during this maturation interval providing a suitable feedstock for microbial ecosystems in geological time spans. Investigation...... of kerogen-bound high molecular weight fatty acids show for the long chain fatty acids (C20-C30), representing a terrestrial plant material signal, a constant decrease during diagenesis and early catagenesis. In contrast the short chain fatty acids (mainly C16 and C18) show an increase again during early...

AtlA Mediates Extracellular DNA Release, Which Contributes to Streptococcus mutans Biofilm Formation in an Experimental Rat Model of Infective Endocarditis.

Science.gov (United States)

Jung, Chiau-Jing; Hsu, Ron-Bin; Shun, Chia-Tung; Hsu, Chih-Chieh; Chia, Jean-San

2017-09-01

Host factors, such as platelets, have been shown to enhance biofilm formation by oral commensal streptococci, inducing infective endocarditis (IE), but how bacterial components contribute to biofilm formation in vivo is still not clear. We demonstrated previously that an isogenic mutant strain of Streptococcus mutans deficient in autolysin AtlA (Δ atlA ) showed a reduced ability to cause vegetation in a rat model of bacterial endocarditis. However, the role of AtlA in bacterial biofilm formation is unclear. In this study, confocal laser scanning microscopy analysis showed that extracellular DNA (eDNA) was embedded in S. mutans GS5 floes during biofilm formation on damaged heart valves, but an Δ atlA strain could not form bacterial aggregates. Semiquantification of eDNA by PCR with bacterial 16S rRNA primers demonstrated that the Δ atlA mutant strain produced dramatically less eDNA than the wild type. Similar results were observed with in vitro biofilm models. The addition of polyanethol sulfonate, a chemical lysis inhibitor, revealed that eDNA release mediated by bacterial cell lysis is required for biofilm initiation and maturation in the wild-type strain. Supplementation of cultures with calcium ions reduced wild-type growth but increased eDNA release and biofilm mass. The effect of calcium ions on biofilm formation was abolished in Δ atlA cultures and by the addition of polyanethol sulfonate. The VicK sensor, but not CiaH, was found to be required for the induction of eDNA release or the stimulation of biofilm formation by calcium ions. These data suggest that calcium ion-regulated AtlA maturation mediates the release of eDNA by S. mutans , which contributes to biofilm formation in infective endocarditis. Copyright © 2017 American Society for Microbiology.

Influence of Calcium on Microbial Reduction of Solid Phase Uranium (VI)

International Nuclear Information System (INIS)

Liu, Chongxuan; Jeon, Byong-Hun; Zachara, John M.; Wang, Zheming

2007-01-01

The effect of calcium on microbial reduction of a solid phase U(VI), sodium boltwoodite (NaUO2SiO3OH · 1.5H2O), was evaluated in a culture of a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. Batch experiments were performed in a non-growth bicarbonate medium with lactate as electron donor at pH 7 buffered with PIPES. Calcium increased both the rate and extent of Na-boltwoodite dissolution by increasing its solubility through the formation of a ternary aqueous calcium-uranyl-carbonate species. The ternary species, however, decreased the rates of microbial reduction of aqueous U(VI). Laser-induced fluorescence spectroscopy (LIFS) and transmission electron microscopy (TEM) revealed that microbial reduction of solid phase U(VI) is a sequentially coupled process of Na-boltwoodite dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) to U(IV) that accumulated on bacterial surfaces/periplasm. The overall rates of microbial reduction of solid phase U(VI) can be described by the coupled rates of dissolution and microbial reduction that were both influenced by calcium. The results demonstrated that dissolved U(VI) concentration during microbial reduction was a complex function of solid phase U(VI) dissolution kinetics, aqueous U(VI) speciation, and microbial activity

Microbial consortia in Oman oil fields: a possible use in enhanced oil recovery.

Science.gov (United States)

Al-Bahry, Saif N; Elshafie, Abdulkader E; Al-Wahaibi, Yahya M; Al-Bemani, Ali S; Joshi, Sanket J; Al-Maaini, Ratiba A; Al-Alawi, Wafa J; Sugai, Yuichi; Al-Mandhari, Mussalam

2013-01-01

Microbial enhanced oil recovery (MEOR) is one of the most economical and efficient methods for extending the life of production wells in a declining reservoir. Microbial consortia from Wafra oil wells and Suwaihat production water, Al-Wusta region, Oman were screened. Microbial consortia in brine samples were identified using denaturing gradient gel electrophoresis and 16S rRNA gene sequences. The detected microbial consortia of Wafra oil wells were completely different from microbial consortia of Suwaihat formation water. A total of 33 genera and 58 species were identified in Wafra oil wells and Suwaihat production water. All of the identified microbial genera were first reported in Oman, with Caminicella sporogenes for the first time reported from oil fields. Most of the identified microorganisms were found to be anaerobic, thermophilic, and halophilic, and produced biogases, biosolvants, and biosurfactants as by-products, which may be good candidates for MEOR.

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

Science.gov (United States)

Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

2016-07-01

Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

Electricity production from microbial fuel cell by using yeast

International Nuclear Information System (INIS)

Vorasingha, A.; Souvakon, C.; Boonchom, K.

2006-01-01

The continuous search for methods to generate electricity from renewable sources such as water, solar energy, wind, nuclear or chemicals was discussed with particular focus on attaining the full power of the microbial fuel cell (MFC). Under ideal environmental conditions, the only byproducts of a biofuel cell would be water and carbon dioxide (CO 2 ). The production of energy from renewables such as biomass is important for sustainable development and reducing global emissions of CO 2 . Hydrogen can also be an important component of an energy infrastructure that reduces CO 2 emissions if the hydrogen is produced from renewable sources and used in fuel cells. Hydrogen gas can be biologically produced at high concentration from the fermentation of high sugar substrates such as glucose and sucrose. Some of the issues of MFC design were addressed, including the use of cheap substrates to derive microbial electricity. In the MFC, yeast donates electrons to a chemical electron mediator, which in turn transfers the electrons to an electrode, producing electricity. Experimental results showed that glucose yielded the highest peak voltage, but a semi-processed sugar and molasses were similar to glucose in the electricity production pattern. It was noted that this technology is only at the research stages, and more research is needed before household microbial fuel cells can be made available for producing power for prolonged periods of time. Future research efforts will focus on increasing the efficiency, finding alternatives to hazardous electron mediators and finding new microbes. 12 refs., 6 figs

Antibiotic tolerance and microbial biofilms

DEFF Research Database (Denmark)

Folkesson, Anders

Increased tolerance to antimicrobial agents is thought to be an important feature of microbes growing in biofilms. We study the dynamics of antibiotic action within hydrodynamic flow chamber biofilms of Escherichia coli and Pseudomonas aeruginosa using isogenic mutants and fluorescent gene...... expression reporters and we address the question of how biofilm organization affects antibiotic susceptibility. The dynamics of microbial killing is monitored by viable count determination, and confocal laser microscopy. Our work shows that the apparent increased antibiotic tolerance is due to the formation...... of antibiotic tolerant subpopulations within the biofilm. The formation of these subpopulations is highly variable and dependent on the antibiotic used, the biofilm structural organization and the induction of specific tolerance mechanisms....

Managing Impression Formation in Computer-Mediated Communication.

Science.gov (United States)

Liu, Yuliang; Ginther, Dean

2001-01-01

Offers suggestions for online instructors regarding verbal and nonverbal impression management. The recommendations should facilitate computer mediated teacher-student or manager-client interactions and help develop constructive relationships that promote learning and productivity. (EV)

Formation of palladium(0) nanoparticles at microbial surfaces

DEFF Research Database (Denmark)

Bunge, Michael; Søbjerg, Lina S; Rotaru, Amelia-Elena

2010-01-01

) nanoparticles were still deposited on autoclaved cells of C. necator that had no hydrogenase activity, suggesting a hydrogenase-independent formation mechanism. The catalytic properties of Pd(0) and bioPd(0) were determined by the amount of hydrogen released in a reaction with hypophosphite. Generally, bioPd(0...... potential. Hitherto, bacteria with the property of dissimilatory metal reduction have been in focus, although the biochemical reactions linking enzymatic Pd(II) reduction and Pd(0) deposition have not yet been identified. In this study we investigated Pd(II) reduction with formate as the electron donor......) demonstrated a lower level of activity than the Pd(0) control, possibly due to the inaccessibility of the Pd(0) fraction embedded in the cell envelope. Our results demonstrate the suitability of bacterial cells for the recovery of Pd(0), and formation and immobilization of Pd(0) nanoparticles inside the cell...

Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

Science.gov (United States)

Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

2016-01-01

Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

Solar energy powered microbial fuel cell with a reversible bioelectrode.

Science.gov (United States)

Strik, David P B T B; Hamelers, Hubertus V M; Buisman, Cees J N

2010-01-01

The solar energy powered microbial fuel cell is an emerging technology for electricity generation via electrochemically active microorganisms fueled by solar energy via in situ photosynthesized metabolites from algae, cyanobacteria, or living higher plants. A general problem with microbial fuel cells is the pH membrane gradient which reduces cell voltage and power output. This problem is caused by acid production at the anode, alkaline production at the cathode, and the nonspecific proton exchange through the membrane. Here we report a solution for a new kind of solar energy powered microbial fuel cell via development of a reversible bioelectrode responsible for both biocatalyzed anodic and cathodic electron transfer. Anodic produced protons were used for the cathodic reduction reaction which held the formation of a pH membrane gradient. The microbial fuel cell continuously generated electricity and repeatedly reversed polarity dependent on aeration or solar energy exposure. Identified organisms within biocatalyzing biofilm of the reversible bioelectrode were algae, (cyano)bacteria and protozoa. These results encourage application of solar energy powered microbial fuel cells.

Enhanced microbial decolorization of methyl red with oxidized carbon fiber as redox mediator

Energy Technology Data Exchange (ETDEWEB)

Emilia Rios-Del Toro, E. [División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), Camino a la Presa San José 2055, Col. Lomas 4a Sección, San Luis Potosí, SLP 78216 (Mexico); Celis, Lourdes B. [División de Geociencias Aplicadas, Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), Camino a la Presa San José 2055, Col. Lomas 4a Sección, San Luis Potosí, SLP 78216 (Mexico); Cervantes, Francisco J. [División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), Camino a la Presa San José 2055, Col. Lomas 4a Sección, San Luis Potosí, SLP 78216 (Mexico); Rangel-Mendez, J. Rene, E-mail: rene@ipicyt.edu.mx [División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), Camino a la Presa San José 2055, Col. Lomas 4a Sección, San Luis Potosí, SLP 78216 (Mexico)

2013-09-15

Highlights: • Activated carbon fibers (ACFs) act as redox mediator. • Electron accepting capacity increased with oxidation time of ACF. •ACFs increased 8-fold the reduction of methyl red in biological assays. •Biofilm formed on the ACFs partly blocked their redox mediator capacity. -- Abstract: The anaerobic degradation of azo dyes under anaerobic conditions is possible but at a slow rate. Redox mediators (quinones, activated carbon) are used to improve the reduction rate. The aim of this work was to use activated carbon fiber (ACF) as a redox mediator for the anaerobic reduction of the azo dye methyl red. ACF was chemically modified with 8 M HNO{sub 3} to increase its redox-mediating capacity and used in chemical and anaerobic biological batch assays for the reduction of methyl red. ACF increased its redox-mediating capacity up to 3-fold in chemical assays; in biological assays ACF increased the reduction rate up to 8-fold compared to controls without ACF. However, since the ACF served as support for biomass, a biofilm formed on the fiber significantly reduced its redox-mediating capacity; substrate consumption suggested that the electron transport from ACF to methyl red was the rate-limiting step in the process. These results are the first evidence of the role of ACF as a redox mediator in the reductive decolorization of methyl red, in addition to the effect of biofilm attached to ACF on methyl red reduction. Due to the versatile characteristics of ACF and its redox-mediating capacity, carbon fibers could be used in biological wastewater treatment systems to accelerate the reductive transformation of pollutants commonly found in industrial effluents.

Enhanced microbial decolorization of methyl red with oxidized carbon fiber as redox mediator

International Nuclear Information System (INIS)

Emilia Rios-Del Toro, E.; Celis, Lourdes B.; Cervantes, Francisco J.; Rangel-Mendez, J. Rene

2013-01-01

Highlights: • Activated carbon fibers (ACFs) act as redox mediator. • Electron accepting capacity increased with oxidation time of ACF. •ACFs increased 8-fold the reduction of methyl red in biological assays. •Biofilm formed on the ACFs partly blocked their redox mediator capacity. -- Abstract: The anaerobic degradation of azo dyes under anaerobic conditions is possible but at a slow rate. Redox mediators (quinones, activated carbon) are used to improve the reduction rate. The aim of this work was to use activated carbon fiber (ACF) as a redox mediator for the anaerobic reduction of the azo dye methyl red. ACF was chemically modified with 8 M HNO 3 to increase its redox-mediating capacity and used in chemical and anaerobic biological batch assays for the reduction of methyl red. ACF increased its redox-mediating capacity up to 3-fold in chemical assays; in biological assays ACF increased the reduction rate up to 8-fold compared to controls without ACF. However, since the ACF served as support for biomass, a biofilm formed on the fiber significantly reduced its redox-mediating capacity; substrate consumption suggested that the electron transport from ACF to methyl red was the rate-limiting step in the process. These results are the first evidence of the role of ACF as a redox mediator in the reductive decolorization of methyl red, in addition to the effect of biofilm attached to ACF on methyl red reduction. Due to the versatile characteristics of ACF and its redox-mediating capacity, carbon fibers could be used in biological wastewater treatment systems to accelerate the reductive transformation of pollutants commonly found in industrial effluents

Immune-mediated diseases and microbial exposure in early life

DEFF Research Database (Denmark)

Bisgaard, H; Bønnelykke, K; Stokholm, Jacob

2014-01-01

The non-communicable disease pandemic includes immune-mediated diseases such as asthma and allergy, which are likely originating in early life where the immature immune system is prone to alterations caused by the exposome. The timing of exposure seems critical for the developing immune system...

Palladium- and copper-mediated N-aryl bond formation reactions for the synthesis of biological active compounds

Directory of Open Access Journals (Sweden)

Burkhard Koenig

2011-01-01

Full Text Available N-Arylated aliphatic and aromatic amines are important substituents in many biologically active compounds. In the last few years, transition-metal-mediated N-aryl bond formation has become a standard procedure for the introduction of amines into aromatic systems. While N-arylation of simple aromatic halides by simple amines works with many of the described methods in high yield, the reactions may require detailed optimization if applied to the synthesis of complex molecules with additional functional groups, such as natural products or drugs. We discuss and compare in this review the three main N-arylation methods in their application to the synthesis of biologically active compounds: Palladium-catalysed Buchwald–Hartwig-type reactions, copper-mediated Ullmann-type and Chan–Lam-type N-arylation reactions. The discussed examples show that palladium-catalysed reactions are favoured for large-scale applications and tolerate sterically demanding substituents on the coupling partners better than Chan–Lam reactions. Chan–Lam N-arylations are particularly mild and do not require additional ligands, which facilitates the work-up. However, reaction times can be very long. Ullmann- and Buchwald–Hartwig-type methods have been used in intramolecular reactions, giving access to complex ring structures. All three N-arylation methods have specific advantages and disadvantages that should be considered when selecting the reaction conditions for a desired C–N bond formation in the course of a total synthesis or drug synthesis.

Microbial activity in the marine deep biosphere: progress and prospects.

Science.gov (United States)

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Microbial contributions to the persistence of coral reefs.

Science.gov (United States)

Webster, Nicole S; Reusch, Thorsten B H

2017-10-01

On contemplating the adaptive capacity of reef organisms to a rapidly changing environment, the microbiome offers significant and greatly unrecognised potential. Microbial symbionts contribute to the physiology, development, immunity and behaviour of their hosts, and can respond very rapidly to changing environmental conditions, providing a powerful mechanism for acclimatisation and also possibly rapid evolution of coral reef holobionts. Environmentally acquired fluctuations in the microbiome can have significant functional consequences for the holobiont phenotype upon which selection can act. Environmentally induced changes in microbial abundance may be analogous to host gene duplication, symbiont switching / shuffling as a result of environmental change can either remove or introduce raw genetic material into the holobiont; and horizontal gene transfer can facilitate rapid evolution within microbial strains. Vertical transmission of symbionts is a key feature of many reef holobionts and this would enable environmentally acquired microbial traits to be faithfully passed to future generations, ultimately facilitating microbiome-mediated transgenerational acclimatisation (MMTA) and potentially even adaptation of reef species in a rapidly changing climate. In this commentary, we highlight the capacity and mechanisms for MMTA in reef species, propose a modified Price equation as a framework for assessing MMTA and recommend future areas of research to better understand how microorganisms contribute to the transgenerational acclimatisation of reef organisms, which is essential if we are to reliably predict the consequences of global change for reef ecosystems.

Microbial Regulation in Gorgonian Corals

Directory of Open Access Journals (Sweden)

Laura D. Mydlarz

2012-06-01

Full Text Available Gorgonian corals possess many novel natural products that could potentially mediate coral-bacterial interactions. Since many bacteria use quorum sensing (QS signals to facilitate colonization of host organisms, regulation of prokaryotic cell-to-cell communication may represent an important bacterial control mechanism. In the present study, we examined extracts of twelve species of Caribbean gorgonian corals, for mechanisms that regulate microbial colonization, such as antibacterial activity and QS regulatory activity. Ethanol extracts of gorgonians collected from Puerto Rico and the Florida Keys showed a range of both antibacterial and QS activities using a specific Pseudomonas aeruginosa QS reporter, sensitive to long chain AHLs and a short chain N-acylhomoserine lactones (AHL biosensor, Chromobacterium violaceium. Overall, the gorgonian corals had higher antimicrobial activity against non-marine strains when compared to marine strains. Pseudopterogorgia americana, Pseusopterogorgia acerosa, and Pseudoplexuara flexuosa had the highest QS inhibitory effect. Interestingly, Pseudoplexuara porosa extracts stimulated QS activity with a striking 17-fold increase in signal. The stimulation of QS by P. porosa or other elements of the holobiont may encourage colonization or recruitment of specific microbial species. Overall, these results suggest the presence of novel stimulatory QS, inhibitory QS and bactericidal compounds in gorgonian corals. A better understanding of these compounds may reveal insight into coral-microbial ecology and whether a therapeutic potential exists.

Uranium bioprecipitation mediated by yeasts utilizing organic phosphorus substrates.

Science.gov (United States)

Liang, Xinjin; Csetenyi, Laszlo; Gadd, Geoffrey Michael

2016-06-01

In this research, we have demonstrated the ability of several yeast species to mediate U(VI) biomineralization through uranium phosphate biomineral formation when utilizing an organic source of phosphorus (glycerol 2-phosphate disodium salt hydrate (C3H7Na2O6P·xH2O (G2P)) or phytic acid sodium salt hydrate (C6H18O24P6·xNa(+)·yH2O (PyA))) in the presence of soluble UO2(NO3)2. The formation of meta-ankoleite (K2(UO2)2(PO4)2·6(H2O)), chernikovite ((H3O)2(UO2)2(PO4)2·6(H2O)), bassetite (Fe(++)(UO2)2(PO4)2·8(H2O)), and uramphite ((NH4)(UO2)(PO4)·3(H2O)) on cell surfaces was confirmed by X-ray diffraction in yeasts grown in a defined liquid medium amended with uranium and an organic phosphorus source, as well as in yeasts pre-grown in organic phosphorus-containing media and then subsequently exposed to UO2(NO3)2. The resulting minerals depended on the yeast species as well as physico-chemical conditions. The results obtained in this study demonstrate that phosphatase-mediated uranium biomineralization can occur in yeasts supplied with an organic phosphate substrate as sole source of phosphorus. Further understanding of yeast interactions with uranium may be relevant to development of potential treatment methods for uranium waste and utilization of organic phosphate sources and for prediction of microbial impacts on the fate of uranium in the environment.

Microbial Contribution to Organic Carbon Sequestration in Mineral Soil

Science.gov (United States)

Soil productivity and sustainability are dependent on soil organic matter (SOM). Our understanding on how organic inputs to soil from microbial processes become converted to SOM is still limited. This study aims to understand how microbes affect carbon (C) sequestration and the formation of recalcit...

Salivary Thromboxane A2-Binding Proteins from Triatomine Vectors of Chagas Disease Inhibit Platelet-Mediated Neutrophil Extracellular Traps (NETs Formation and Arterial Thrombosis.

Directory of Open Access Journals (Sweden)

Daniella M Mizurini

Full Text Available The saliva of blood-feeding arthropods contains a notable diversity of molecules that target the hemostatic and immune systems of the host. Dipetalodipin and triplatin are triatomine salivary proteins that exhibit high affinity binding to prostanoids, such as TXA2, thus resulting in potent inhibitory effect on platelet aggregation in vitro. It was recently demonstrated that platelet-derived TXA2 mediates the formation of neutrophil extracellular traps (NETs, a newly recognized link between inflammation and thrombosis that promote thrombus growth and stability.This study evaluated the ability of dipetalodipin and triplatin to block NETs formation in vitro. We also investigated the in vivo antithrombotic activity of TXA2 binding proteins by employing two murine models of experimental thrombosis. Remarkably, we observed that both inhibitors abolished the platelet-mediated formation of NETs in vitro. Dipetalodipin and triplatin significantly increased carotid artery occlusion time in a FeCl3-induced injury model. Treatment with TXA2-binding proteins also protected mice from lethal pulmonary thromboembolism evoked by the intravenous injection of collagen and epinephrine. Effective antithrombotic doses of dipetalodipin and triplatin did not increase blood loss, which was estimated using the tail transection method.Salivary TXA2-binding proteins, dipetalodipin and triplatin, are capable to prevent platelet-mediated NETs formation in vitro. This ability may contribute to the antithrombotic effects in vivo. Notably, both molecules inhibit arterial thrombosis without promoting excessive bleeding. Our results provide new insight into the antihemostatic effects of TXA2-binding proteins and may have important significance in elucidating the mechanisms of saliva to avoid host's hemostatic responses and innate immune system.

High power density yeast catalyzed microbial fuel cells

Science.gov (United States)

Ganguli, Rahul

Microbial fuel cells leverage whole cell biocatalysis to convert the energy stored in energy-rich renewable biomolecules such as sugar, directly to electrical energy at high efficiencies. Advantages of the process include ambient temperature operation, operation in natural streams such as wastewater without the need to clean electrodes, minimal balance-of-plant requirements compared to conventional fuel cells, and environmentally friendly operation. These make the technology very attractive as portable power sources and waste-to-energy converters. The principal problem facing the technology is the low power densities compared to other conventional portable power sources such as batteries and traditional fuel cells. In this work we examined the yeast catalyzed microbial fuel cell and developed methods to increase the power density from such fuel cells. A combination of cyclic voltammetry and optical absorption measurements were used to establish significant adsorption of electron mediators by the microbes. Mediator adsorption was demonstrated to be an important limitation in achieving high power densities in yeast-catalyzed microbial fuel cells. Specifically, the power densities are low for the length of time mediator adsorption continues to occur. Once the mediator adsorption stops, the power densities increase. Rotating disk chronoamperometry was used to extract reaction rate information, and a simple kinetic expression was developed for the current observed in the anodic half-cell. Since the rate expression showed that the current was directly related to microbe concentration close to the electrode, methods to increase cell mass attached to the anode was investigated. Electrically biased electrodes were demonstrated to develop biofilm-like layers of the Baker's yeast with a high concentration of cells directly connected to the electrode. The increased cell mass did increase the power density 2 times compared to a non biofilm fuel cell, but the power density

Syringe test screening of microbial gas production activity: Cases denitrification and biogas formation.

Science.gov (United States)

Østgaard, Kjetill; Kowarz, Viktoria; Shuai, Wang; Henry, Ingrid A; Sposob, Michal; Haugen, Hildegunn Hegna; Bakke, Rune

2017-01-01

Mass produced plastic syringes may be applied as vessels for cheap, simple and large scale batch culture testing. As illustrated for the cases of denitrification and of biogas formation, metabolic activity was monitored by direct reading of the piston movement due to the gas volume formed. Pressure buildup due to friction was shown to be moderate. A piston pull and slide back routine can be applied before recording gas volume to minimize experimental errors due to friction. Inoculum handling and activity may be conveniently standardized as illustrated by applying biofilm carriers. A robust set of positive as well as negative controls ("blanks") should be included to ensure quality of the actual testing. The denitrification test showed saturation response at increasing amounts of inoculum in the form of adapted moving bed biofilm reactor (MBBR) carriers, with well correlated nitrate consumption vs. gas volume formed. As shown, the denitrification test efficiently screened different inocula at standardized substrates. Also, different substrates were successfully screened and compared at standardized inocula. The biogas potential test showed efficient screening of different substrates with effects of relative amounts of carbohydrate, protein, fat. A second case with CO 2 capture reclaimer waste as substrate demonstrated successful use of co-feeding to support waste treatment and how temperature effects on kinetics and stoichiometry can be observed. In total, syringe test screening of microbial gas production seems highly efficient at a low cost when properly applied. Copyright © 2016 Elsevier B.V. All rights reserved.

Laser engineering of microbial systems

Science.gov (United States)

Yusupov, V. I.; Gorlenko, M. V.; Cheptsov, V. S.; Minaev, N. V.; Churbanova, E. S.; Zhigarkov, V. S.; Chutko, E. A.; Evlashin, S. A.; Chichkov, B. N.; Bagratashvili, V. N.

2018-06-01

A technology of laser engineering of microbial systems (LEMS) based on the method of laser-induced transfer of heterogeneous mixtures containing microorganisms (laser bioprinting) is described. This technology involves laser printing of soil microparticles by focusing near-infrared laser pulses on a specially prepared gel/soil mixture spread onto a gold-coated glass plate. The optimal range of laser energies from the point of view of the formation of stable jets and droplets with minimal negative impact on living systems of giant accelerations, laser pulse irradiation, and Au nanoparticles was found. Microsamples of soil were printed on glucose-peptone-yeast agar plates to estimate the LEMS process influence on structural and morphological microbial diversity. The obtained results were compared with traditionally treated soil samples. It was shown that LEMS technology allows significantly increasing the biodiversity of printed organisms and is effective for isolating rare or unculturable microorganisms.

Microbial syntrophy: interaction for the common good.

Science.gov (United States)

Morris, Brandon E L; Henneberger, Ruth; Huber, Harald; Moissl-Eichinger, Christine

2013-05-01

Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.

Science.gov (United States)

He, Tianliang; Li, Hongyun; Zhang, Xiaobo

2017-07-11

Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found

Marine and estuarine natural microbial biofilms: ecological and biogeochemical dimensions

Directory of Open Access Journals (Sweden)

O. Roger Anderson

2016-08-01

Full Text Available Marine and estuarine microbial biofilms are ubiquitously distributed worldwide and are increasingly of interest in basic and applied sciences because of their unique structural and functional features that make them remarkably different from the biota in the plankton. This is a review of some current scientific knowledge of naturally occurring microbial marine and estuarine biofilms including prokaryotic and microeukaryotic biota, but excluding research specifically on engineering and applied aspects of biofilms such as biofouling. Because the microbial communities including bacteria and protists are integral to the fundamental ecological and biogeochemical processes that support biofilm communities, particular attention is given to the structural and ecological aspects of microbial biofilm formation, succession, and maturation, as well as the dynamics of the interactions of the microbiota in biofilms. The intent is to highlight current state of scientific knowledge and possible avenues of future productive research, especially focusing on the ecological and biogeochemical dimensions.

Adenoviral Mediated Expression of BMP2 by Bone Marrow Stromal Cells Cultured in 3D Copolymer Scaffolds Enhances Bone Formation.

Science.gov (United States)

Sharma, Sunita; Sapkota, Dipak; Xue, Ying; Sun, Yang; Finne-Wistrand, Anna; Bruland, Ove; Mustafa, Kamal

2016-01-01

Selection of appropriate osteoinductive growth factors, suitable delivery method and proper supportive scaffold are critical for a successful outcome in bone tissue engineering using bone marrow stromal cells (BMSC). This study examined the molecular and functional effect of a combination of adenoviral mediated expression of bone morphogenetic protein-2 (BMP2) in BMSC and recently developed and characterized, biodegradable Poly(L-lactide-co-є-caprolactone){poly(LLA-co-CL)}scaffolds in osteogenic molecular changes and ectopic bone formation by using in vitro and in vivo approaches. Pathway-focused custom PCR array, validation using TaqMan based quantitative RT-PCR (qRT-PCR) and ALP staining showed significant up-regulation of several osteogenic and angiogenic molecules, including ALPL and RUNX2 in ad-BMP2 BMSC group grown in poly(LLA-co-CL) scaffolds both at 3 and 14 days. Micro CT and histological analyses of the subcutaneously implanted scaffolds in NOD/SCID mice revealed significantly increased radiopaque areas, percentage bone volume and formation of vital bone in ad-BMP2 scaffolds as compared to the control groups both at 2 and 8 weeks. The increased bone formation in the ad-BMP2 group in vivo was paralleled at the molecular level with concomitant over-expression of a number of osteogenic and angiogenic genes including ALPL, RUNX2, SPP1, ANGPT1. The increased bone formation in ad-BMP2 explants was not found to be associated with enhanced endochondral activity as evidenced by qRT-PCR (SOX9 and FGF2) and Safranin O staining. Taken together, combination of adenoviral mediated BMP-2 expression in BMSC grown in the newly developed poly(LLA-co-CL) scaffolds induced expression of osteogenic markers and enhanced bone formation in vivo.

Microbial adhesion to silicone hydrogel lenses: a review.

Science.gov (United States)

Willcox, Mark D P

2013-01-01

Microbial adhesion to contact lenses is believed to be one of the initiating events in the formation of many corneal infiltrative events, including microbial keratitis, that occur during contact lens wear. The advent of silicone hydrogel lenses has not reduced the incidence of these events. This may partly be related to the ability of microbes to adhere to these lenses. The aim of this study was to review the published literature on microbial adhesion to contact lenses, focusing on adhesion to silicone hydrogel lenses. The literature on microbial adhesion to contact lenses was searched, along with associated literature on adverse events that occur during contact lens wear. Particular reference was paid to the years 1995 through 2012 because this encompasses the time when the first clinical trials of silicone hydrogel lenses were reported, and their commercial availability and the publication of epidemiology studies on adverse events were studied. In vitro studies of bacterial adhesion to unworn silicone hydrogel lens have shown that generally, bacteria adhere to these lenses in greater numbers than to the hydroxyethyl methacrylate-based soft lenses. Lens wear has different effects on microbial adhesion, and this is dependent on the type of lens and microbial species/genera that is studied. Biofilms that can be formed on any lens type tend to protect the bacteria and fungi from the effects on disinfectants. Fungal hyphae can penetrate the surface of most types of lenses. Acanthamoeba adhere in greater numbers to first-generation silicone hydrogel lenses compared with the second-generation or hydroxyethyl methacrylate-based soft lenses. Microbial adhesion to silicone hydrogel lenses occurs and is associated with the production of corneal infiltrative events during lens wear.

Effect of calcium on microbial aggregation during UASB reactor start-up

Energy Technology Data Exchange (ETDEWEB)

Mahoney, E.M.; Varangu, L.K.; Cairns, W.L.; Kosaric, N.; Murray, R.G.E.

1987-01-01

The dynamics of granule formation were studied using cells from two bench-scale UASB reactors. The objective was to elucidate factors which influence formation and maintenance of highly active self-agglomerated microbial biomass. Simultaneous examination of biological and physical parameters was performed during the start-up of a calcium-positive (100 mg/l) reactor and a reactor without added calcium. The influence of carbon nutrients and Ca++ on the cell surface and microbial aggregation was studied. The granules formed in both reactors but were larger in the calcium-positive reactor in which they settled 3-4 times faster. A higher rate of biomass accumulation also was evident in the calcium-positive reactor and this allowed a more frequent increase in the substrate loading rate and earlier development of the granular sludge. (Refs. 17).

Spatial Distribution of Viruses Associated with Planktonic and Attached Microbial Communities in Hydrothermal Environments

Science.gov (United States)

Nunoura, Takuro; Kazama, Hiromi; Noguchi, Takuroh; Inoue, Kazuhiro; Akashi, Hironori; Yamanaka, Toshiro; Toki, Tomohiro; Yamamoto, Masahiro; Furushima, Yasuo; Ueno, Yuichiro; Yamamoto, Hiroyuki; Takai, Ken

2012-01-01

Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments. PMID:22210205

Hydrogen production profiles using furans in microbial electrolysis cells.

Science.gov (United States)

Catal, Tunc; Gover, Tansu; Yaman, Bugra; Droguetti, Jessica; Yilancioglu, Kaan

2017-06-01

Microbial electrochemical cells including microbial fuel cells (MFCs) and microbial electrolysis cells (MECs) are novel biotechnological tools that can convert organic substances in wastewater or biomass into electricity or hydrogen. Electroactive microbial biofilms used in this technology have ability to transfer electrons from organic compounds to anodes. Evaluation of biofilm formation on anode is crucial for enhancing our understanding of hydrogen generation in terms of substrate utilization by microorganisms. In this study, furfural and hydroxymethylfurfural (HMF) were analyzed for hydrogen generation using single chamber membrane-free MECs (17 mL), and anode biofilms were also examined. MECs were inoculated with mixed bacterial culture enriched using chloroethane sulphonate. Hydrogen was succesfully produced in the presence of HMF, but not furfural. MECs generated similar current densities (5.9 and 6 mA/cm 2 furfural and HMF, respectively). Biofilm samples obtained on the 24th and 40th day of cultivation using aromatic compounds were evaluated by using epi-fluorescent microscope. Our results show a correlation between biofilm density and hydrogen generation in single chamber MECs.

Natural attenuation process via microbial oxidation of arsenic in a high Andean watershed.

Science.gov (United States)

Leiva, Eduardo D; Rámila, Consuelo d P; Vargas, Ignacio T; Escauriaza, Cristian R; Bonilla, Carlos A; Pizarro, Gonzalo E; Regan, John M; Pasten, Pablo A

2014-01-01

Rivers in northern Chile have arsenic (As) concentrations at levels that are toxic for humans and other organisms. Microorganism-mediated redox reactions have a crucial role in the As cycle; the microbial oxidation of As (As(III) to As(V)) is a critical transformation because it favors the immobilization of As in the solid phase. We studied the role of microbial As oxidation for controlling the mobility of As in the extreme environment found in the Chilean Altiplano (i.e., > 4000 meters above sea level (masl) and Azufre River sub-basin, where the natural attenuation of As from hydrothermal discharge (pH 4-6) was observed. As(III) was actively oxidized by a microbial consortium, leading to a significant decrease in the dissolved As concentrations and a corresponding increase in the sediment's As concentration downstream of the hydrothermal source. In-situ oxidation experiments demonstrated that the As oxidation required biological activity, and microbiological molecular analysis confirmed the presence of As(III)-oxidizing groups (aroA-like genes) in the system. In addition, the pH measurements and solid phase analysis strongly suggested that the As removal mechanism involved adsorption or coprecipitation with Fe-oxyhydroxides. Taken together, these results indicate that the microorganism-mediated As oxidation contributed to the attenuation of As concentrations and the stabilization of As in the solid phase, therefore controlling the amount of As transported downstream. This study is the first to demonstrate the microbial oxidation of As in Altiplano basins and its relevance in the immobilization of As. © 2013.

Formation of Microbial Mats and Salt in Radioactive Paddy Soils in Fukushima, Japan

Directory of Open Access Journals (Sweden)

Kazue Tazaki

2015-12-01

Full Text Available Coastal areas in Minami-soma City, Fukushima, Japan, were seriously damaged by radioactive contamination from the Fukushima Daiichi Nuclear Power Plant (FDNPP accident that caused multiple pollution by tsunami and radionuclide exposure, after the Great East Japan Earthquake, on 11 March 2011. Some areas will remain no-go zones because radiation levels remain high. In Minami-soma, only 26 percent of decontamination work had been finished by the end of July in 2015. Here, we report the characterization of microbial mats and salt found on flooded paddy fields at Karasuzaki, Minami-soma City, Fukushima Prefecture, Japan which have been heavily contaminated by radionuclides, especially by Cs (134Cs, 137Cs, 40K, Sr (89Sr, 90Sr, and 91 or 95Zr even though it is more than 30 km north of the FDNPP. We document the mineralogy, the chemistry, and the micro-morphology, using a combination of micro techniques. The microbial mats were found to consist of diatoms with mineralized halite and gypsum by using X-ray diffraction (XRD. Particular elements concentrated in microbial mats were detected using scanning electron microscopy equipped with energy dispersive spectroscopy (SEM-EDS and X-ray fluorescence (XRF. The objective of this contribution is to illustrate the ability of various diatoms associated with minerals and microorganisms which are capable of absorbing both radionuclides and stable isotopes from polluted paddy soils in extreme conditions. Ge semiconductor analysis of the microbial mats detected 134Cs, 137Cs, and 40K without 131I in 2012 and in 2013. Quantitative analysis associated with the elemental content maps by SEM-EDS indicated the possibility of absorption of radionuclide and stable isotope elements from polluted paddy soils in Fukushima Prefecture. In addition, radionuclides were detected in solar salts made of contaminated sea water collected from the Karasuzaki ocean bath, Minami-soma, Fukushima in 2015, showing high Zr content associated

Stream microbial diversity responds to environmental changes: Review and synthesis of existing research

Directory of Open Access Journals (Sweden)

Lydia eZeglin

2015-05-01

Full Text Available The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of the hundreds of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream organic matter compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

Science.gov (United States)

Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

2018-06-01

Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

Characterization of indigenous oil field microorganisms for microbially enhanced oil recovery (MEOR)

Energy Technology Data Exchange (ETDEWEB)

Sitte, J.; Krueger, M. [Bundesanstalt fuer Geowissenschaften und Rohstoffe (BGR), Hannover (Germany); Biegel, E.; Herold, A. [BASF SE, Ludwigshafen (Germany); Alkan, H. [Wintershall Holding GmbH, Kassel (Germany)

2013-08-01

Microbial activities and their resulting metabolites became a focus of attention for enhanced oil recovery (MEOR, microbial enhanced oil recovery) in the recent years. In order to develop a strategy for a MEOR application in a German oil field operated by Wintershall experiments were performed to investigate different sampling strategies and the microbial communities found in these samples. The objectives of this study were (1) to characterize the indigenous microbial communities, (2) to investigate the dependency of microbial activity/diversity on the different sampling strategies, and (3) to study the influence of the in situ pressure on bacterial growth and metabolite production. Fluids were sampled at the well head (surface) and in situ in approx. 785 m depth to collect uncontaminated production water directly from the reservoir horizon and under the in situ pressure of 31 bar (subsurface). In the lab the pressure was either released quickly or slowly to assess the sensitivity of microorganisms to rapid pressure changes. Quantitative PCR resulted in higher microbial cell numbers in the subsurface than in the surface sample. Biogenic CO{sub 2} and CH{sub 4} formation rates were determined under atmospheric and high pressure conditions in the original fluids, with highest rates found in the surface fluid. Interestingly, no methane was formed in the native fluid samples. While nitrate reduction was exclusively detected in the surface samples, sulfide formation also occurred in the subsurface fluids. Increased CO{sub 2} formation was measured after addition of a variety of substrates in the surface fluids, while only fructose and glucose showed a stimulating effect on CO{sub 2} production for the subsurface sample. Stable enrichment cultures were obtained in complex medium inoculated with the subsurface fluid, both under atmospheric and in situ pressure. Growth experiments with constant or changing pressure, and subsequent DGGE analysis of bacterial 16S rRNA genes

Effect of ion exchange on the rate of aerobic microbial oxidation of ammonium in hyporheic zone sediments.

Science.gov (United States)

Yan, Ailan; Liu, Chongxuan; Liu, Yuanyuan; Xu, Fen

2018-03-01

Microbially mediated ammonium oxidation is a major process affecting nitrogen transformation and cycling in natural environments. This study investigated whether ion exchange process can affect microbially mediated aerobic oxidation of ammonium in a hyporheic zone (HZ) sediments from the Columbia River at US Department of Energy's Hanford site, Washington State. Experiments were conducted using synthetic groundwater and river water to investigate their effect on ammonium oxidation. Results indicated that ammonium sorption through ion exchange reactions decreased the rate of ammonium oxidation, apparently resulting from the influence of the ion exchange on dissolved ammonium concentration, thus decreasing the bioavailability of ammonium for microbial oxidation. However, with the decrease in dissolved ammonium concentration, the sorbed ammonium released back to aqueous phase, and became bioavailable so that all the ammonium in the suspensions were oxidized. Our results implied a dynamic change in ammonium oxidation rates in an environment such as at HZ where river water and groundwater with different chemical compositions exchange frequently that can affect ammonium sorption and desorption through ion exchange reactions.

Microbial healing of cracks in concrete: a review.

Science.gov (United States)

Joshi, Sumit; Goyal, Shweta; Mukherjee, Abhijit; Reddy, M Sudhakara

2017-11-01

Concrete is the most widely used construction material of the world and maintaining concrete structures from premature deterioration is proving to be a great challenge. Early age formation of micro-cracking in concrete structure severely affects the serviceability leading to high cost of maintenance. Apart from conventional methods of repairing cracks with sealants or treating the concrete with adhesive chemicals to prevent the cracks from widening, a microbial crack-healing approach has shown promising results. The unique feature of the microbial system is that it enables self-healing of concrete. The effectiveness of microbially induced calcium carbonate precipitation (MICCP) in improving durability of cementitious building materials, restoration of stone monuments and soil bioclogging is discussed. Main emphasis has been laid on the potential of bacteria-based crack repair in concrete structure and the applications of different bacterial treatments to self-healing cracks. Furthermore, recommendations to employ the MICCP technology at commercial scale and reduction in the cost of application are provided in this review.

A unique model system of microbial carbonate precipitation: Stromatolites of Lagoa Vermelha, Brazil

Science.gov (United States)

Warthmann, R. J.; Vasoncelos, C.; van Lith, Y.; Visscher, P. T.; McKenzie, J. A.

2003-04-01

Modern stromatolites are recognized as analogues to fossil laminated structures, which are remains of microbial activity that are widely found in sedimentary rocks beginning in the Neo-Archean, but are quite rare today. The key difference of modern microbial mats and stromatolites compared to ancient examples is the type of lithification. A few marine and hypersaline microbial mats have been observed to precipitate carbonates, and only in Shark Bay (Western, Australia) and Highborne Cay (Bahamas) has the formation of continuous laminae of carbonates been observed. Lagoa Vermelha, a moderate hypersaline lagoon in Rio de Janeiro, Brazil, offers the ideal conditions to promote lithification. Calcified, sometimes dolomitic stromatolites grow on the sediment surface, whereas within the sediments dolomite precipitates. The factors controlling carbonate precipitation in Lagoa Vermelha are the changing water chemistry and the special hydrology, combined with a high primary production by cyanobacteria, a high rate of respiration and the absence of higher organisms. Here, we present a study of the physico-chemical parameters, microbial processes and bio-minerals associated with these stromatolites and microbial mats. This approach provides boundary conditions to better understand dolomite formation. Several discrete lithified calcium carbonate layers are present. The first lithified layer is found beneath a 2-mm-thick biofilm, which contains Gloeocapsa. Below the underlying dense Microcoleus layer, the second micrite deposit is observed at 4-5 mm depth. Successive micritic laminae are preserved in the layer of decaying cyanobacteria that harbors large numbers of purple sulfur bacteria, heterotrophic microbes and sulfate-reducing bacteria. C-isotope studies of the carbonate layers indicate a contribution of organic derived carbon associated with microbial processes, such as sulfate reduction. The O-isotopic values indicate an evaporitic enrichment of the water. Understanding

Methymercury Formation in Marine and Freshwater Systems: Sediment Characteristics, Microbial Activity and SRB Phylogeny Control Formation Rates and Food-Chain Exposure

Science.gov (United States)

King, J. K.; Saunders, F. M.

2004-05-01

Mercury research in freshwater and marine systems suggests that sediment characteristics such as organic substrate, mercury speciation, and sulfate/sulfide concentrations influence availability of inorganic mercury for methylation. Similarly, sediment characteristics also influence sulfate-reducing bacterial (SRB) respiration as well as the presence/distribution of phylogenetic groups responsible for mercury methylation. Our work illustrates that the process of methylmercury formation in freshwater and marine systems are not dissimilar. Rather, the same geochemical parameters and SRB phylogenetic groups determine the propensity for methylmercury formation and are applicable in both fresh- and marine-water systems. The presentation will include our integration of sediment geochemical and microbial parameters affecting mercury methylation in specific freshwater and marine systems. Constructed wetlands planted with Schoenoplectus californicus and amended with gypsum (CaSO4) have demonstrated a capacity to remove inorganic mercury from industrial outfalls. However, bioaccumulation studies of periphyton, eastern mosquitofish (Gambusia holbrooki) and lake chubsucker (Erimyzon sucetta) were conducted in order to ascertain the availability of wetland-generated methylmercury to biota. Total mercury concentrations in mosquitofish from non-sulfate treated controls and the reference location were significantly lower than those from the low and high sulfate treatments while mean total mercury concentrations in lake chubsuckers were also significantly elevated in the high sulfate treatment compared to the low sulfate, control and reference populations. Methylmercury concentrations in periphyton also corresponded with mercury levels found in the tissue of the lake chubsuckers, and these findings fit well given the trophic levels identified for both species of fish. Overall, data from this study suggest that the initial use of gypsum to accelerate the maturity of a constructed

A marine microbial consortium apparently mediating anaerobic oxidation of methane

DEFF Research Database (Denmark)

Boetius, A.; Ravenschlag, K.; Schubert, CJ

2000-01-01

microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria(5-7). Here we provide microscopic...... cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.......A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments(1). Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles(2), radiotracer experiments(3) and stable carbon isotope data(4). But the elusive...

Microbial production of branched-chain dicarboxylate 2-methylsuccinic acid via enoate reductase-mediated bioreduction.

Science.gov (United States)

Wang, Jian; Yang, Yaping; Zhang, Ruihua; Shen, Xiaolin; Chen, Zhenya; Wang, Jia; Yuan, Qipeng; Yan, Yajun

2018-01-01

2-Methylsuccinic acid (2-MSA) is a C5 branched-chain dicarboxylate that serves as an attractive synthon for the synthesis of polymers with extensive applications in coatings, cosmetic solvents and bioplastics. However, the lack of natural pathways for 2-MSA biosynthesis has limited its application as a promising bio-replacement. Herein, we conceived a non-natural three-step biosynthetic route for 2-MSA, via employing the citramalate pathway in combination with enoate reductase-mediated bioreduction of the pathway intermediate citraconate. First, over-expression of codon-optimized citramalate synthase variant CimA* from Methanococcus jannaschii, endogenous isopropylmalate isomerase EcLeuCD and enoate reductase YqjM from Bacillus subtilis allowed the production of 2-MSA in Escherichia coli for the first time, with a titer of 0.35g/L in shake flask experiments. Subsequent screening of YqjM-like enoate reductases of different bacterial origins enabled identification and characterization of a new NAD(P)H-dependent enoate reductase KpnER from Klebsiella pneumoniae, which exhibited higher activity towards citraconate than YqjM. Incorporation of KpnER into the 2-MSA biosynthetic pathway led to 2-MSA production improvement to a titer of 0.96g/L in aerobic condition. Subsequent optimizations including cofactor regeneration, microaerobic cultivation and host strain engineering, boosted 2-MSA titer to 3.61g/L with a molar yield of 0.36 in shake flask experiments. This work established a promising platform for 2-MSA bioproduction, which enabled the highest titer of 2-MSA production in microbial hosts so far. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Proteomic analysis of HIV-1 Nef cellular binding partners reveals a role for exocyst complex proteins in mediating enhancement of intercellular nanotube formation

Directory of Open Access Journals (Sweden)

Mukerji Joya

2012-06-01

Full Text Available Abstract Background HIV-1 Nef protein contributes to pathogenesis via multiple functions that include enhancement of viral replication and infectivity, alteration of intracellular trafficking, and modulation of cellular signaling pathways. Nef stimulates formation of tunneling nanotubes and virological synapses, and is transferred to bystander cells via these intercellular contacts and secreted microvesicles. Nef associates with and activates Pak2, a kinase that regulates T-cell signaling and actin cytoskeleton dynamics, but how Nef promotes nanotube formation is unknown. Results To identify Nef binding partners involved in Pak2-association dependent Nef functions, we employed tandem mass spectrometry analysis of Nef immunocomplexes from Jurkat cells expressing wild-type Nef or Nef mutants defective for the ability to associate with Pak2 (F85L, F89H, H191F and A72P, A75P in NL4-3. We report that wild-type, but not mutant Nef, was associated with 5 components of the exocyst complex (EXOC1, EXOC2, EXOC3, EXOC4, and EXOC6, an octameric complex that tethers vesicles at the plasma membrane, regulates polarized exocytosis, and recruits membranes and proteins required for nanotube formation. Additionally, Pak2 kinase was associated exclusively with wild-type Nef. Association of EXOC1, EXOC2, EXOC3, and EXOC4 with wild-type, but not mutant Nef, was verified by co-immunoprecipitation assays in Jurkat cells. Furthermore, shRNA-mediated depletion of EXOC2 in Jurkat cells abrogated Nef-mediated enhancement of nanotube formation. Using bioinformatic tools, we visualized protein interaction networks that reveal functional linkages between Nef, the exocyst complex, and the cellular endocytic and exocytic trafficking machinery. Conclusions Exocyst complex proteins are likely a key effector of Nef-mediated enhancement of nanotube formation, and possibly microvesicle secretion. Linkages revealed between Nef and the exocyst complex suggest a new paradigm of

Electricity generation by microbial fuel cells fuelled with wheat straw hydrolysate

DEFF Research Database (Denmark)

Thygesen, Anders; Poulsen, Finn Willy; Angelidaki, Irini

2011-01-01

Electricity production from microbial fuel cells fueled with hydrolysate produced by hydrothermal treatment of wheat straw can achieve both energy production and domestic wastewater purification. The hydrolysate contained mainly xylan, carboxylic acids, and phenolic compounds. Power generation...... in 95% degradation of the xylan and glucan. The study demonstrates that lignocellulosic hydrolysate can be used for co-treatment with domestic wastewater for power generation in microbial fuel cells....... density with the hydrolysate was higher than the one with only xylan (120 mW m−2) and carboxylic acids as fuel. The higher power density can be caused by the presence of phenolic compounds in the hydrolysates, which could mediate electron transport. Electricity generation with the hydrolysate resulted...

Microbial oxidation of lithospheric organic carbon in rapidly eroding tropical mountain soils.

Science.gov (United States)

Hemingway, Jordon D; Hilton, Robert G; Hovius, Niels; Eglinton, Timothy I; Haghipour, Negar; Wacker, Lukas; Chen, Meng-Chiang; Galy, Valier V

2018-04-13

Lithospheric organic carbon ("petrogenic"; OC petro ) is oxidized during exhumation and subsequent erosion of mountain ranges. This process is a considerable source of carbon dioxide (CO 2 ) to the atmosphere over geologic time scales, but the mechanisms that govern oxidation rates in mountain landscapes are poorly constrained. We demonstrate that, on average, 67 ± 11% of the OC petro initially present in bedrock exhumed from the tropical, rapidly eroding Central Range of Taiwan is oxidized in soils, leading to CO 2 emissions of 6.1 to 18.6 metric tons of carbon per square kilometer per year. The molecular and isotopic evolution of bulk OC and lipid biomarkers during soil formation reveals that OC petro remineralization is microbially mediated. Rapid oxidation in mountain soils drives CO 2 emission fluxes that increase with erosion rate, thereby counteracting CO 2 drawdown by silicate weathering and biospheric OC burial. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Bioremediation of PAHs and VOCs: Advances in clay mineral-microbial interaction.

Science.gov (United States)

Biswas, Bhabananda; Sarkar, Binoy; Rusmin, Ruhaida; Naidu, Ravi

2015-12-01

Bioremediation is an effective strategy for cleaning up organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs). Advanced bioremediation implies that biotic agents are more efficient in degrading the contaminants completely. Bioremediation by microbial degradation is often employed and to make this process efficient, natural and cost-effective materials can serve as supportive matrices. Clay/modified clay minerals are effective adsorbents of PAHs/VOCs, and readily available substrate and habitat for microorganisms in the natural soil and sediment. However, the mechanism underpinning clay-mediated biodegradation of organic compounds is often unclear, and this requires critical investigation. This review describes the role of clay/modified clay minerals in hydrocarbon bioremediation through interaction with microbial agents in specific scenarios. The vision is on a faster, more efficient and cost-effective bioremediation technique using clay-based products. This review also proposes future research directions in the field of clay modulated microbial degradation of hydrocarbons. Copyright © 2015 Elsevier Ltd. All rights reserved.

Caffeine suppresses homologous recombination through interference with RAD51-mediated joint molecule formation

Science.gov (United States)

Zelensky, Alex N.; Sanchez, Humberto; Ristic, Dejan; Vidic, Iztok; van Rossum-Fikkert, Sari E.; Essers, Jeroen; Wyman, Claire; Kanaar, Roland

2013-01-01

Caffeine is a widely used inhibitor of the protein kinases that play a central role in the DNA damage response. We used chemical inhibitors and genetically deficient mouse embryonic stem cell lines to study the role of DNA damage response in stable integration of the transfected DNA and found that caffeine rapidly, efficiently and reversibly inhibited homologous integration of the transfected DNA as measured by several homologous recombination-mediated gene-targeting assays. Biochemical and structural biology experiments revealed that caffeine interfered with a pivotal step in homologous recombination, homologous joint molecule formation, through increasing interactions of the RAD51 nucleoprotein filament with non-homologous DNA. Our results suggest that recombination pathways dependent on extensive homology search are caffeine-sensitive and stress the importance of considering direct checkpoint-independent mechanisms in the interpretation of the effects of caffeine on DNA repair. PMID:23666627

Evaluation of catalytic properties of tungsten carbide for the anode of microbial fuel cells

Energy Technology Data Exchange (ETDEWEB)

Rosenbaum, Miriam; Zhao, Feng; Quaas, Marion; Wulff, Harm; Schroeder, Uwe; Scholz, Fritz [Universitaet Greifswald, Institut fuer Biochemie, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany)

2007-07-31

In this communication we discuss the properties of tungsten carbide, WC, as anodic electrocatalyst for microbial fuel cell application. The electrocatalytic activity of tungsten carbide is evaluated in the light of its preparation procedure, its structural properties as well as the pH and the composition of the anolyte solution and the catalyst load. The activity of the noble-metal-free electrocatalyst towards the oxidation of several common microbial fermentation products (hydrogen, formate, lactate, ethanol) is studied for microbial fuel cell conditions (e.g., pH 5, room temperature and ambient pressure). Current densities of up to 8.8 mA cm{sup -2} are achieved for hydrogen (hydrogen saturated electrolyte solution), and up to 2 mA cm{sup -2} for formate and lactate, respectively. No activity was observed for ethanol electrooxidation. The electrocatalytic activity and chemical stability of tungsten carbide is excellent in acidic to pH neutral potassium chloride electrolyte solutions, whereas higher phosphate concentrations at neutral pH support an oxidative degradation. (author)

Rac1 switching at the right time and location is essential for Fcγ receptor-mediated phagosome formation.

Science.gov (United States)

Ikeda, Yuka; Kawai, Katsuhisa; Ikawa, Akira; Kawamoto, Kyoko; Egami, Youhei; Araki, Nobukazu

2017-08-01

Lamellipodia are sheet-like cell protrusions driven by actin polymerization mainly through Rac1, a GTPase molecular switch. In Fcγ receptor-mediated phagocytosis of IgG-opsonized erythrocytes (IgG-Es), Rac1 activation is required for lamellipodial extension along the surface of IgG-Es. However, the significance of Rac1 deactivation in phagosome formation is poorly understood. Our live-cell imaging and electron microscopy revealed that RAW264 macrophages expressing a constitutively active Rac1 mutant showed defects in phagocytic cup formation, while lamellipodia were formed around IgG-Es. Because activated Rac1 reduced the phosphorylation levels of myosin light chains, failure of the cup formation is probably due to inhibition of actin/myosin II contractility. Reversible photo-manipulation of the Rac1 switch in macrophages fed with IgG-Es could phenocopy two lamellipodial motilities: outward-extension and cup-constriction by Rac1 ON and OFF, respectively. In conjunction with fluorescence resonance energy transfer imaging of Rac1 activity, we provide a novel mechanistic model of phagosome formation spatiotemporally controlled by Rac1 switching within a phagocytic cup. © 2017. Published by The Company of Biologists Ltd.

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

Science.gov (United States)

Karl, David M

2014-01-01

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

Mediating Dynamic Supply Chain Formation by Collaborative Single Machine Earliness/Tardiness Agents in Supply Mesh

Directory of Open Access Journals (Sweden)

Hang Yang

2014-01-01

Full Text Available Nowadays, a trend of forming dynamic supply chains with different trading partners over different e-marketplaces has emerged. These supply chains, which are called “supply mesh,” generally refer to heterogeneous electronic marketplaces in which dynamic supply chains, as per project (often make-to-order, are formed across different parties. Conceptually, in a supply mesh a dynamic supply chain is formed vertically, mediating several companies for a project. Companies that are on the same level horizontally are either competitors or cohorts. A complex scenario such as this makes it challenging to find the right group of members for a dynamic supply chain. Earlier on, a multiagent model called the collaborative single machine earliness/tardiness (CSET model was proposed for the optimal formation of make-to-order supply chains. This paper contributes the particular agent designs, for enabling the mediation of CSET in a supply mesh, and the possibilities are discussed. It is demonstrated via a computer simulation, based on samples from the U.S. textile industry, that by using intelligent agents under the CSET model it is possible to automatically find an ideal group of trading partners from a supply mesh.

Microbial activity in the marine deep biosphere: Progress and prospects

Directory of Open Access Journals (Sweden)

Beth N Orcutt

2013-07-01

Full Text Available The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists – all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive. Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI "theme team" on microbial activity (www.darkenergybiosphere.org.

Microbial activity in the marine deep biosphere: progress and prospects

Science.gov (United States)

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome.

Science.gov (United States)

Medina, Daniel A; Pinto, Francisco; Ovalle, Aline; Thomson, Pamela; Garrido, Daniel

2017-10-04

Composition of the gut microbiome is influenced by diet. Milk or formula oligosaccharides act as prebiotics, bioactives that promote the growth of beneficial gut microbes. The influence of prebiotics on microbial interactions is not well understood. Here we investigated the transformation of prebiotics by a consortium of four representative species of the infant gut microbiome, and how their interactions changed with dietary substrates. First, we optimized a culture medium resembling certain infant gut parameters. A consortium containing Bifidobacterium longum subsp. infantis , Bacteroides vulgatus , Escherichia coli and Lactobacillus acidophilus was grown on fructooligosaccharides (FOS) or 2'-fucosyllactose (2FL) in mono- or co-culture. While Bi. infantis and Ba. vulgatus dominated growth on 2FL, their combined growth was reduced. Besides, interaction coefficients indicated strong competition, especially on FOS. While FOS was rapidly consumed by the consortium, B. infantis was the only microbe displaying significant consumption of 2FL. Acid production by the consortium resembled the metabolism of microorganisms dominating growth in each substrate. Finally, the consortium was tested in a bioreactor, observing similar predominance but more pronounced acid production and substrate consumption. This study indicates that the chemical nature of prebiotics modulate microbial interactions in a consortium of infant gut species.

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome

Directory of Open Access Journals (Sweden)

Daniel A. Medina

2017-10-01

Full Text Available Composition of the gut microbiome is influenced by diet. Milk or formula oligosaccharides act as prebiotics, bioactives that promote the growth of beneficial gut microbes. The influence of prebiotics on microbial interactions is not well understood. Here we investigated the transformation of prebiotics by a consortium of four representative species of the infant gut microbiome, and how their interactions changed with dietary substrates. First, we optimized a culture medium resembling certain infant gut parameters. A consortium containing Bifidobacterium longum subsp. infantis, Bacteroides vulgatus, Escherichia coli and Lactobacillus acidophilus was grown on fructooligosaccharides (FOS or 2′-fucosyllactose (2FL in mono- or co-culture. While Bi. infantis and Ba. vulgatus dominated growth on 2FL, their combined growth was reduced. Besides, interaction coefficients indicated strong competition, especially on FOS. While FOS was rapidly consumed by the consortium, B. infantis was the only microbe displaying significant consumption of 2FL. Acid production by the consortium resembled the metabolism of microorganisms dominating growth in each substrate. Finally, the consortium was tested in a bioreactor, observing similar predominance but more pronounced acid production and substrate consumption. This study indicates that the chemical nature of prebiotics modulate microbial interactions in a consortium of infant gut species.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Microbial interactions: ecology in a molecular perspective.

Science.gov (United States)

Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

2016-12-01

The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Augmented BMPRIA-mediated BMP signaling in cranial neural crest lineage leads to cleft palate formation and delayed tooth differentiation.

Directory of Open Access Journals (Sweden)

Lu Li

Full Text Available The importance of BMP receptor Ia (BMPRIa mediated signaling in the development of craniofacial organs, including the tooth and palate, has been well illuminated in several mouse models of loss of function, and by its mutations associated with juvenile polyposis syndrome and facial defects in humans. In this study, we took a gain-of-function approach to further address the role of BMPR-IA-mediated signaling in the mesenchymal compartment during tooth and palate development. We generated transgenic mice expressing a constitutively active form of BmprIa (caBmprIa in cranial neural crest (CNC cells that contributes to the dental and palatal mesenchyme. Mice bearing enhanced BMPRIa-mediated signaling in CNC cells exhibit complete cleft palate and delayed odontogenic differentiation. We showed that the cleft palate defect in the transgenic animals is attributed to an altered cell proliferation rate in the anterior palatal mesenchyme and to the delayed palatal elevation in the posterior portion associated with ectopic cartilage formation. Despite enhanced activity of BMP signaling in the dental mesenchyme, tooth development and patterning in transgenic mice appeared normal except delayed odontogenic differentiation. These data support the hypothesis that a finely tuned level of BMPRIa-mediated signaling is essential for normal palate and tooth development.

The complex formation of selected actinides (U, Np, Cm) with microbial ligands

International Nuclear Information System (INIS)

Glorius, Maja

2009-01-01

One of the urgent tasks in the field of nuclear technology is the final storage of radioactive substances. As a part of the safety requirements the protection of humans and the environment from the danger of radioactive substances in case of the release from the final storage is essential. For performing long-term safety calculations the detailed understanding of the physico-chemical effects and influences which cause the mobilisation and transport of actinides are necessary. The presented work was a discrete part of a project, which was focused on the clarification of the influence of microorganisms on the migration of actinides in case of the release of actinides from a final storage. The influence of microbial produced substances on the mobilisation of selected actinides was studied thereby. The microbial produced substances studied in this project were synthesized by bacteria from the Pseudomonas genus under special conditions. Fluorescent Pseudomonads secrete bacterial pyoverdin-type siderophores with a high potential to complex and transport metals, especially iron(III). The aim of the project was to determine how and under which conditions the bioligands are able to complex also radioactive substances and therefore to transport them. For this work the alpha-emitting actinides uranium, curium and neptunium were chosen because their long-life cycle and their radiotoxicity are a matter of particular interest. This work dealed with the interaction of the actinides U(VI), Np(V) and Cm(III) with model ligands simulating the functionality of the pyoverdins. So, such bioligands can essentially influence the behaviour of actinides in the environment. The results of this work contribute to a better understanding and assessment of the influence of the microbial ligands to the mobilisation and migration of the radionuclides. The outcomes could be used to quantify the actinide-mobilising effect of the bioligands, which are released, for example, in the vicinity of a

Microbial Decomposers Not Constrained by Climate History Along a Mediterranean Climate Gradient

Science.gov (United States)

Baker, N. R.; Khalili, B.; Martiny, J. B. H.; Allison, S. D.

2017-12-01

The return of organic carbon to the atmosphere through terrestrial decomposition is mediated through the breakdown of complex organic polymers by extracellular enzymes produced by microbial decomposer communities. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. To address this question, we deployed fine-pore nylon mesh "microbial cage" litterbags containing grassland litter with and without local inoculum across five sites in southern California, spanning a gradient of 10.3-22.8° C in mean annual temperature and 100-400+ mm mean annual precipitation. Litterbags were deployed in October 2014 and collected four times over the course of 14 months. Recovered litter was assayed for mass loss, litter chemistry, microbial biomass, extracellular enzymes (Vmax and Km­), and enzyme temperature sensitivities. We hypothesized that grassland litter would decompose most rapidly in the grassland site, and that access to local microbial communities would enhance litter decomposition rates and microbial activity in the other sites along the gradient. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbes were not restricted in their ability to decompose litter under different climate conditions. Although we observed a strong correlation between bacterial biomass and mass loss across the gradient, litter that was inoculated with local microbial communities lost less mass despite having greater bacterial biomass and potentially accumulating more microbial residues. Our results suggest that microbial community composition may not constrain C-cycling rates under climate change in our system. However, there may be community constraints on decomposition if climate change alters litter chemistry, a

The Use of Boron-doped Diamond Electrode on Yeast-based Microbial Fuel Cell for Electricity Production

Science.gov (United States)

Hanzhola, G.; Tribidasari, A. I.; Endang, S.

2018-01-01

The dependency of fossil energy in Indonesia caused the crude oil production to be drastically decreased since 2001, while energy consumption increased. In addition, The use of fossil energy can cause several environmental problems. Therefore, we need an alternative environment-friendly energy as solution for these problems. A microbial fuel cell is one of the prospective alternative source of an environment-friendly energy source to be developed. In this study, Boron-doped diamond electrode was used as working electrode and Candida fukuyamaensis as biocatalyst in microbial fuel cell. Different pH of anode compartment (pH 6.5-7.5) and mediator concentration (10-100 μM) was used to produce an optimal electricity. MFC was operated for 3 hours. During operation, the current and voltage density was measured with potensiostat. The maximum power and current density are 425,82 mW/m2 and 440 mA/m2, respectively, for MFC using pH 7.5 at anode compartment without addition of methylene blue. The addition of redox mediator is lowering the produced electricity because of its anti microbial properties that can kill the microbe.

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

NARCIS (Netherlands)

Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk; Salles, Joana Falcao

2015-01-01

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events

Science.gov (United States)

Mooshammer, Maria; Hofhansl, Florian; Frank, Alexander H.; Wanek, Wolfgang; Hämmerle, Ieda; Leitner, Sonja; Schnecker, Jörg; Wild, Birgit; Watzka, Margarete; Keiblinger, Katharina M.; Zechmeister-Boltenstern, Sophie; Richter, Andreas

2017-01-01

Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling. In contrast to the fast recovery of the initially stimulated C and N processes, we found a slow recovery of P mineralization rates, which was not accompanied by significant changes in community composition. The functional and structural responses to the two distinct temperature disturbances were markedly similar, suggesting that direct negative physical effects and costs associated with the stress response were comparable. Moreover, the stress response of extracellular enzyme activities, but not that of intracellular microbial processes (for example, respiration or N mineralization), was dependent on the nutrient content of the resource through its effect on microbial physiology and community composition. Our laboratory study provides novel insights into the mechanisms of microbial functional stress responses that can serve as a basis for field studies and, in particular, illustrates the need for a closer integration of microbial C-N-P interactions into climate extremes research. PMID:28508070

The contribution of microbial mats to the arsenic geochemistry of an ancient gold mine

International Nuclear Information System (INIS)

Drewniak, Lukasz; Maryan, Natalia; Lewandowski, Wiktor; Kaczanowski, Szymon; Sklodowska, Aleksandra

2012-01-01

The ancient Zloty Stok (SW Poland) gold mine is such an environment, where different microbial communities, able to utilize inorganic arsenic species As(III) and As(V), are found. The purpose of the present study was to (i) estimate prokaryotic diversity in the microbial mats in bottom sediments of this gold mine, (ii) identify microorganisms that can metabolize arsenic, and (iii) estimate their potential role in the arsenic geochemistry of the mine and in the environment. The oxidation/reduction experiments showed that the microbial mat community may significantly contribute to arsenic contamination in groundwater. The presence of both arsenite oxidizing and dissimilatory arsenate reducing bacteria in the mat was confirmed by the detection of arsenite oxidase and dissimilatory arsenate reductase genes, respectively. This work also demonstrated that microorganisms utilizing other compounds that naturally co-occur with arsenic are present within the microbial mat community and may contribute to the arsenic geochemistry in the environment. - Highlights: ► The microbial mats from this ancient gold mine are highly diverse community. ► As(III) oxidizing and As(V) reducing bacteria are present in the mats. ► As redox transformations are linked to the metabolism of microbial mats bacteria. ► Microbial mats play a crucial role in the As biogeochemical cycle within the mine. - The microbial mats from this ancient gold mine can mediate oxidation/reduction reaction of arsenic and in this way may significantly contribute to arsenic contamination in groundwater.

Mac-1 (CD11b/CD18) is essential for Fc receptor-mediated neutrophil cytotoxicity and immunologic synapse formation.

Science.gov (United States)

van Spriel, A B; Leusen, J H; van Egmond, M; Dijkman, H B; Assmann, K J; Mayadas, T N; van de Winkel, J G

2001-04-15

Receptors for human immunoglobulin (Ig)G and IgA initiate potent cytolysis of antibody (Ab)-coated targets by polymorphonuclear leukocytes (PMNs). Mac-1 (complement receptor type 3, CD11b/CD18) has previously been implicated in receptor cooperation with Fc receptors (FcRs). The role of Mac-1 in FcR-mediated lysis of tumor cells was characterized by studying normal human PMNs, Mac-1-deficient mouse PMNs, and mouse PMNs transgenic for human FcR. All PMNs efficiently phagocytosed Ab-coated particles. However, antibody-dependent cellular cytotoxicity (ADCC) was abrogated in Mac-1(-/-) PMNs and in human PMNs blocked with anti-Mac-1 monoclonal Ab (mAb). Mac-1(-/-) PMNs were unable to spread on Ab-opsonized target cells and other Ab-coated surfaces. Confocal laser scanning and electron microscopy revealed a striking difference in immunologic synapse formation between Mac-1(-/-) and wild-type PMNs. Also, respiratory burst activity could be measured outside membrane-enclosed compartments by using Mac-1(-/-) PMNs bound to Ab-coated tumor cells, in contrast to wild-type PMNs. In summary, these data document an absolute requirement of Mac-1 for FcR-mediated PMN cytotoxicity toward tumor targets. Mac-1(-/-) PMNs exhibit defective spreading on Ab-coated targets, impaired formation of immunologic synapses, and absent tumor cytolysis.

Microbially-mediated fluorescent organic matter transformations in the deep ocean

DEFF Research Database (Denmark)

Aparicio, Fran L.; Nieto-Cid, Mar; Borrull, Encarna

2015-01-01

The refractory nature of marine dissolved organic matter (DOM) increases while it travels from surface waters to the deep ocean. This resistant fraction is in part composed of fluorescent humic-like material, which is relatively difficult to metabolize by deep water prokaryotes, and it can also b....... These findings contribute to the understanding of FDOM variability in deep waters and provide valuable information for studies where fluorescent compounds are used in order to track water masses and/or microbial processes.......The refractory nature of marine dissolved organic matter (DOM) increases while it travels from surface waters to the deep ocean. This resistant fraction is in part composed of fluorescent humic-like material, which is relatively difficult to metabolize by deep water prokaryotes, and it can also...

Inhibition of peroxynitrite-mediated DNA strand cleavage and hydroxyl radical formation by aspirin at pharmacologically relevant concentrations: Implications for cancer intervention

Energy Technology Data Exchange (ETDEWEB)

Chen, Wei [Division of Biomedical Sciences, Edward Via Virginia College of Osteopathic Medicine, Virginia Tech Corporate Research Center, Blacksburg, VA 24060 (United States); College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035 (China); Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 (United States); Zhu, Hong; Jia, Zhenquan [Division of Biomedical Sciences, Edward Via Virginia College of Osteopathic Medicine, Virginia Tech Corporate Research Center, Blacksburg, VA 24060 (United States); Li, Jianrong [College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035 (China); Misra, Hara P. [Division of Biomedical Sciences, Edward Via Virginia College of Osteopathic Medicine, Virginia Tech Corporate Research Center, Blacksburg, VA 24060 (United States); Zhou, Kequan, E-mail: kzhou@wayne.edu [Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202 (United States); Li, Yunbo, E-mail: yli@vcom.vt.edu [Division of Biomedical Sciences, Edward Via Virginia College of Osteopathic Medicine, Virginia Tech Corporate Research Center, Blacksburg, VA 24060 (United States)

2009-12-04

Epidemiological studies have suggested that the long-term use of aspirin is associated with a decreased incidence of human malignancies, especially colorectal cancer. Since accumulating evidence indicates that peroxynitrite is critically involved in multistage carcinogenesis, this study was undertaken to investigate the ability of aspirin to inhibit peroxynitrite-mediated DNA damage. Peroxynitrite and its generator 3-morpholinosydnonimine (SIN-1) were used to cause DNA strand breaks in {phi}X-174 plasmid DNA. We demonstrated that the presence of aspirin at concentrations (0.25-2 mM) compatible with amounts in plasma during chronic anti-inflammatory therapy resulted in a significant inhibition of DNA cleavage induced by both peroxynitrite and SIN-1. Moreover, the consumption of oxygen caused by 250 {mu}M SIN-1 was found to be decreased in the presence of aspirin, indicating that aspirin might affect the auto-oxidation of SIN-1. Furthermore, EPR spectroscopy using 5,5-dimethylpyrroline-N-oxide (DMPO) as a spin trap demonstrated the formation of DMPO-hydroxyl radical adduct (DMPO-OH) from authentic peroxynitrite, and that aspirin at 0.25-2 mM potently diminished the radical adduct formation in a concentration-dependent manner. Taken together, these results demonstrate for the first time that aspirin at pharmacologically relevant concentrations can inhibit peroxynitrite-mediated DNA strand breakage and hydroxyl radical formation. These results may have implications for cancer intervention by aspirin.

Inhibition of peroxynitrite-mediated DNA strand cleavage and hydroxyl radical formation by aspirin at pharmacologically relevant concentrations: Implications for cancer intervention

International Nuclear Information System (INIS)

Chen, Wei; Zhu, Hong; Jia, Zhenquan; Li, Jianrong; Misra, Hara P.; Zhou, Kequan; Li, Yunbo

2009-01-01

Epidemiological studies have suggested that the long-term use of aspirin is associated with a decreased incidence of human malignancies, especially colorectal cancer. Since accumulating evidence indicates that peroxynitrite is critically involved in multistage carcinogenesis, this study was undertaken to investigate the ability of aspirin to inhibit peroxynitrite-mediated DNA damage. Peroxynitrite and its generator 3-morpholinosydnonimine (SIN-1) were used to cause DNA strand breaks in φX-174 plasmid DNA. We demonstrated that the presence of aspirin at concentrations (0.25-2 mM) compatible with amounts in plasma during chronic anti-inflammatory therapy resulted in a significant inhibition of DNA cleavage induced by both peroxynitrite and SIN-1. Moreover, the consumption of oxygen caused by 250 μM SIN-1 was found to be decreased in the presence of aspirin, indicating that aspirin might affect the auto-oxidation of SIN-1. Furthermore, EPR spectroscopy using 5,5-dimethylpyrroline-N-oxide (DMPO) as a spin trap demonstrated the formation of DMPO-hydroxyl radical adduct (DMPO-OH) from authentic peroxynitrite, and that aspirin at 0.25-2 mM potently diminished the radical adduct formation in a concentration-dependent manner. Taken together, these results demonstrate for the first time that aspirin at pharmacologically relevant concentrations can inhibit peroxynitrite-mediated DNA strand breakage and hydroxyl radical formation. These results may have implications for cancer intervention by aspirin.

Degradation of vinasse in soil under different humidity levels: CO sub 2 liberation, microbial biomass formation and immobilization of added nitrogen. Decomposicao de vinhaca em solo sob diferentes niveis de umidade: liberacao de CO sub 2 , formacao de biomassa microbiana e imobilizacao do nitrogenio adicionado

Energy Technology Data Exchange (ETDEWEB)

Minhoni, M T.A. [UNESP, Botucatu, SP (Brazil). Dept. de Defesa Fitossanitaria; Cerri, C C [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)

1987-01-01

Degradation of vinasse added to a sandy Red-Yellow Latosol at the rate of 200m{sup 3}/ha and kept at 40,60 and 80% of the holding capacity (w.h.c.), was studied and compared for liberation of CO{sub 2}, formation of microbial biomass and immobilization of nitrogen added. The CO{sub 2} liberated was evaluated by NaOH retention followed by titration with HCl. The microbial biomass was determined by using gamma radiation as biocide. Nitrogen immobilization was determined using the Kjeldahl method and {sup 15}N enrichment according to Rittemberg's method. Soil moisture, which affected the oxygen level of the soil, had a significant influence in CO{sub 2} liberation, formation of microbial biomassa and nitrogen immobilization. Samples kept under drier conditions (40% w.h.c.) showed initially greater Co{sub 2} liberation. However, at the end of 3 month incubation period, total carbon evolved was similar at all misture levels used, with an average of 3805{mu}g C/g soil. The microbial biomass showed greater formation for the drier samples (40% w.h.c.), reaching a maximum of 519{mu}g C/g soil. Immobilization of the N added showed an increasing initial rate, which was greater with dryness of the soil, followed by stabilization. Nevertheless, at the end of 3 month incubation period, the percentages of immobilization were similar and about 40% of total {sup 15}N irrespective of the soil moisture content. Therefore, the increasing rate of carbon assimilation was not totally acompanied by an increasing immobilization for the N added. The greatest intensity was reached by CO{sub 2} liberation in residue degradation, 2/3 of the carbon having evolved to CO{sub 2} and than 1/3 having been immobilized by the microbial biomass. (author).

Mast cells mediate malignant pleural effusion formation.

Science.gov (United States)

Giannou, Anastasios D; Marazioti, Antonia; Spella, Magda; Kanellakis, Nikolaos I; Apostolopoulou, Hara; Psallidas, Ioannis; Prijovich, Zeljko M; Vreka, Malamati; Zazara, Dimitra E; Lilis, Ioannis; Papaleonidopoulos, Vassilios; Kairi, Chrysoula A; Patmanidi, Alexandra L; Giopanou, Ioanna; Spiropoulou, Nikolitsa; Harokopos, Vaggelis; Aidinis, Vassilis; Spyratos, Dionisios; Teliousi, Stamatia; Papadaki, Helen; Taraviras, Stavros; Snyder, Linda A; Eickelberg, Oliver; Kardamakis, Dimitrios; Iwakura, Yoichiro; Feyerabend, Thorsten B; Rodewald, Hans-Reimer; Kalomenidis, Ioannis; Blackwell, Timothy S; Agalioti, Theodora; Stathopoulos, Georgios T

2015-06-01

Mast cells (MCs) have been identified in various tumors; however, the role of these cells in tumorigenesis remains controversial. Here, we quantified MCs in human and murine malignant pleural effusions (MPEs) and evaluated the fate and function of these cells in MPE development. Evaluation of murine MPE-competent lung and colon adenocarcinomas revealed that these tumors actively attract and subsequently degranulate MCs in the pleural space by elaborating CCL2 and osteopontin. MCs were required for effusion development, as MPEs did not form in mice lacking MCs, and pleural infusion of MCs with MPE-incompetent cells promoted MPE formation. Once homed to the pleural space, MCs released tryptase AB1 and IL-1β, which in turn induced pleural vasculature leakiness and triggered NF-κB activation in pleural tumor cells, thereby fostering pleural fluid accumulation and tumor growth. Evaluation of human effusions revealed that MCs are elevated in MPEs compared with benign effusions. Moreover, MC abundance correlated with MPE formation in a human cancer cell-induced effusion model. Treatment of mice with the c-KIT inhibitor imatinib mesylate limited effusion precipitation by mouse and human adenocarcinoma cells. Together, the results of this study indicate that MCs are required for MPE formation and suggest that MC-dependent effusion formation is therapeutically addressable.

The Impact of Microbially Influenced Corrosion on Spent Nuclear Fuel and Storage Life

International Nuclear Information System (INIS)

Wolfram, J. H.; Mizia, R. E.; Jex, R.; Nelson, L.; Garcia, K. M.

1996-01-01

A study was performed to evaluate if microbial activity could be considered a threat to spent nuclear fuel integrity. The existing data regarding the impact of microbial influenced corrosion (MIC) on spent nuclear fuel storage does not allow a clear assessment to be made. In order to identify what further data are needed, a literature survey on MIC was accomplished with emphasis on materials used in nuclear fuel fabrication, e.g., A1, 304 SS, and zirconium. In addition, a survey was done at Savannah River, Oak Ridge, Hanford, and the INEL on the condition of their wet storage facilities. The topics discussed were the SNF path forward, the types of fuel, ramifications of damaged fuel, involvement of microbial processes, dry storage scenarios, ability to identify microbial activity, definitions of water quality, and the use of biocides. Information was also obtained at international meetings in the area of biological mediated problems in spent fuel and high level wastes. Topics dis cussed included receiving foreign reactor research fuels into existing pools, synergism between different microbes and other forms of corrosion, and cross contamination

Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

Science.gov (United States)

Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

2016-01-01

In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P nitrogen cycle in recently abandoned croplands.

The Impact of Microbially Influenced Corrosion on Spent Nuclear Fuel and Storage Life

Energy Technology Data Exchange (ETDEWEB)

J. H. Wolfram; R. E. Mizia; R. Jex; L. Nelson; K. M. Garcia

1996-10-01

A study was performed to evaluate if microbial activity could be considered a threat to spent nuclear fuel integrity. The existing data regarding the impact of microbial influenced corrosion (MIC) on spent nuclear fuel storage does not allow a clear assessment to be made. In order to identify what further data are needed, a literature survey on MIC was accomplished with emphasis on materials used in nuclear fuel fabrication, e.g., A1, 304 SS, and zirconium. In addition, a survey was done at Savannah River, Oak Ridge, Hanford, and the INEL on the condition of their wet storage facilities. The topics discussed were the SNF path forward, the types of fuel, ramifications of damaged fuel, involvement of microbial processes, dry storage scenarios, ability to identify microbial activity, definitions of water quality, and the use of biocides. Information was also obtained at international meetings in the area of biological mediated problems in spent fuel and high level wastes. Topics dis cussed included receiving foreign reactor research fuels into existing pools, synergism between different microbes and other forms of corrosion, and cross contamination.

Neurokinin 1 Receptor Mediates Membrane Blebbing and Sheer Stress-Induced Microparticle Formation in HEK293 Cells

Science.gov (United States)

Chen, Panpan; Douglas, Steven D.; Meshki, John; Tuluc, Florin

2012-01-01

Cell-derived microparticles participate in intercellular communication similar to the classical messenger systems of small and macro-molecules that bind to specialized membrane receptors. Microparticles have been implicated in the regulation of a variety of complex physiopathologic processes, such as thrombosis, the control of innate and adaptive immunity, and cancer. The neurokinin 1 receptor (NK1R) is a Gq-coupled receptor present on the membrane of a variety of tissues, including neurons in the central and peripheral nervous system, immune cells, endocrine and exocrine glands, and smooth muscle. The endogenous agonist of NK1R is the undecapeptide substance P (SP). We have previously described intracellular signaling mechanisms that regulate NK1R-mediated rapid cell shape changes in HEK293 cells and U373MG cells. In the present study, we show that the activation of NK1R in HEK293 cells, but not in U373MG cells, leads to formation of sheer-stress induced microparticles that stain positive with the membrane-selective fluorescent dye FM 2–10. SP-induced microparticle formation is independent of elevated intracellular calcium concentrations and activation of NK1R present on HEK293-derived microparticles triggers detectable calcium increase in SP-induced microparticles. The ROCK inhibitor Y27632 and the dynamin inhibitor dynasore inhibited membrane blebbing and microparticle formation in HEK293 cells, strongly suggesting that microparticle formation in this cell type is dependent on membrane blebbing. PMID:23024816

Neurokinin 1 receptor mediates membrane blebbing and sheer stress-induced microparticle formation in HEK293 cells.

Directory of Open Access Journals (Sweden)

Panpan Chen

Full Text Available Cell-derived microparticles participate in intercellular communication similar to the classical messenger systems of small and macro-molecules that bind to specialized membrane receptors. Microparticles have been implicated in the regulation of a variety of complex physiopathologic processes, such as thrombosis, the control of innate and adaptive immunity, and cancer. The neurokinin 1 receptor (NK1R is a Gq-coupled receptor present on the membrane of a variety of tissues, including neurons in the central and peripheral nervous system, immune cells, endocrine and exocrine glands, and smooth muscle. The endogenous agonist of NK1R is the undecapeptide substance P (SP. We have previously described intracellular signaling mechanisms that regulate NK1R-mediated rapid cell shape changes in HEK293 cells and U373MG cells. In the present study, we show that the activation of NK1R in HEK293 cells, but not in U373MG cells, leads to formation of sheer-stress induced microparticles that stain positive with the membrane-selective fluorescent dye FM 2-10. SP-induced microparticle formation is independent of elevated intracellular calcium concentrations and activation of NK1R present on HEK293-derived microparticles triggers detectable calcium increase in SP-induced microparticles. The ROCK inhibitor Y27632 and the dynamin inhibitor dynasore inhibited membrane blebbing and microparticle formation in HEK293 cells, strongly suggesting that microparticle formation in this cell type is dependent on membrane blebbing.

tri-n-butyltin hydride-mediated radical reaction of a 2-iodobenzamide: formation of an unexpected carbon-tin bond

International Nuclear Information System (INIS)

Oliveira, Marcelo T.; Alves, Rosemeire B.; Cesar, Amary; Prado, Maria Auxiliadora F.; Alves, Ricardo J.; Queiroga, Carla G.; Santos, Leonardo S.; Eberlin, Marcos N.

2007-01-01

The tri-n-butyltin hydride-mediated reaction of methyl 2,3-di-O-benzyl-4-O-trans-cinnamyl- 6-deoxy-6-(2-iodobenzoylamino)-α-D-galactopyranoside afforded an unexpected aryltributyltin compound. The structure of this new tetraorganotin(IV) product has been elucidated by 1 H, 13 C NMR spectroscopy, COSY and HMQC experiments and electrospray ionization mass spectrometry (ESI-MS). The formation of this new compound via a radical coupling reaction and a radical addition-elimination process is discussed. (author)

Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model.

Science.gov (United States)

Miki, Takeshi; Ushio, Masayuki; Fukui, Shin; Kondoh, Michio

2010-08-10

Theory and empirical evidence suggest that plant-soil feedback (PSF) determines the structure of a plant community and nutrient cycling in terrestrial ecosystems. The plant community alters the nutrient pool size in soil by affecting litter decomposition processes, which in turn shapes the plant community, forming a PSF system. However, the role of microbial decomposers in PSF function is often overlooked, and it remains unclear whether decomposers reinforce or weaken litter-mediated plant control over nutrient cycling. Here, we present a theoretical model incorporating the functional diversity of both plants and microbial decomposers. Two fundamental microbial processes are included that control nutrient mineralization from plant litter: (i) assimilation of mineralized nutrient into the microbial biomass (microbial immobilization), and (ii) release of the microbial nutrients into the inorganic nutrient pool (net mineralization). With this model, we show that microbial diversity may act as a buffer that weakens plant control over the soil nutrient pool, reversing the sign of PSF from positive to negative and facilitating plant coexistence. This is explained by the decoupling of litter decomposability and nutrient pool size arising from a flexible change in the microbial community composition and decomposition processes in response to variations in plant litter decomposability. Our results suggest that the microbial community plays a central role in PSF function and the plant community structure. Furthermore, the results strongly imply that the plant-centered view of nutrient cycling should be changed to a plant-microbe-soil feedback system, by incorporating the community ecology of microbial decomposers and their functional diversity.

Effect of multiwalled carbon nanotubes on UASB microbial consortium.

Science.gov (United States)

Yadav, Tushar; Mungray, Alka A; Mungray, Arvind K

2016-03-01

The continuous rise in production and applications of carbon nanotubes (CNTs) has grown a concern about their fate and toxicity in the environment. After use, these nanomaterials pass through sewage and accumulate in wastewater treatment plants. Since, such plants rely on biological degradation of wastes; their activity may decrease due to the presence of CNTs. This study investigated the effect of multiwalled carbon nanotubes (MWCNTs) on upflow anaerobic sludge blanket (UASB) microbial activity. The toxic effect on microbial viability, extracellular polymeric substances (EPS), volatile fatty acids (VFA), and biogas generation was determined. The reduction in a colony-forming unit (CFU) was 29 and 58 % in 1 and 100 mg/L test samples, respectively, as compared to control. The volatile fatty acids and biogas production was also found reduced. The scanning electron microscopy (SEM) and fluorescent microscopy images confirmed that the MWCNT mediated microbial cell damage. This damage caused the increase in EPS carbohydrate, protein, and DNA concentration. Fourier transform infrared (FTIR) spectroscopy results supported the alterations in sludge EPS due to MWCNT. Our observations offer a new insight to understand the nanotoxic effect of MWCNTs on UASB microflora in a complex environment system.

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.

Science.gov (United States)

Dini-Andreote, Francisco; Stegen, James C; van Elsas, Jan Dirk; Salles, Joana Falcão

2015-03-17

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages--which provide a larger spatiotemporal scale relative to within stage analyses--revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended--and experimentally testable--conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.

Microbial Transformations of Actinides and Fission Products in Radioactive Waste

Energy Technology Data Exchange (ETDEWEB)

Francis, A. J. [Pohang Univ. Science and Technology, Pohang (Korea, Republic of)

2011-07-01

The environmental factors that can affect microbial growth and activity include moisture, temperature, ph, Eh, availability of organic and inorganic nutrients, and radiation. The microbial activity in a specific repository is influenced by the ambient environment of the repository, and the materials to be emplaced. For example, a repository in unsaturated igneous rock formations such as volcanic tuff rocks at Yucca Mountain is generally expected to be oxidizing; a repository in a hydrologically expected to be oxidizing; a repository in a hydrologically saturated zone, especially in sedimentary rocks, could be reducing. Sedimentary rocks contain a certain amount of organic matter, which may stimulate microbial activities and, thus maintain the repository and its surrounding areas at reducing conditions. Although the impacts of microbial activity on high-level nuclear waste and the long-term performance of the repository have not fully investigated, little microbial activity is expected in the near-field because of the radiation, lack of nutrients and the harsh conditions. However in the far-field microbial effects could be significant. Much of our understanding of the microbial effects on radionuclides stems from studies conducted with selected transuranic elements and fission products and limited studies with low-level radioactive wastes. Significant aerobic- and anaerobic-microbial activity is expected to occur in the waste because of the presence of electron donors and acceptors. The actinides initially may be present as soluble- or insoluble-forms but, after disposal, may be converted from one to the other by microorganisms. The direct enzymatic or indirect non-enzymatic actions of microbes could alter the speciation, solubility, and sorption properties of the actinides, thereby increasing or decreasing their concentrations in solution.

Microbial brokers of insect-plant interactions revisited.

Science.gov (United States)

Douglas, Angela E

2013-07-01

Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis.

The role of microbial iron reduction in the formation of Proterozoic molar tooth structures

Science.gov (United States)

Hodgskiss, Malcolm S. W.; Kunzmann, Marcus; Poirier, André; Halverson, Galen P.

2018-01-01

Molar tooth structures are poorly understood early diagenetic, microspar-filled voids in clay-rich carbonate sediments. They are a common structure in sedimentary successions dating from 2600-720 Ma, but do not occur in rocks older or younger, with the exception of two isolated Ediacaran occurrences. Despite being locally volumetrically significant in carbonate rocks of this age, their formation and disappearance in the geological record remain enigmatic. Here we present iron isotope data, supported by carbon and oxygen isotopes, major and minor element concentrations, and total organic carbon and sulphur contents for 87 samples from units in ten different basins spanning ca. 1900-635 Ma. The iron isotope composition of molar tooth structures is almost always lighter (modal depletion of 2‰) than the carbonate or residue components in the host sediment. We interpret the isotopically light iron in molar tooth structures to have been produced by dissimilatory iron reduction utilising Fe-rich smectites and Fe-oxyhydroxides in the upper sediment column. The microbial conversion of smectite to illite results in a volume reduction of clay minerals (∼30%) while simultaneously increasing pore water alkalinity. When coupled with wave loading, this biogeochemical process is a viable mechanism to produce voids and subsequently precipitate carbonate minerals. The disappearance of molar tooth structures in the mid-Neoproterozoic is likely linked to a combination of a decrease in smectite abundance, a decline in the marine DIC reservoir, and an increase in the concentration of O2 in shallow seawater.

Interaction mediated by the putative tip regions of MdsA and MdsC in the formation of a Salmonella-specific tripartite efflux pump.

Directory of Open Access Journals (Sweden)

Saemee Song

Full Text Available To survive in the presence of a wide range of toxic compounds, gram-negative bacteria expel such compounds via tripartite efflux pumps that span both the inner and outer membranes. The Salmonella-specific MdsAB pump consists of MdsB, a resistance-nodulation-division (RND-type inner membrane transporter (IMT that requires the membrane fusion protein (MFP MdsA, and an outer membrane protein (OMP; MdsC or TolC to form a tripartite efflux complex. In this study, we investigated the role of the putative tip regions of MdsA and its OMPs, MdsC and TolC, in the formation of a functional MdsAB-mediated efflux pump. Comparative analysis indicated that although sequence homologies of MdsA and MdsC with other MFPs and OMPs, respectively, are extremely low, key residues in the putative tip regions of these proteins are well conserved. Mutagenesis studies on these conserved sites demonstrated their importance for the physical and functional interactions required to form an MdsAB-mediated pump. Our studies suggest that, despite differences in the primary amino acid sequences and functions of various OMPs and MFPs, interactions mediated by the conserved tip regions of OMP and MFP are required for the formation of functional tripartite efflux pumps in gram-negative bacteria.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Directory of Open Access Journals (Sweden)

Muneer A. Malla

2018-06-01

Full Text Available Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Extracellular enzymes facilitate electron uptake in biocorrosion and bioelectrosynthesis.

Science.gov (United States)

Deutzmann, Jörg S; Sahin, Merve; Spormann, Alfred M

2015-04-21

Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. The intriguing trait of some microbial organisms to engage in direct electron transfer is thought to be widespread in nature. Consequently, direct uptake of electrons into microbial cells from solid surfaces is assumed

Oncoidal granular iron formation in the Mesoarchaean Pongola Supergroup, southern Africa: Textural and geochemical evidence for biological activity during iron deposition.

Science.gov (United States)

Smith, A J B; Beukes, N J; Gutzmer, J; Czaja, A D; Johnson, C M; Nhleko, N

2017-11-01

We document the discovery of the first granular iron formation (GIF) of Archaean age and present textural and geochemical results that suggest these formed through microbial iron oxidation. The GIF occurs in the Nconga Formation of the ca. 3.0-2.8 Ga Pongola Supergroup in South Africa and Swaziland. It is interbedded with oxide and silicate facies micritic iron formation (MIF). There is a strong textural control on iron mineralization in the GIF not observed in the associated MIF. The GIF is marked by oncoids with chert cores surrounded by magnetite and calcite rims. These rims show laminated domal textures, similar in appearance to microstromatolites. The GIF is enriched in silica and depleted in Fe relative to the interbedded MIF. Very low Al and trace element contents in the GIF indicate that chemically precipitated chert was reworked above wave base into granules in an environment devoid of siliciclastic input. Microbially mediated iron precipitation resulted in the formation of irregular, domal rims around the chert granules. During storm surges, oncoids were transported and deposited in deeper water environments. Textural features, along with positive δ 56 Fe values in magnetite, suggest that iron precipitation occurred through incomplete oxidation of hydrothermal Fe 2+ by iron-oxidizing bacteria. The initial Fe 3+ -oxyhydroxide precipitates were then post-depositionally transformed to magnetite. Comparison of the Fe isotope compositions of the oncoidal GIF with those reported for the interbedded deeper water iron formation (IF) illustrates that the Fe 2+ pathways and sources for these units were distinct. It is suggested that the deeper water IF was deposited from the evolved margin of a buoyant Fe 2+ aq -rich hydrothermal plume distal to its source. In contrast, oncolitic magnetite rims of chert granules were sourced from ambient Fe 2+ aq -depleted shallow ocean water beyond the plume. © 2017 John Wiley & Sons Ltd.

Switchgrass ecotypes alter microbial contribution to deep-soil C

Science.gov (United States)

Roosendaal, Damaris; Stewart, Catherine E.; Denef, Karolien; Follett, Ronald F.; Pruessner, Elizabeth; Comas, Louise H.; Varvel, Gary E.; Saathoff, Aaron; Palmer, Nathan; Sarath, Gautam; Jin, Virginia L.; Schmer, Marty; Soundararajan, Madhavan

2016-05-01

Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on microbial communities down deep in the soil profiles. Microbial dynamics in deeper soils are likely to exert considerable control on ecosystem services, including C and nutrient cycles, due to their involvement in such processes as soil formation and ecosystem biogeochemistry. Differences in root biomass and rooting characteristics of switchgrass ecotypes could lead to distinct differences in belowground microbial biomass and microbial community composition. We quantified root abundance and root architecture and the associated microbial abundance, composition, and rhizodeposit C uptake for two switchgrass ecotypes using stable-isotope probing of microbial phospholipid fatty acids (PLFAs) after 13CO2 pulse-chase labeling. Kanlow, a lowland ecotype with thicker roots, had greater plant biomass above- and belowground (g m-2), greater root mass density (mg cm-3), and lower specific root length (m g-1) compared to Summer, an upland ecotype with finer root architecture. The relative abundance of bacterial biomarkers dominated microbial PLFA profiles for soils under both Kanlow and Summer (55.4 and 53.5 %, respectively; P = 0.0367), with differences attributable to a greater relative abundance of Gram-negative bacteria in soils under Kanlow (18.1 %) compared to soils under Summer (16.3 %; P = 0.0455). The two ecotypes also had distinctly different microbial communities process rhizodeposit C: greater relative atom % 13C excess in Gram-negative bacteria (44.1 ± 2.3 %) under the thicker roots of Kanlow and greater relative atom % 13C excess in saprotrophic fungi under the thinner roots of Summer (48.5 ± 2.2 %). For bioenergy production systems, variation between switchgrass

Electron Transfer Strategies Regulate Carbonate Mineral and Micropore Formation.

Science.gov (United States)

Zeng, Zhirui; Tice, Michael M

2018-01-01

Some microbial carbonates are robust biosignatures due to their distinct morphologies and compositions. However, whether carbonates induced by microbial iron reduction have such features is unknown. Iron-reducing bacteria use various strategies to transfer electrons to iron oxide minerals (e.g., membrane-bound enzymes, soluble electron shuttles, nanowires, as well as different mechanisms for moving over or attaching to mineral surfaces). This diversity has the potential to create mineral biosignatures through manipulating the microenvironments in which carbonate precipitation occurs. We used Shewanella oneidensis MR-1, Geothrix fermentans, and Geobacter metallireducens GS-15, representing three different strategies, to reduce solid ferric hydroxide in order to evaluate their influence on carbonate and micropore formation (micro-size porosity in mineral rocks). Our results indicate that electron transfer strategies determined the morphology (rhombohedral, spherical, or long-chained) of precipitated calcium-rich siderite by controlling the level of carbonate saturation and the location of carbonate formation. Remarkably, electron transfer strategies also produced distinctive cell-shaped micropores in both carbonate and hydroxide minerals, thus producing suites of features that could potentially serve as biosignatures recording information about the sizes, shapes, and physiologies of iron-reducing organisms. Key Words: Microbial iron reduction-Micropore-Electron transfer strategies-Microbial carbonate. Astrobiology 18, 28-36.

Microbial Species and Functional Diversity in Rice Rhizosphere of High-yield Special Ecological Areas

Directory of Open Access Journals (Sweden)

PAN Li-yuan

2016-11-01

Full Text Available Taoyuan, Yunnan Province is a special eco-site which keeps the highest yield records of rice cultivation in small planting areas. Soil microbial species and functional diversity were evaluated using cultivation method and BIOLOG ecoplates. The results showed that the microbial community of the high yield region was more abundant, and the total microbial population was 2 times of the control, furthermore, the areas belonged to the healthy "bacteria" soil, which was showed as bacteria > actinomycetes > fungi. Bacteria were the dominant populations in the rhizosphere of high yielding rice field, and the yield formation of rice was not correlated with the depth of soil layers. In order to obtain more species diversity information, Shannon diversity index H, Shannon evenness index E and Simpson index D were analyzed, and the results showed that microbial community diversity and evenness were not the main differences between the high and general yield areas. Then, the functional diversity of soil microbial community was investigated through the average well color development(AWCD and diversity index analyses. The results of AWCD analysis indicated that the metabolic activity of soil microbial community in high yield paddy soils were stronger than the control. Moreover, the difference range from large to small showed as tillering stage > harvest period > seedling period > rotation period, the stronger the rice growth, the greater the difference between the high yield region and the control. At tillering stage and harvest stage, due to the vigorous plant growth, the root exudates were rich, and the microbial communities of high yield paddy soils showed a strong metabolic activity and strong ability to use carbon sources. The results of Shannon, Simpson and McIntosh indices analysis indicated that common microbial species was not a key factor affecting the yield of rice. Tillering stage was a key period for the growth of high yield rice, and many

Biofilm and dental implant: The microbial link

Directory of Open Access Journals (Sweden)

Sangeeta Dhir

2013-01-01

Full Text Available Mouth provides a congenial environment for the growth of the microorganisms as compared to any other part of the human body by exhibiting an ideal nonshedding surface. Dental plaque happens to be a diverse community of the microorganisms found on the tooth surface. Periodontal disease and the peri-implant disease are specific infections that are originating from these resident microbial species when the balance between the host and the microbial pathogenicity gets disrupted. This review discusses the biofilms in relation to the peri-implant region, factors affecting its presence, and the associated treatment to manage this complex microbial colony. Search Methodology: Electronic search of the medline was done with the search words: Implants and biofilms/dental biofilm formation/microbiology at implant abutment interface/surface free energy/roughness and implant, periimplantitis/local drug delivery and dental implant. Hand search across the journals - clinical oral implant research, implant dentistry, journal of dental research, international journal of oral implantology, journal of prosthetic dentistry, perioodntology 2000, journal of periodontology were performed. The articles included in the review comprised of in vivo studies, in vivo (animal and human studies, abstracts, review articles.

Amorphous Ca-phosphate precursors for Ca-carbonate biominerals mediated by Chromohalobacter marismortui

NARCIS (Netherlands)

Rivadeneyra, María Angustias; Martín-Algarra, Agustín; Sánchez-Román, Mónica; Sánchez-Navas, Antonio; Martín-Ramos, José Daniel

Although diverse microbial metabolisms are known to induce the precipitation of carbonate minerals, the mechanisms involved in the bacterial mediation, in particular nucleation, are still debated. The study of aragonite precipitation by Chromohalobacter marismortui during the early stages (3-7 days)

Microbial ecology-based engineering of Microbial Electrochemical Technologies.

Science.gov (United States)

Koch, Christin; Korth, Benjamin; Harnisch, Falk

2018-01-01

Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial Biotechnology 2020; microbiology of fossil fuel resources.

Science.gov (United States)

Head, Ian M; Gray, Neil D

2016-09-01

This roadmap examines the future of microbiology research and technology in fossil fuel energy recovery. Globally, the human population will be reliant on fossil fuels for energy and chemical feedstocks for at least the medium term. Microbiology is already important in many areas relevant to both upstream and downstream activities in the oil industry. However, the discipline has struggled for recognition in a world dominated by geophysicists and engineers despite widely known but still poorly understood microbially mediated processes e.g. reservoir biodegradation, reservoir souring and control, microbial enhanced oil recovery. The role of microbiology is even less understood in developing industries such as shale gas recovery by fracking or carbon capture by geological storage. In the future, innovative biotechnologies may offer new routes to reduced emissions pathways especially when applied to the vast unconventional heavy oil resources formed, paradoxically, from microbial activities in the geological past. However, despite this potential, recent low oil prices may make industry funding hard to come by and recruitment of microbiologists by the oil and gas industry may not be a high priority. With regards to public funded research and the imperative for cheap secure energy for economic growth in a growing world population, there are signs of inherent conflicts between policies aimed at a low carbon future using renewable technologies and policies which encourage technologies which maximize recovery from our conventional and unconventional fossil fuel assets. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

Science.gov (United States)

Cong, Jing; Liu, Xueduan; Lu, Hui; Xu, Han; Li, Yide; Deng, Ye; Li, Diqiang; Zhang, Yuguang

2015-08-20

Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Something new from something old? Fracking stimulated microbial processes

Science.gov (United States)

Wrighton, K. C.; Daly, R. A.; Hoyt, D.; Trexler, R.; McRae, J.; Wilkins, M.; Mouser, P. J.

2015-12-01

Hydraulic fracturing, colloquially known as "fracking", is employed for effective gas and oil recovery in deep shales. This process injects organisms and liquids from the surface into the deep subsurface (~2500 m), exposing microorganisms to high pressures, elevated temperatures, chemical additives, and brine-level salinities. Here we use assembly-based metagenomics to create a metabolic blueprint from an energy-producing Marcellus shale well over a 328-day period. Using this approach we ask the question: What abiotic and biotic factors drive microbial metabolism and thus biogeochemical cycling during natural gas extraction? We found that after 49 days, increased salinity in produced waters corresponded to a shift in the microbial community, with only organisms that encode salinity adaptations detected. We posit that organic compatible solutes, produced by organisms adapting to increased salinity, fuels a methylamine-driven ecosystem in fractured shale. This metabolic network ultimately results in biogenic methane production from members of Methanohalophilus and Methanolobus. Proton NMR validated these genomic hypotheses, with mono-methylamine being highest in the input material, but detected throughout the sampling. Beyond abiotic constraints, our genomic investigations revealed that viruses can be linked to key members of the microbial community, potentially releasing methylamine osmoprotectants and impacting bacterial strain variation. Collectively our results indicate that adaptation to high salinity, metabolism in the absence of oxidized electron acceptors, and viral predation are controlling factors mediating microbial community metabolism during hydraulic fracturing of the deep subsurface.

2010 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 18-23, 2010

Energy Technology Data Exchange (ETDEWEB)

Sarah Ades

2011-07-23

The 2010 Gordon Research Conference on Microbial Stress Responses provides an open and exciting forum for the exchange of scientific discoveries on the remarkable mechanisms used by microbes to survive in nearly every niche on the planet. Understanding these stress responses is critical for our ability to control microbial survival, whether in the context of biotechnology, ecology, or pathogenesis. From its inception in 1994, this conference has traditionally employed a very broad definition of stress in microbial systems. Sessions will cover the major steps of stress responses from signal sensing to transcriptional regulation to the effectors that mediate responses. A wide range of stresses will be represented. Some examples include (but are not limited to) oxidative stress, protein quality control, antibiotic-induced stress and survival, envelope stress, DNA damage, and nutritional stress. The 2010 meeting will also focus on the role of stress responses in microbial communities, applied and environmental microbiology, and microbial development. This conference brings together researchers from both the biological and physical sciences investigating stress responses in medically- and environmentally relevant microbes, as well as model organisms, using cutting-edge techniques. Computational, systems-level, and biophysical approaches to exploring stress responsive circuits will be integrated throughout the sessions alongside the more traditional molecular, physiological, and genetic approaches. The broad range of excellent speakers and topics, together with the intimate and pleasant setting at Mount Holyoke College, provide a fertile ground for the exchange of new ideas and approaches.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

KAUST Repository

Wang, Yong

2015-10-20

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea.

Directory of Open Access Journals (Sweden)

Yong Wang

Full Text Available In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

KAUST Repository

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon B.; Al-Suwailem, Abdulaziz M.; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

Auxin-dependent compositional change in Mediator in ARF7- and ARF19-mediated transcription.

Science.gov (United States)

Ito, Jun; Fukaki, Hidehiro; Onoda, Makoto; Li, Lin; Li, Chuanyou; Tasaka, Masao; Furutani, Masahiko

2016-06-07

Mediator is a multiprotein complex that integrates the signals from transcription factors binding to the promoter and transmits them to achieve gene transcription. The subunits of Mediator complex reside in four modules: the head, middle, tail, and dissociable CDK8 kinase module (CKM). The head, middle, and tail modules form the core Mediator complex, and the association of CKM can modify the function of Mediator in transcription. Here, we show genetic and biochemical evidence that CKM-associated Mediator transmits auxin-dependent transcriptional repression in lateral root (LR) formation. The AUXIN/INDOLE 3-ACETIC ACID 14 (Aux/IAA14) transcriptional repressor inhibits the transcriptional activity of its binding partners AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 by making a complex with the CKM-associated Mediator. In addition, TOPLESS (TPL), a transcriptional corepressor, forms a bridge between IAA14 and the CKM component MED13 through the physical interaction. ChIP assays show that auxin induces the dissociation of MED13 but not the tail module component MED25 from the ARF7 binding region upstream of its target gene. These findings indicate that auxin-induced degradation of IAA14 changes the module composition of Mediator interacting with ARF7 and ARF19 in the upstream region of their target genes involved in LR formation. We suggest that this regulation leads to a quick switch of signal transmission from ARFs to target gene expression in response to auxin.

Investigating the role of biofilms in trihalomethane formation in water distribution systems with a multicomponent model.

Science.gov (United States)

Abokifa, Ahmed A; Yang, Y Jeffrey; Lo, Cynthia S; Biswas, Pratim

2016-11-01

Biofilms are ubiquitous in the pipes of drinking water distribution systems (DWDSs), and recent experimental studies revealed that the chlorination of the microbial carbon associated with the biofilm contributes to the total disinfection by-products (DBPs) formation with distinct mechanisms from those formed from precursors derived from natural organic matter (NOM). A multiple species reactive-transport model was developed to explain the role of biofilms in DBPs formation by accounting for the simultaneous transport and interactions of disinfectants, organic compounds, and biomass. Using parameter values from experimental studies in the literature, the model equations were solved to predict chlorine decay and microbial regrowth dynamics in an actual DWDS, and trihalomethanes (THMs) formation in a pilot-scale distribution system simulator. The model's capability of reproducing the measured concentrations of free chlorine, suspended biomass, and THMs under different hydrodynamic and temperature conditions was demonstrated. The contribution of bacteria-derived precursors to the total THMs production was found to have a significant dependence on the system's hydraulics, seasonal variables, and the quality of the treated drinking water. Under system conditions that promoted fast bacterial re-growth, the transformation of non-microbial into microbial carbon DBP precursors by the biofilms showed a noticeable effect on the kinetics of THMs formation, especially when a high initial chlorine dose was applied. These conditions included elevated water temperature and high concentrations of nutrients in the influent water. The fraction of THMs formed from microbial sources was found to reach a peak of 12% of the total produced THMs under the investigated scenarios. The results demonstrated the importance of integrating bacterial regrowth dynamics in predictive DBPs formation models. Copyright © 2016 Elsevier Ltd. All rights reserved.

Manipulatiaon of Biofilm Microbial Ecology

Energy Technology Data Exchange (ETDEWEB)

Burkhalter, R.; Macnaughton, S.J.; Palmer, R.J.; Smith, C.A.; Whitaker, K.W.; White, D.C.; Zinn, M.; kirkegaard, R.

1998-08-09

The Biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms by generated. The most effective monitoring of biofilm formation, succession and desquamation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in the distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

Manipulation of Biofilm Microbial Ecology

Energy Technology Data Exchange (ETDEWEB)

White, D.C.; Palmer, R.J., Jr.; Zinn, M.; Smith, C.A.; Burkhalter, R.; Macnaughton, S.J.; Whitaker, K.W.; Kirkegaard, R.D.

1998-08-15

The biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms be generated. The most effective monitoring of biofilm formation, succession and desaturation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

Alpha 1-adrenergic receptor-mediated phosphoinositide hydrolysis and prostaglandin E2 formation in Madin-Darby canine kidney cells. Possible parallel activation of phospholipase C and phospholipase A2

International Nuclear Information System (INIS)

Slivka, S.R.; Insel, P.A.

1987-01-01

alpha 1-Adrenergic receptors mediate two effects on phospholipid metabolism in Madin-Darby canine kidney (MDCK-D1) cells: hydrolysis of phosphoinositides and arachidonic acid release with generation of prostaglandin E2 (PGE2). The similarity in concentration dependence for the agonist (-)-epinephrine in eliciting these two responses implies that they are mediated by a single population of alpha 1-adrenergic receptors. However, we find that the kinetics of the two responses are quite different, PGE2 production occurring more rapidly and transiently than the hydrolysis of phosphoinositides. The antibiotic neomycin selectively decreases alpha 1-receptor-mediated phosphatidylinositol 4,5-bisphosphate hydrolysis without decreasing alpha 1-receptor-mediated arachidonic acid release and PGE2 generation. In addition, receptor-mediated inositol trisphosphate formation is independent of extracellular calcium, whereas release of labeled arachidonic acid is largely calcium-dependent. Moreover, based on studies obtained with labeled arachidonic acid, receptor-mediated generation of arachidonic acid cannot be accounted for by breakdown of phosphatidylinositol monophosphate, phosphatidylinositol bisphosphate, or phosphatidic acid. Further studies indicate that epinephrine produces changes in formation or turnover of several classes of membrane phospholipids in MDCK cells. We conclude that alpha 1-adrenergic receptors in MDCK cells appear to regulate phospholipid metabolism by the parallel activation of phospholipase C and phospholipase A2. This parallel activation of phospholipases contrasts with models described in other systems which imply sequential activation of phospholipase C and diacylglycerol lipase or phospholipase A2

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces.

Science.gov (United States)

Tecon, Robin; Or, Dani

2017-03-06

Mounting evidence suggests that natural microbial communities exhibit a high level of spatial organization at the micrometric scale that facilitate ecological interactions and support biogeochemical cycles. Microbial patterns are difficult to study definitively in natural environments due to complex biodiversity, observability and variable physicochemical factors. Here, we examine how trophic dependencies give rise to self-organized spatial patterns of a well-defined bacterial consortium grown on hydrated surfaces. The model consortium consisted of two Pseudomonas putida mutant strains that can fully degrade the aromatic hydrocarbon toluene. We demonstrated that obligate cooperation in toluene degradation (cooperative mutualism) favored convergence of 1:1 partner ratio and strong intermixing at the microscale (10-100 μm). In contrast, competition for benzoate, a compound degraded independently by both strains, led to distinct segregation patterns. Emergence of a persistent spatial pattern has been predicted for surface attached microbial activity in liquid films that mediate diffusive exchanges while permitting limited cell movement (colony expansion). This study of a simple microbial consortium offers mechanistic glimpses into the rules governing the assembly and functioning of complex sessile communities, and points to general principles of spatial organization with potential applications for natural and engineered microbial systems.

Growth-Phase Sterigmatocystin Formation on Lactose Is Mediated via Low Specific Growth Rates in Aspergillus nidulans

Directory of Open Access Journals (Sweden)

Zoltán Németh

2016-11-01

Full Text Available Seed contamination with polyketide mycotoxins such as sterigmatocystin (ST produced by Aspergilli is a worldwide issue. The ST biosynthetic pathway is well-characterized in A. nidulans, but regulatory aspects related to the carbon source are still enigmatic. This is particularly true for lactose, inasmuch as some ST production mutant strains still synthesize ST on lactose but not on other carbon substrates. Here, kinetic data revealed that on d-glucose, ST forms only after the sugar is depleted from the medium, while on lactose, ST appears when most of the carbon source is still available. Biomass-specified ST production on lactose was significantly higher than on d-glucose, suggesting that ST formation may either be mediated by a carbon catabolite regulatory mechanism, or induced by low specific growth rates attainable on lactose. These hypotheses were tested by d-glucose limited chemostat-type continuous fermentations. No ST formed at a high growth rate, while a low growth rate led to the formation of 0.4 mg·L−1 ST. Similar results were obtained with a CreA mutant strain. We concluded that low specific growth rates may be the primary cause of mid-growth ST formation on lactose in A. nidulans, and that carbon utilization rates likely play a general regulatory role during biosynthesis.

Microbial Endocrinology in the Pathogenesis of Infectious Disease.

Science.gov (United States)

Lyte, Mark

2016-04-01

Microbial endocrinology represents the intersection of two seemingly disparate fields, microbiology and neurobiology, and is based on the shared presence of neurochemicals that are exactly the same in host as well as in the microorganism. The ability of microorganisms to not only respond to, but also produce, many of the same neurochemicals that are produced by the host, such as during periods of stress, has led to the introduction of this evolutionary-based mechanism which has a role in the pathogenesis of infectious disease. The consideration of microbial endocrinology-based mechanisms has demonstrated, for example, that the prevalent use of catecholamine-based synthetic drugs in the clinical setting contributes to the formation of biofilms in indwelling medical devices. Production of neurochemicals by microorganisms most often employs the same biosynthetic pathways as those utilized by the host, indicating that acquisition of host neurochemical-based signaling system in the host may have been acquired due to lateral gene transfer from microorganisms. That both host and microorganism produce and respond to the very same neurochemicals means that there is bidirectionality contained with the theoretical underpinnings of microbial endocrinology. This can be seen in the role of microbial endocrinology in the microbiota-gut-brain axis and its relevance to infectious disease. Such shared pathways argue for a role of microorganism-neurochemical interactions in infectious disease.

Formation of Fructose-Mediated Advanced Glycation End Products and Their Roles in Metabolic and Inflammatory Diseases.

Science.gov (United States)

Gugliucci, Alejandro

2017-01-01

Fructose is associated with the biochemical alterations that promote the development of metabolic syndrome (MetS), nonalcoholic fatty liver disease, and type 2 diabetes. Its consumption has increased in parallel with MetS. It is metabolized by the liver, where it stimulates de novo lipogenesis. The triglycerides synthesized lead to hepatic insulin resistance and dyslipidemia. Fructose-derived advanced glycation end products (AGEs) may be involved via the Maillard reaction. Fructose has not been a main focus of glycation research because of the difficulty in measuring its adducts, and, more importantly, because although it is 10 times more reactive than glucose, its plasma concentration is only 1% of that of glucose. In this focused review, I summarize exogenous and endogenous fructose metabolism, fructose glycation, and in vitro, animal, and human data. Fructose is elevated in several tissues of diabetic patients where the polyol pathway is active, reaching the same order of magnitude as glucose. It is plausible that the high reactivity of fructose, directly or via its metabolites, may contribute to the formation of intracellular AGEs and to vascular complications. The evidence, however, is still unconvincing. Two areas that have been overlooked so far and should be actively explored include the following: 1) enteral formation of fructose AGEs, generating an inflammatory response to the receptor for AGEs (which may explain the strong association between fructose consumption and asthma, chronic bronchitis, and arthritis); and 2) inactivation of hepatic AMP-activated protein kinase by a fructose-mediated increase in methylglyoxal flux (perpetuating lipogenesis, fatty liver, and insulin resistance). If proven correct, these mechanisms would put the fructose-mediated Maillard reaction in the limelight again as a contributing factor in chronic inflammatory diseases and MetS. © 2017 American Society for Nutrition.

Sub-soil microbial activity under rotational cotton crops in Australia

Science.gov (United States)

Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

2016-04-01

Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

Performance of Microbial Concrete Developed Using Bacillus Subtilus JC3

Science.gov (United States)

Rao, M. V. Seshagiri; Reddy, V. Srinivasa; Sasikala, Ch.

2017-12-01

Concrete is vulnerable to deterioration, corrosion, and cracks, and the consequent damage and loss of strength requires immensely expensive remediation and repair. So need for special concrete that they would respond to crack formation with an autonomous self-healing action lead to research and development of microbial concrete. The microbial concrete works on the principle of calcite mineral precipitation by a specific group of alkali-resistant spore-forming bacteria related to the genus Bacillus called Bacillus subtilis JC3, this phenomenon is called biomineralization or Microbiologically Induced Calcite Crystal Precipitation. Bacillus subtilis JC3, a common soil bacterium, has inherent ability to precipitate calcite crystals continuously which enhances the strength and durability performance of concrete enormously. This microbial concrete can be called as a "Self healing Bacterial Concrete" because it can remediate its cracks by itself without any human intervention and would make the concrete more durable and sustainable. This paper discuss the incorporation of microorganism Bacillus subtilis JC3 (developed at JNTU, India) into concrete and presents the results of experimental investigations carried out to study the improved durability and sustainability characteristics of microbial concrete.

Effects of microbial redox cycling of iron on cast iron pipe corrosion in drinking water distribution systems.

Science.gov (United States)

Wang, Haibo; Hu, Chun; Zhang, Lili; Li, Xiaoxiao; Zhang, Yu; Yang, Min

2014-11-15

Bacterial characteristics in corrosion products and their effect on the formation of dense corrosion scales on cast iron coupons were studied in drinking water, with sterile water acting as a reference. The corrosion process and corrosion scales were characterized by electrochemical and physico-chemical measurements. The results indicated that the corrosion was more rapidly inhibited and iron release was lower due to formation of more dense protective corrosion scales in drinking water than in sterile water. The microbial community and denitrifying functional genes were analyzed by pyrosequencing and quantitative polymerase chain reactions (qPCR), respectively. Principal component analysis (PCA) showed that the bacteria in corrosion products played an important role in the corrosion process in drinking water. Nitrate-reducing bacteria (NRB) Acidovorax and Hydrogenophaga enhanced iron corrosion before 6 days. After 20 days, the dominant bacteria became NRB Dechloromonas (40.08%) with the protective corrosion layer formation. The Dechloromonas exhibited the stronger corrosion inhibition by inducing the redox cycling of iron, to enhance the precipitation of iron oxides and formation of Fe3O4. Subsequently, other minor bacteria appeared in the corrosion scales, including iron-respiring bacteria and Rhizobium which captured iron by the produced siderophores, having a weaker corrosion-inhibition effect. Therefore, the microbially-driven redox cycling of iron with associated microbial capture of iron caused more compact corrosion scales formation and lower iron release. Copyright © 2014 Elsevier Ltd. All rights reserved.

Synbiotic preparation with Lactic acid bacteria and inulin as a functional food: In vivo evaluation of microbial activities, and preneoplastic aberrant crypt foci

Directory of Open Access Journals (Sweden)

Chaiyavat CHAIYASUT

Full Text Available Abstract Host microbiome and metabolome are associated with the incidence of colorectal cancer (CC, one of the major health problems in developed countries. The pro and prebiotic supplementation helps to improve the host health. Inulin is one such prebiotic used for the enhancement of naïve probiotic bacterial population. This paper explains the impact of inulin (PRE extracted from Jerusalem artichoke (JA, Lactobacillus plantarum HII11 (PRO, and synbiotic (SYN; inulin + L. plantarum HII11 preparation on Azoxymethane mediated CC induced rat model with respect to changes in microbial load, microbial enzymes, and preneoplastic aberrant crypt foci. The results suggested that the PRE and SYN supplementation effectively reduced the selected pathogenic bacteria (Salmonella spp., and Escherichia coli, microbial enzymes and increased the probiotic load. The intervention of SYN significantly reduced the colonic ACF in CC model. The study results revealed that the supplementation of SYN diet (inulin and L. plantarum HII11 protects the AOM-mediated colon cancer induced host.

Peatland Microbial Carbon Use Under Warming using Isotopic Fractionation

Science.gov (United States)

Gutknecht, J.

2016-12-01

Peatlands are a critical natural resource, especially in their role as carbon sinks. Most of the world's peatlands are located in Northern ecosystems where the climate is changing at a rapid pace, and there is great interest and concern with how climate change will influence them. Although studies regarding the response of peatlands to climate change have emerged, the microbial mediation of C cycling in these systems is still less well understood. In this study, 13CPLFA analysis was used to characterize the microbial community and it's carbon use at the Spruce and Peatland Responses Under Climatic and Environmental Change (SPRUCE) Project. The SPRUCE project is an extensive study of the response of peatlands to climatic manipulation in the Marcell Experimental Forest in northern Minnesota. Heating rods were installed in peatland plots where peat is being warmed at several levels including ambient, +2.5, +4.5, +6.75, and +9 degrees Celsius, at a depth of 3 meters, beginning July of 2014. Samples were taken June 2014, September 2014, and June 2015, throughout the depth profile. We found very high microbial, and especially fungal growth at shallow depths, owing in part to the influence of fungal-like lipids present in Sphagnum stems, and in part to dense mycorrhizal colonization in shrub and tree species. Isotopic data shows that microbial biomass has an enriched δ13C lower in the peat profile, indicating as expected that microbes at depth utilize older carbon or carbon more enriched in 13C. The increase over depth in the δ13C signature may also reflect the increased dominance of pre-industrial carbon that is more enriched in 13C. In this early period of warming we did not see clear effects of warming, either due to the highly heterogeneous microbial growth across the bog, or to the short term deep warming only. We expect that with the initiation of aboveground warming in July 2016, warming will begin to show stronger effects on microbial C cycling.

Recognition of microbial glycolipids by Natural Killer T cells

Directory of Open Access Journals (Sweden)

Dirk Michael Zajonc

2015-08-01

Full Text Available T cells can recognize microbial antigens when presented by dedicated antigen-presenting molecules. While peptides are presented by classical members of the Major Histocompatibility (MHC family (MHC I and II, lipids, glycolipids and lipopeptides can be presented by the non-classical MHC member CD1. The best studied subset of lipid-reactive T cells are Type I Natural killer T (iNKT cells that recognize a variety of different antigens when presented by the non-classical MHCI homolog CD1d. iNKT cells have been shown to be important for the protection against various microbial pathogens, including B. burgdorferi the causative agents of Lyme disease and S. pneumoniae, which causes pneumococcal meningitis and community-acquired pneumonia. Both pathogens carry microbial glycolipids that can trigger the T cell antigen receptor (TCR, leading to iNKT cell activation. iNKT cells have an evolutionary conserved TCR alpha chain, yet retain the ability to recognize structurally diverse glycolipids. They do so using a conserved recognition mode, in which the TCR enforces a conserved binding orientation on CD1d. TCR binding is accompanied by structural changes within the TCR binding site of CD1d, as well as the glycolipid antigen itself. In addition to direct recognition of microbial antigens, iNKT cells can also be activated by a combination of cytokines (IL-12/IL-18 and TCR stimulation. Many microbes carry TLR antigens and microbial infections can lead to TLR activation. The subsequent cytokine response in turn lower the threshold of TCR mediated iNKT cell activation, especially when weak microbial or even self-antigens are presented during the cause of the infection. In summary, iNKT cells can be directly activated through TCR triggering of strong antigens, while cytokines produced by the innate immune response may be necessary for TCR triggering and iNKT cell activation in the presence of weak antigens. Here we will review the molecular basis of iNKT cell

Protein kinase C mediates platelet secretion and thrombus formation through protein kinase D2.

Science.gov (United States)

Konopatskaya, Olga; Matthews, Sharon A; Harper, Matthew T; Gilio, Karen; Cosemans, Judith M E M; Williams, Christopher M; Navarro, Maria N; Carter, Deborah A; Heemskerk, Johan W M; Leitges, Michael; Cantrell, Doreen; Poole, Alastair W

2011-07-14

Platelets are highly specialized blood cells critically involved in hemostasis and thrombosis. Members of the protein kinase C (PKC) family have established roles in regulating platelet function and thrombosis, but the molecular mechanisms are not clearly understood. In particular, the conventional PKC isoform, PKCα, is a major regulator of platelet granule secretion, but the molecular pathway from PKCα to secretion is not defined. Protein kinase D (PKD) is a family of 3 kinases activated by PKC, which may represent a step in the PKC signaling pathway to secretion. In the present study, we show that PKD2 is the sole PKD member regulated downstream of PKC in platelets, and that the conventional, but not novel, PKC isoforms provide the upstream signal. Platelets from a gene knock-in mouse in which 2 key phosphorylation sites in PKD2 have been mutated (Ser707Ala/Ser711Ala) show a significant reduction in agonist-induced dense granule secretion, but not in α-granule secretion. This deficiency in dense granule release was responsible for a reduced platelet aggregation and a marked reduction in thrombus formation. Our results show that in the molecular pathway to secretion, PKD2 is a key component of the PKC-mediated pathway to platelet activation and thrombus formation through its selective regulation of dense granule secretion.

Biochar and microbial signaling: production conditions determine effects on microbial communication

Science.gov (United States)

Masiello, Caroline A.; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R.; Rudgers, Jennifer A.; Wagner, Daniel S.; Zygourakis, Kyriacos; Silberg, Jonathan J.

2013-01-01

Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700°C (surface area of 301 m2/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300°C (surface area of 3 m2/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops. PMID:24066613

Biochar and microbial signaling: production conditions determine effects on microbial communication.

Science.gov (United States)

Masiello, Caroline A; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R; Rudgers, Jennifer A; Wagner, Daniel S; Zygourakis, Kyriacos; Silberg, Jonathan J

2013-10-15

Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m(2)/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m(2)/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

NARCIS (Netherlands)

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

Continuous power generation and microbial community structure of the anode biofilms in a three-stage microbial fuel cell system

Energy Technology Data Exchange (ETDEWEB)

Chung, Kyungmi; Okabe, Satoshi [Hokkaido Univ., Sapporo (Japan). Dept. of Urban and Environmental Engineering

2009-07-15

A mediator-less three-stage two-chamber microbial fuel cell (MFC) system was developed and operated continuously for more than 1.5 years to evaluate continuous power generation while treating artificial wastewater containing glucose (10 mM) concurrently. A stable power density of 28 W/m3 was attained with an anode hydraulic retention time of 4.5 h and phosphate buffer as the cathode electrolyte. An overall dissolved organic carbon removal ratio was about 85%, and coulombic efficiency was about 46% in this MFC system. We also analyzed the microbial community structure of anode biofilms in each MFC. Since the environment in each MFC was different due to passing on the products to the next MFC in series, the microbial community structure was different accordingly. The anode biofilm in the first MFC consisted mainly of bacteria belonging to the Gammaproteobacteria, identified as Aeromonas sp., while the Firmicutes dominated the anode biofilms in the second and third MFCs that were mainly fed with acetate. Cyclic voltammetric results supported the presence of a redox compound(s) associated with the anode biofilm matrix, rather than mobile (dissolved) forms, which could be responsible for the electron transfer to the anode. Scanning electron microscopy revealed that the anode biofilms were comprised of morphologically different cells that were firmly attached on the anode surface and interconnected each other with anchor-like filamentous appendages, which might support the results of cyclic voltammetry. (orig.)

Density-dependent microbial turnover improves soil carbon model predictions of long-term litter manipulations

Science.gov (United States)

Georgiou, Katerina; Abramoff, Rose; Harte, John; Riley, William; Torn, Margaret

2017-04-01

Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity via abiotic effects on soil or mediated by changes in plant inputs. Recently, many promising microbial models of soil organic carbon (SOC) decomposition have been proposed to advance understanding and prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the sources of instability in four models that span the range of complexity of these recent microbial models, by sequentially adding complexity to a simple model to include microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We propose a formulation that introduces density-dependence of microbial turnover, which acts to limit population sizes and reduce oscillations. We compare these models to results from 24 long-term C-input field manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that widely used first-order models and microbial models without density-dependence cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures. The proposed formulation improves predictions of long-term C-input changes, and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to common microbial models. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in Earth System Models.

Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial immune system.

Science.gov (United States)

Koo, Yoon; Ka, Donghyun; Kim, Eun-Jin; Suh, Nayoung; Bae, Euiyoung

2013-10-23

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form an RNA-mediated microbial immune system against invading foreign genetic elements. Cas5 proteins constitute one of the most prevalent Cas protein families in CRISPR-Cas systems and are predicted to have RNA recognition motif (RRM) domains. Cas5d is a subtype I-C-specific Cas5 protein that can be divided into two distinct subgroups, one of which has extra C-terminal residues while the other contains a longer insertion in the middle of its N-terminal RRM domain. Here, we report crystal structures of Cas5d from Streptococcus pyogenes and Xanthomonas oryzae, which respectively represent the two Cas5d subgroups. Despite a common domain architecture consisting of an N-terminal RRM domain and a C-terminal β-sheet domain, the structural differences between the two Cas5d proteins are highlighted by the presence of a unique extended helical region protruding from the N-terminal RRM domain of X. oryzae Cas5d. We also demonstrate that Cas5d proteins possess not only specific endoribonuclease activity for CRISPR RNAs but also nonspecific double-stranded DNA binding affinity. These findings suggest that Cas5d may play multiple roles in CRISPR-mediated immunity. Furthermore, the specific RNA processing was also observed between S. pyogenes Cas5d protein and X. oryzae CRISPR RNA and vice versa. This cross-species activity of Cas5d provides a special opportunity for elucidating conserved features of the CRISPR RNA processing event. Copyright © 2013 Elsevier Ltd. All rights reserved.

Extreme CO2 disturbance and the resilience of soil microbial communities

Science.gov (United States)

McFarland, Jack W.; Waldrop, Mark P.; Haw, Monica

2013-01-01

Carbon capture and storage (CSS) technology has the potential to inadvertently release large quantities of CO2 through geologic substrates and into surrounding soils and ecosystems. Such a disturbance has the potential to not only alter the structure and function of plant and animal communities, but also soils, soil microbial communities, and the biogeochemical processes they mediate. At Mammoth Mountain, we assessed the soil microbial community response to CO2 disturbance (derived from volcanic ‘cold’ CO2) that resulted in localized tree kill; soil CO2 concentrations in our study area ranged from 0.6% to 60%. Our objectives were to examine how microbial communities and their activities are restructured by extreme CO2 disturbance, and assess the response of major microbial taxa to the reintroduction of limited plant communities following an extensive period (15–20 years) with no plants. We found that CO2-induced tree kill reduced soil carbon (C) availability along our sampling transect. In response, soil microbial biomass decreased by an order of magnitude from healthy forest to impacted areas. Soil microorganisms were most sensitive to changes in soil organic C, which explained almost 60% of the variation for microbial biomass C (MBC) along the CO2gradient. We employed phospholipid fatty acid analysis and quantitative PCR (qPCR) to determine compositional changes among microbial communities in affected areas and found substantial reductions in microbial biomass linked to the loss of soil fungi. In contrast, archaeal populations responded positively to the CO2 disturbance, presumably due to reduced competition of bacteria and fungi, and perhaps unique adaptations to energy stress. Enzyme activities important in the cycling of soil C, nitrogen (N), and phosphorus (P) declined with increasing CO2, though specific activities (per unit MBC) remained stable or increased suggesting functional redundancy among restructured communities. We conclude that both the

Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches.

Science.gov (United States)

Beltrán, Yislem; Cerqueda-García, Daniel; Taş, Neslihan; Thomé, Patricia E; Iglesias-Prieto, Roberto; Falcón, Luisa I

2016-01-01

Coral reefs are among the most productive ecosystems on the planet, but are rapidly declining due to global-warming-mediated changes in the oceans. Particularly for the Caribbean region, Acropora sp. stony corals have lost ∼80% of their original coverage, resulting in vast extensions of dead coral rubble. We analyzed the microbial composition of biofilms that colonize and lithify dead Acropora palmata rubble in the Mexican Caribbean and identified the microbial assemblages that can persist under scenarios of global change, including high temperature and low pH. Lithifying biofilms have a mineral composition that includes aragonite and magnesium calcite (16 mole% MgCO(3)) and calcite, while the mineral phase corresponding to coral skeleton is basically aragonite. Microbial composition of the lithifying biofilms are different in comparison to surrounding biotopes, including a microbial mat, water column, sediments and live A. palmata microbiome. Significant shifts in biofilm composition were detected in samples incubated in mesocosms. The combined effect of low pH and increased temperature showed a strong effect after two-week incubations for biofilm composition. Findings suggest that lithifying biofilms could remain as a secondary structure on reef rubble possibly impacting the functional role of coral reefs. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis.

Directory of Open Access Journals (Sweden)

Chen-hua Li

Full Text Available The conversion of virgin desert into oasis farmland creates two contrasting types of land-cover. During oasis formation with irrigation and fertilizer application, however, the changes in the soil microbial population, which play critical roles in the ecosystem, remain poorly understood. We applied high-throughput pyrosequencing to investigate bacterial and archaeal communities throughout the profile (0-3 m in an experimental field, where irrigation and fertilization began in 1990 and cropped with winter wheat since then. To assess the effects of cultivation, the following treatments were compared with the virgin desert: CK (no fertilizer, PK, NK, NP, NPK, NPKR, and NPKM (R: straw residue; M: manure fertilizer. Irrigation had a greater impact on the overall microbial community than fertilizer application. The greatest impact occurred in topsoil (0-0.2 m, e.g., Cyanobacteria (25% total abundance were most abundant in desert soil, while Actinobacteria (26% were most abundant in oasis soil. The proportions of extremophilic and photosynthetic groups (e.g., Deinococcus-Thermus and Cyanobacteria decreased, while the proportions of R-strategy (e.g., Gammaproteobacteria including Xanthomonadales, nitrifying (e.g., Nitrospirae, and anaerobic bacteria (e.g., Anaerolineae increased throughout the oasis profile. Archaea occurred only in oasis soil. The impact of fertilizer application was mainly reflected in the non-dominant communities or finer taxonomic divisions. Oasis formation led to a dramatic shift in microbial community and enhanced soil enzyme activities. The rapidly increased soil moisture and decreased salt caused by irrigation were responsible for this shift. Furthermore, difference in fertilization and crop growth altered the organic carbon contents in the soil, which resulted in differences of microbial communities within oasis.

Electricity generation using microbial fuel cells

Energy Technology Data Exchange (ETDEWEB)

Mohan, Y.; Manoj Muthu Kumar, S.; Das, D. [Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India)

2008-01-15

Conversion of biomass into electricity is possible using microbial fuel cells (MFCs). The present paper deals with the studies of a two-chambered salt bridge MFC using Enterobacter cloacae IIT-BT 08 in MYG medium. The effect of different electron mediators, concentration of the mediator, ionic strength (salt concentration) of the medium and the surface area of the salt-bridge in contact with the anode and cathode chambers on the power generation in MFCs are reported. In the case of methyl viologen (MV) (0.1 mM) as the electron mediator, the voltage generation was 0.4 V but no current was detected. Different concentrations of methylene blue (MB) were also studied as the mediator. A maximum voltage of 0.37 V was seen at 0.05 mM MB, whereas a maximum current and power of 56.7{mu} A and 19.2{mu} W, respectively, were observed in the case of 0.03 mM MB with a voltage of 0.34 V. The corresponding power density and current density of 9.3mW/m{sup 2} and 27.6mA/m{sup 2}, respectively, were obtained. When the surface area of the salt bridge in contact with the anode and cathode chambers was increased, a proportionate improvement in the power output from 19.2 to 708{mu} W was detected. The maximum power density and current density of 236mW/m{sup 2} and 666.7mA/m{sup 2}, respectively, which are found to be very promising for a salt bridge MFC were observed. (author)

An Evaluation of Subsurface Microbial Activity Conditional to Subsurface Temperature, Porosity, and Permeability at North American Carbon Sequestration Sites

Energy Technology Data Exchange (ETDEWEB)

Wilson, B. [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); National Energy Technology Lab. (NETL), Albany, OR (United States); Mordensky, S. [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); National Energy Technology Lab. (NETL), Albany, OR (United States); Verba, Circe [National Energy Technology Lab. (NETL), Albany, OR (United States); Rabjohns, K. [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); National Energy Technology Lab. (NETL), Albany, OR (United States); Colwell, F. [National Energy Technology Lab. (NETL), Albany, OR (United States); Oregon State Univ., Corvallis, OR (United States). College of Earth, Ocean, and Atmospheric Sciences

2016-06-21

Several nations, including the United States, recognize global climate change as a force transforming the global ecosphere. Carbon dioxide (CO₂) is a greenhouse gas that contributes to the evolving climate. Reduction of atmospheric CO₂ levels is a goal for many nations and carbon sequestration which traps CO₂ in the Earth’s subsurface is one method to reduce atmospheric CO₂ levels. Among the variables that must be considered in developing this technology to a national scale is microbial activity. Microbial activity or biomass can change rock permeability, alter artificial seals around boreholes, and play a key role in biogeochemistry and accordingly may determine how CO₂ is sequestered underground. Certain physical parameters of a reservoir found in literature (e.g., temperature, porosity, and permeability) may indicate whether a reservoir can host microbial communities. In order to estimate which subsurface formations may host microbes, this report examines the subsurface temperature, porosity, and permeability of underground rock formations that have high potential to be targeted for CO₂ sequestration. Of the 268 North American wellbore locations from the National Carbon Sequestration Database (NATCARB; National Energy and Technology Laboratory, 2015) and 35 sites from Nelson and Kibler (2003), 96 sequestration sites contain temperature data. Of these 96 sites, 36 sites have temperatures that would be favorable for microbial survival, 48 sites have mixed conditions for supporting microbial populations, and 11 sites would appear to be unfavorable to support microbial populations. Future studies of microbe viability would benefit from a larger database with more formation parameters (e.g. mineralogy, structure, and groundwater chemistry), which would help to increase understanding of where CO₂ sequestration could be most efficiently implemented.

Post-fire spatial patterns of soil nitrogen mineralization and microbial abundance.

Directory of Open Access Journals (Sweden)

Erica A H Smithwick

Full Text Available Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1 quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2 determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA. Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m. Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R²<0.29. Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21(st Century.

Enabling fast electron transfer through both bacterial outer-membrane redox centers and endogenous electron mediators by polyaniline hybridized large-mesoporous carbon anode for high-performance microbial fuel cells

International Nuclear Information System (INIS)

Zou, Long; Qiao, Yan; Zhong, Canyu; Li, Chang Ming

2017-01-01

Both physical structure and chemical property of an electrode play critical roles in extracellular electron transfer from microbes to electrodes in microbial fuel cells (MFCs). Herein a novel polyaniline hybridized large mesoporous carbon (PANI-LMC) anode is fabricated from natural biomass by nanostructured CaCO 3 template-assisted carbonization followed by in situ chemical polymerizing PANI to enable fast extracellular electron transfer, in which the LMC with rich disorder-interconnected large mesopores (∼20−50 nm) and large surface area facilitates a fast mediated electron transfer through electron mediators, while the decorated PANI on LMC surface enables the direct electron transfer via bacterial outer-membrane redox centers. Owing to the unique synergistic effect from both excellent electron transfer paths, the PANI-LMC hybrid anode harvests high power electricity with a maximum output power density of 1280 mW m −2 in Shewanella putrefaciens CN32 MFCs, 10-fold higher than that of conventional carbon cloth. The findings from this work suggest a new insight on design of high-efficient anode according to the multiple and flexible electrochemical process for practical MFC applications.

Preparation of a differentially expressed, full-length cDNA expression library by RecA-mediated triple-strand formation with subtractively enriched cDNA fragments

NARCIS (Netherlands)

Hakvoort, T. B.; Spijkers, J. A.; Vermeulen, J. L.; Lamers, W. H.

1996-01-01

We have developed a fast and general method to obtain an enriched, full-length cDNA expression library with subtractively enriched cDNA fragments. The procedure relies on RecA-mediated triple-helix formation of single-stranded cDNA fragments with a double-stranded cDNA plasmid library. The complexes

Microbial Rechargeable Battery

NARCIS (Netherlands)

Molenaar, Sam D.; Mol, Annemerel R.; Sleutels, Tom H.J.A.; Heijne, Ter Annemiek; Buisman, Cees J.N.

2016-01-01

Bioelectrochemical systems hold potential for both conversion of electricity into chemicals through microbial electrosynthesis (MES) and the provision of electrical power by oxidation of organics using microbial fuel cells (MFCs). This study provides a proof of concept for a microbial

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

Science.gov (United States)

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Silver nanoparticles impede the biofilm formation by Pseudomonas aeruginosa and Staphylococcus epidermidis.

Science.gov (United States)

Kalishwaralal, Kalimuthu; BarathManiKanth, Selvaraj; Pandian, Sureshbabu Ram Kumar; Deepak, Venkataraman; Gurunathan, Sangiliyandi

2010-09-01

Biofilms are ensued due to bacteria that attach to surfaces and aggregate in a hydrated polymeric matrix. Formation of these sessile communities and their inherent resistance to anti-microbial agents are the source of many relentless and chronic bacterial infections. Such biofilms are responsible play a major role in development of ocular related infectious diseases in human namely microbial keratitis. Different approaches have been used for preventing biofilm related infections in health care settings. Many of these methods have their own demerits that include chemical based complications; emergent antibiotic resistant strains, etc. silver nanoparticles are renowned for their influential anti-microbial activity. Hence the present study over the biologically synthesized silver nanoparticles, exhibited a potential anti-biofilm activity that was tested in vitro on biofilms formed by Pseudomonas aeruginosa and Staphylococcus epidermidis during 24-h treatment. Treating these organisms with silver nanoparticles resulted in more than 95% inhibition in biofilm formation. The inhibition was known to be invariable of the species tested. As a result this study demonstrates the futuristic application of silver nanoparticles in treating microbial keratitis based on its potential anti-biofilm activity. Copyright 2010 Elsevier B.V. All rights reserved.

Nrp2 is sufficient to instruct circuit formation of mitral-cells to mediate odour-induced attractive social responses.

Science.gov (United States)

Inokuchi, Kasumi; Imamura, Fumiaki; Takeuchi, Haruki; Kim, Ryang; Okuno, Hiroyuki; Nishizumi, Hirofumi; Bito, Haruhiko; Kikusui, Takefumi; Sakano, Hitoshi

2017-07-21

Odour information induces various innate responses that are critical to the survival of the individual and for the species. An axon guidance molecule, Neuropilin 2 (Nrp2), is known to mediate targeting of olfactory sensory neurons (primary neurons), to the posteroventral main olfactory bulb (PV MOB) in mice. Here we report that Nrp2-positive (Nrp2 + ) mitral cells (MCs, second-order neurons) play crucial roles in transmitting attractive social signals from the PV MOB to the anterior part of medial amygdala (MeA). Semaphorin 3F, a repulsive ligand to Nrp2, regulates both migration of Nrp2 + MCs to the PV MOB and their axonal projection to the anterior MeA. In the MC-specific Nrp2 knockout mice, circuit formation of Nrp2 + MCs and odour-induced attractive social responses are impaired. In utero, electroporation demonstrates that activation of the Nrp2 gene in MCs is sufficient to instruct their circuit formation from the PV MOB to the anterior MeA.

Ferrihydrite-associated organic matter (OM stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

Directory of Open Access Journals (Sweden)

R. E. Cooper

2017-11-01

Full Text Available The formation of Fe(III oxides in natural environments occurs in the presence of natural organic matter (OM, resulting in the formation of OM–mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III reduction in natural environments most often occurs in the presence of OM–mineral complexes rather than pure Fe(III minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III reduction by Shewanella oneidensis MR-1, a model Fe(III-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite–OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose mimics S. oneidensis under the same experimental Fe(III-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM–ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria during pure ferrihydrite incubations which are known to use Fe(III as an electron sink. Instead, OM–mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and

Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

Science.gov (United States)

Cooper, Rebecca Elizabeth; Eusterhues, Karin; Wegner, Carl-Eric; Totsche, Kai Uwe; Küsel, Kirsten

2017-11-01

The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM-mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM-mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite-OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM-ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM-mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and acetate as an electron

Soil microbial activities beneath Stipa tenacissima L. and in surrounding bare soil

Science.gov (United States)

Novosadová, I.; Ruiz Sinoga, J. D.; Záhora, J.; Fišerová, H.

2010-05-01

Open steppes dominated by Stipa tenacissima L. constitute one of the most representative ecosystems of the semi-arid zones of Eastern Mediterranean Basin (Iberian Peninsula, North of Africa). These steppes show a higher degree of variability in composition and structure. Ecosystem functioning is strongly related to the spatial pattern of grass tussocks. Soils beneath S. tenacissima grass show higher fertility and improved microclimatic conditions, favouring the formation of "resource islands" (Maestre et al., 2007). On the other hand in "resource islands" and in surrounding bare soil exists the belowground zone of influence. The competition for water and resources between plants and microorganisms is strong and mediated trough an enormous variety of exudates and resource depletion intended to regulate soil microbial communities in the rhizosphere, control herbivory, encourage beneficial symbioses, and change chemical and physical properties in soil (Pugnaire et Armas, 2008). Secondary compounds and allelopathy restrict other species growth and contribute to patchy plant distribution. Active root segregation affects not only neighbourś growth but also soil microbial activities. The objective of this study was to assess the effect of Stipa tenacissima on the key soil microbial activities under controlled incubation conditions (basal and potential respiration; net nitrogen mineralization). The experimental plots were located in the province Almería in Sierra de los Filabres Mountains near the village Gérgal (southeast Spain) in the small catchment which is situated between 1090 - 1165 m a.s.l. The area with extent of 82 000 m2 is affected by soil degradation. The climate is semiarid Mediterranean. The mean annual rainfall is of about 240 mm mostly concentrated in autumn and spring. The mean annual temperature is 13.9° C. The studied soil has a loam to sandy clay texture and is classified as Lithosol (FAO-ISRIC and ISSS, 1998). The vegetation of these areas is an

Microbial biosensors

International Nuclear Information System (INIS)

Le Yu; Chen, Wilfred; Mulchandani, Ashok

2006-01-01

A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

Childhood microbial keratitis

Directory of Open Access Journals (Sweden)

Abdullah G Al Otaibi

2012-01-01

Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

Final report - Microbial pathways for the reduction of mercury in saturated subsurface sediments

Energy Technology Data Exchange (ETDEWEB)

Tamar barkay; Lily Young; Gerben Zylstra

2009-08-25

Mercury is a component of mixed wastes that have contaminated vast areas of the deep subsurface as a result of nuclear weapon and energy production. While this mercury is mostly bound to soil constituents episodes of groundwater contamination are known in some cases resulting in potable water super saturated with Hg(0). Microbial processes that reduce Hg(II) to the elemental form Hg(0) in the saturated subsurface sediments may contribute to this problem. When we started the project, only one microbial pathway for the reduction of Hg(II), the one mediated by the mer operon in mercury resistant bacteria was known. As we had previously demonstrated that the mer mediated process occurred in highly contaminated environments (Schaefer et al., 2004), and mercury concentrations in the subsurface were reported to be low (Krabbenhoft and Babiarz, 1992), we hypothesized that other microbial processes might be active in reducing Hg(II) to Hg(0) in saturated subsurface environments. The specific goals of our projects were: (1) Investigating the potential for Hg(II) reduction under varying electron accepting conditions in subsurface sediments and relating these potential to mer gene distribution; and (2) Examining the physiological and biochemical characteristics of the interactions of anaerobic bacteria with mercury. The results are briefly summarized with references to published papers and manuscripts in preparation where details about our research can be found. Additional information may be found in copies of our published manuscripts and conference proceedings, and our yearly reports that were submitted through the RIMS system.

Photosynthetic solar cell using nanostructured proton exchange membrane for microbial biofilm prevention.

Science.gov (United States)

Lee, Dong Hyun; Oh, Hwa Jin; Bai, Seoung Jae; Song, Young Seok

2014-06-24

Unwanted biofilm formation has a detrimental effect on bioelectrical energy harvesting in microbial cells. This issue still needs to be solved for higher power and longer durability and could be resolved with the help of nanoengineering in designing and manufacturing. Here, we demonstrate a photosynthetic solar cell (PSC) that contains a nanostructure to prevent the formation of biofilm by micro-organisms. Nanostructures were fabricated using nanoimprint lithography, where a film heater array system was introduced to precisely control the local wall temperature. To understand the heat and mass transfer phenomena behind the manufacturing and energy harvesting processes of PSC, we carried out a numerical simulation and experimental measurements. It revealed that the nanostructures developed on the proton exchange membrane enable PSC to produce enhanced output power due to the retarded microbial attachment on the Nafion membrane. We anticipate that this strategy can provide a pathway where PSC can ensure more renewable, sustainable, and efficient energy harvesting performance.

Biogeographic patterns of microbial communities from different oil-contaminated fields in China

Energy Technology Data Exchange (ETDEWEB)

Liang, Yuting; Li, Guanghe [School of Environment, Tsinghua University (China); Zhou, Ji zhong [Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma (United States)], email: jzhou@ou.edu

2011-07-01

Some striking biological challenges of the 21st century include linking biodiversity to ecosystem functions, information scaling, and linking genomics to ecology. This paper discusses the biogeographic patterns of microbial communities from various oil-contaminated fields in China. Two kinds of high throughput approaches are used, open format and closed format. Key differences between them are outlined. The GeoChip, or functional gene array (FGA) approach is presented. This is a high throughput tool for linking community structure to functions. Its main advantages are its high resolution and detecting functions. This approach was applied to soils, bioreactors and ground waters, among others. Issues related to specificity, sensitivity and quantification are listed. An overview of the microarray analysis is given. This is applied to the BP oil spill. 100 samples were chosen from representative oil fields to study the biogeographic patterns of microbial communities in China. The complete study is presented with the results.

Secapin, a bee venom peptide, exhibits anti-fibrinolytic, anti-elastolytic, and anti-microbial activities.

Science.gov (United States)

Lee, Kwang Sik; Kim, Bo Yeon; Yoon, Hyung Joo; Choi, Yong Soo; Jin, Byung Rae

2016-10-01

Bee venom contains a variety of peptide constituents that have various biological, toxicological, and pharmacological actions. However, the biological actions of secapin, a venom peptide in bee venom, remain largely unknown. Here, we provide the evidence that Asiatic honeybee (Apis cerana) secapin (AcSecapin-1) exhibits anti-fibrinolytic, anti-elastolytic, and anti-microbial activities. The recombinant mature AcSecapin-1 peptide was expressed in baculovirus-infected insect cells. AcSecapin-1 functions as a serine protease inhibitor-like peptide that has inhibitory effects against plasmin, elastases, microbial serine proteases, trypsin, and chymotrypsin. Consistent with these functions, AcSecapin-1 inhibited the plasmin-mediated degradation of fibrin to fibrin degradation products, thus indicating the role of AcSecapin-1 as an anti-fibrinolytic agent. AcSecapin-1 also inhibited both human neutrophil and porcine pancreatic elastases. Furthermore, AcSecapin-1 bound to bacterial and fungal surfaces and exhibited anti-microbial activity against fungi and gram-positive and gram-negative bacteria. Taken together, our data demonstrated that the bee venom peptide secapin has multifunctional roles as an anti-fibrinolytic agent during fibrinolysis and an anti-microbial agent in the innate immune response. Copyright © 2016 Elsevier Ltd. All rights reserved.

Importance of PGPR application and its effect on microbial activity in maize rhizosphere

Directory of Open Access Journals (Sweden)

Mrkovački Nastasija

2012-01-01

Full Text Available Microorganisms are involved in the formation of soil fertility, both potential and effective. They facilitate the processes of humification and dehumification and play a key role in the cycling of nutrients - macro and microelements. Rhizosphere is the soil in direct contact with plant roots and influenced by plant exudates. Root exudates of maize significantly affect the composition and abundance of microorganisms in the rhizosphere. Bio-fertilizers are microbial fertilizers composed of highly effective strains of bacteria, algae and fungi isolated from soil. Their application activates microbial processes that secure a better and steadier supply of plants with nitrogen, phosphorus, potassium and some micronutrients. The application of PGPR-containing biofertilizers reduces the need for expensive nitrogen fertilizers, facilitates phosphorus uptake by plants and affects the direction and dynamics of microbial processes.

The microbiology of oral lichen planus: Is microbial infection the cause of oral lichen planus?

Science.gov (United States)

Baek, K; Choi, Y

2018-02-01

Oral lichen planus (OLP) is a variant of lichen planus (LP), a common chronic mucocutaneous inflammatory disease. Cutaneous lesions of LP are self-limiting, but OLP lesions are non-remissive, alternating periods of exacerbation and quiescence, and only symptomatic treatments exist for OLP. The precise etiology and pathogenesis of OLP are hardly understood, which is a major obstacle to the development of new therapeutics for this disease. OLP is considered a T-cell-mediated inflammatory disease. Although various antigens have been considered, what actually triggers the inflammatory response of T cells is unknown. Suggested predisposing factors include genetic factors, stress, trauma, and infection. The aim of this review was to determine whether microbial infection can cause OLP. We first reviewed the association between OLP and microbial factors, including viral, fungal, and bacterial infections. In addition, each microbial factor associated with OLP was assessed by modified guidelines of Fredricks and Relman to determine whether it establishes a causal relationship. In conclusion, no microbial factor yet fulfills the guidelines to establish the causality of OLP. By focusing on the unclarified issues, however, the potential roles of microbial factors in the pathogenesis of OLP will be soon elucidated. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Limiting Factors for Microbial Fe(III)-Reduction In a Landfill Leachate Polluted Aquifer (Vejen, Denmark)

DEFF Research Database (Denmark)

Albrechtsen, Hans-Jørgen; Heron, Gorm; Christensen, Thomas Højlund

1995-01-01

Aquifer sediment samples from two locations within the anaerobic leachate plume of a municipal landfill were compared with respect to microbiology (especially Fe(III)-reduction) and geochemistry. The samples close to the landfill were characterized by low contents of Fe(III), whereas samples from...... the more distant cluster were rich in Fe(III)-oxides. The active microbial population seemed to be less dense in samples more distant from the landfill (measured by ATP and phospholipid fatty acids (PLFA)), but the microbial communities were very similar in the two sample clusters according...... to the composition of PLFA. Very little, if any, Fe(III)-reduction was observed close to the landfill, but all the more distant samples showed evident microbially mediated Fe(III)-reduction. After amendment with both acetate and Fe(III), all the samples showed a potential for Fe(III)-reduction, and the in situ Fe...

Methods in gut microbial ecology for ruminants

International Nuclear Information System (INIS)

Makkar, H.P.S.; McSweeney, C.S.

2005-01-01

This book presents a comprehensive up-to-date account of the methodologies and protocols for conventional and modern molecular techniques that are currently in use for studying the gut microbial ecology of ruminants. Each chapter has been contributed by experts in the field and methods have been presented in a recipe-like format designed for direct practical use in the laboratory and also to provide insight into the most appropriate techniques, their applications and the type of information that could be expected. The techniques and procedures described are also relevant and adaptable to other gastrointestinal ecosystems and the microbiology of anaerobic environments in general. This manual will 'demystify' the methods in molecular microbial ecology for readers who are novice in the field but are excited by the prospects of this technology. It would also be invaluable for the experienced workers striving for giving new dimension to their research - expanding the work in other fields and initiating cross-cutting activities

The group A streptococcal collagen-like protein 1, Scl1, mediates biofilm formation by targeting the EDA-containing variant of cellular fibronectin expressed in wounded tissue

Science.gov (United States)

Oliver-Kozup, Heaven; Martin, Karen H.; Schwegler-Berry, Diane; Green, Brett J.; Betts, Courtney; Shinde, Arti V.; Van De Water, Livingston; Lukomski, Slawomir

2012-01-01

Summary Wounds are known to serve as portals of entry for group A Streptococcus (GAS). Subsequent tissue colonization is mediated by interactions between GAS surface proteins and host extracellular matrix components. We recently reported that the streptococcal collagen-like protein-1, Scl1, selectively binds the cellular form of fibronectin (cFn) and also contributes to GAS biofilm formation on abiotic surfaces. One structural feature of cFn, which is predominantly expressed in response to tissue injury, is the presence of a spliced variant containing extra domain A (EDA/EIIIA). We now report that GAS biofilm formation is mediated by the Scl1 interaction with EDA-containing cFn. Recombinant Scl1 proteins that bound cFn also bound recombinant EDA within the C-C′ loop region recognized by the α9β1 integrin. The extracellular 2-D matrix derived from human dermal fibroblasts supports GAS adherence and biofilm formation. Altogether, this work identifies and characterizes a novel molecular mechanism by which GAS utilizes Scl1 to specifically target an extracellular matrix component that is predominantly expressed at the site of injury in order to secure host tissue colonization. PMID:23217101

Vasculitis related to viral and other microbial agents.

Science.gov (United States)

Teng, Gim Gee; Chatham, W Winn

2015-04-01

Vasculitis due to infection may occur as a consequence of the inflammation of vessel walls due to direct or contiguous infection, type II or immune complex-mediated reaction, cell-mediated hypersensitivity, or inflammation due to immune dysregulation triggered by bacterial toxin and/or superantigen production. As immunosuppressive therapy administered in the absence of antimicrobial therapy may increase morbidity and fail to effect the resolution of infection-associated vascular inflammation, it is important to consider infectious entities as potential inciting factors in vasculitis syndromes. The causality between infection and vasculitis has been established in hepatitis B-associated polyarteritis nodosa (HBV-PAN) and hepatitis C-associated (cryoglobulinemic) vasculitis (HCV-CV). The review summarizes the recent literature on the pathophysiological mechanisms and the approaches to the management of HBV-PAN and HCV-CV. Roles of other viral and microbial infections, which either manifest as vasculitic syndromes or are implicated in the pathogenesis of primary vasculitides, are also discussed. Copyright © 2015. Published by Elsevier Ltd.

Clathrin-Mediated Auxin Efflux and Maxima Regulate Hypocotyl Hook Formation and Light-Stimulated Hook Opening in Arabidopsis.

Science.gov (United States)

Yu, Qinqin; Zhang, Ying; Wang, Juan; Yan, Xu; Wang, Chao; Xu, Jian; Pan, Jianwei

2016-01-04

The establishment of auxin maxima by PIN-FORMED 3 (PIN3)- and AUXIN RESISTANT 1/LIKE AUX1 (LAX) 3 (AUX1/LAX3)-mediated auxin transport is essential for hook formation in Arabidopsis hypocotyls. Until now, however, the underlying regulatory mechanism has remained poorly understood. Here, we show that loss of function of clathrin light chain CLC2 and CLC3 genes enhanced auxin maxima and thereby hook curvature, alleviated the inhibitory effect of auxin overproduction on auxin maxima and hook curvature, and delayed blue light-stimulated auxin maxima reduction and hook opening. Moreover, pharmacological experiments revealed that auxin maxima formation and hook curvature in clc2 clc3 were sensitive to auxin efflux inhibitors 1-naphthylphthalamic acid and 2,3,5-triiodobenzoic acid but not to the auxin influx inhibitor 1-naphthoxyacetic acid. Live-cell imaging analysis further uncovered that loss of CLC2 and CLC3 function impaired PIN3 endocytosis and promoted its lateralization in the cortical cells but did not affect AUX1 localization. Taken together, these results suggest that clathrin regulates auxin maxima and thereby hook formation through modulating PIN3 localization and auxin efflux, providing a novel mechanism that integrates developmental signals and environmental cues to regulate plant skotomorphogenesis and photomorphogenesis. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

The potential significance of microbial activity in radioactive waste disposal

International Nuclear Information System (INIS)

McCabe, A.M.

1987-12-01

The aim of this report is to assess the potential significance of microbial activity in radioactive waste disposal. It outlines the major factors which need to be considered in order to evaluate the importance of microbiological action. These include water and nutritional sources (particularly carbon) hostile conditions (particularly the effects of radiation and pH), the establishment of pH micro-environments and the degradative effect of microbial metabolic by-products on the disposed waste forms. Before an active microbial population can develop there are certain basic requirements for life. These are outlined and the possibility of colonisation occurring within the chemical, radiological and nutritional constraints of a repository are considered. Once colonisation is assumed, the effect of microbial activity is discussed under five headings, i.e. (i) direct attack, (ii) physical disruption (which includes consideration of fissuring processes and void formation), (iii) gas generation (which may be of particular importance), (iv) radionuclide uptake and finally (v) alteration of groundwater chemistry. Particular attention is paid to the possibility of environments becoming established both within the waste form itself (allowing microbes to attack from the inside of the repository outward) or attack on the encapsulant materials (microbes attacking from the outside inward). (author)

Life in the "plastisphere": microbial communities on plastic marine debris.

Science.gov (United States)

Zettler, Erik R; Mincer, Tracy J; Amaral-Zettler, Linda A

2013-07-02

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

Differential sensitivity of total and active soil microbial communities to drought and forest management.

Science.gov (United States)

Bastida, Felipe; Torres, Irene F; Andrés-Abellán, Manuela; Baldrian, Petr; López-Mondéjar, Rubén; Větrovský, Tomáš; Richnow, Hans H; Starke, Robert; Ondoño, Sara; García, Carlos; López-Serrano, Francisco R; Jehmlich, Nico

2017-10-01

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial

Formation of Fructose-Mediated Advanced Glycation End Products and Their Roles in Metabolic and Inflammatory Diseases12

Science.gov (United States)

2017-01-01

Fructose is associated with the biochemical alterations that promote the development of metabolic syndrome (MetS), nonalcoholic fatty liver disease, and type 2 diabetes. Its consumption has increased in parallel with MetS. It is metabolized by the liver, where it stimulates de novo lipogenesis. The triglycerides synthesized lead to hepatic insulin resistance and dyslipidemia. Fructose-derived advanced glycation end products (AGEs) may be involved via the Maillard reaction. Fructose has not been a main focus of glycation research because of the difficulty in measuring its adducts, and, more importantly, because although it is 10 times more reactive than glucose, its plasma concentration is only 1% of that of glucose. In this focused review, I summarize exogenous and endogenous fructose metabolism, fructose glycation, and in vitro, animal, and human data. Fructose is elevated in several tissues of diabetic patients where the polyol pathway is active, reaching the same order of magnitude as glucose. It is plausible that the high reactivity of fructose, directly or via its metabolites, may contribute to the formation of intracellular AGEs and to vascular complications. The evidence, however, is still unconvincing. Two areas that have been overlooked so far and should be actively explored include the following: 1) enteral formation of fructose AGEs, generating an inflammatory response to the receptor for AGEs (which may explain the strong association between fructose consumption and asthma, chronic bronchitis, and arthritis); and 2) inactivation of hepatic AMP-activated protein kinase by a fructose-mediated increase in methylglyoxal flux (perpetuating lipogenesis, fatty liver, and insulin resistance). If proven correct, these mechanisms would put the fructose-mediated Maillard reaction in the limelight again as a contributing factor in chronic inflammatory diseases and MetS. PMID:28096127

Tracing biosignatures from the Recent to the Jurassic in sabkha-associated microbial mats

Science.gov (United States)

van der Land, Cees; Dutton, Kirsten; Andrade, Luiza; Paul, Andreas; Sherry, Angela; Fender, Tom; Hewett, Guy; Jones, Martin; Lokier, Stephen W.; Head, Ian M.

2017-04-01

Microbial mat ecosystems have been operating at the sediment-fluid interface for over 3400 million years, influencing the flux, transformation and preservation of carbon from the biosphere to the physical environment. These ecosystems are excellent recorders of rapid and profound changes in earth surface environments and biota as they often survive crisis-induced extreme paleoenvironmental conditions. Their biosignatures, captured in the preserved organic matter and the biominerals that form the microbialite rock, constitute a significant tool in understanding geobiological processes and the interactions of the microbial communities with sediments and with the prevailing physical chemical parameters, as well as the environmental conditions at a local and global scale. Nevertheless, the exact pathways of diagenetic organic matter transformation and early-lithification, essential for the accretion and preservation in the geological record as microbialites, are not well understood. The Abu Dhabi coastal sabkha system contains a vast microbial mat belt that is dominated by continuous polygonal and internally-laminated microbial mats across the upper and middle intertidal zones. This modern system is believed to be the best analogue for the Upper Jurassic Arab Formation, which is both a prolific hydrocarbon reservoir and source rock facies in the United Arab Emirates and in neighbouring countries. In order to characterise the processes that lead to the formation of microbialites we investigated the modern and Jurassic system using a multidisciplinary approach, including growth of field-sampled microbial mats under controlled conditions in the laboratory and field-based analysis of microbial communities, mat mineralogy and organic biomarker analysis. In this study, we focus on hydrocarbon biomarker data obtained from the surface of microbial mats actively growing in the intertidal zone of the modern system. By comparing these findings to data obtained from recently

Soil structure and microbial activity dynamics in 20-month field-incubated organic-amended soils

DEFF Research Database (Denmark)

Arthur, Emmanuel; Schjønning, Per; Møldrup, Per

2014-01-01

to determine compressive strength. During incubation, the amount of WDC depended on soil carbon content while the trends correlated with moisture content. Organic amendment only yielded modest decreases (mean of 14% across all sampling times and soils) in WDC, but it was sufficient to stimulate the microbial......Soil structure formation is essential to all soil ecosystem functions and services. This study aims to quantify changes in soil structure and microbial activity during and after field incubation and examine the effect of carbon, organic amendment and clay on aggregate characteristics. Five soils...... community (65–100% increase in FDA). Incubation led to significant macroaggregate formation (>2 mm) for all soils. Friability and strength of newly-formed aggregates were negatively correlated with clay content and carbon content, respectively. Soil workability was best for the kaolinite-rich soil...

INITIAL MICROBIAL ADHESION IS A DETERMINANT FOR THE STRENGTH OF BIOFILM ADHESION

NARCIS (Netherlands)

BUSSCHER, HJ; VANDERMEI, HC; Bos, R.R.M.

1995-01-01

This paper presents a hypothesis on the importance of initial microbial adhesion in the overall process of biofilm formation. The hypothesis is based on the realization that dynamic shear conditions exist in many environments, such as in the oral cavity, or on rocks and ship hulls. Recognizing that

Living Dendrolitic Microbial Mats in Hamelin Pool, Shark Bay, Western Australia

Directory of Open Access Journals (Sweden)

Erica P. Suosaari

2018-06-01

Full Text Available Hamelin Pool, Shark Bay, Western Australia, is home to the largest and most diverse assemblage of living marine stromatolites, with shapes and sizes comparable to ancient structures. A recent field-intensive program revealed seasonally ephemeral occurrences of modern dendrolitic microbial mats forming in intertidal, low energy settings. Dominated by filamentous cyanobacteria, dendrolitic microbial mats are formed when filaments provide a supporting framework as a result of gliding mobility, to build a shrubby morphology. Dendrolites, known throughout the rock record, refer to macroscopic microbialites with mesostuctures composed of unlaminated arborescent structures called shrubs. In these modern examples, thick filaments of Lyngbya aestuarii form the “trunk” of the bush, with finer filaments of Lyngbya fragilis, Phormidium sp. and Schizothrix sp. forming the “branches” These biologically-influenced dendrolitic structures provide insight into the complex interplay of microbial communities and the environment, broadening our understanding of shrub and dendrolite formation throughout the rock record.

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

DEFF Research Database (Denmark)

Weitz, Joshua S.; Stock, Charles A.; Wilhelm, Steven W.

2015-01-01

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities......, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic...

NSF- and SNARE-mediated membrane fusion is required for nuclear envelope formation and completion of nuclear pore complex assembly in Xenopus laevis egg extracts.

Science.gov (United States)

Baur, Tina; Ramadan, Kristijan; Schlundt, Andreas; Kartenbeck, Jürgen; Meyer, Hemmo H

2007-08-15

Despite the progress in understanding nuclear envelope (NE) reformation after mitosis, it has remained unclear what drives the required membrane fusion and how exactly this is coordinated with nuclear pore complex (NPC) assembly. Here, we show that, like other intracellular fusion reactions, NE fusion in Xenopus laevis egg extracts is mediated by SNARE proteins that require activation by NSF. Antibodies against Xenopus NSF, depletion of NSF or the dominant-negative NSF(E329Q) variant specifically inhibited NE formation. Staging experiments further revealed that NSF was required until sealing of the envelope was completed. Moreover, excess exogenous alpha-SNAP that blocks SNARE function prevented membrane fusion and caused accumulation of non-flattened vesicles on the chromatin surface. Under these conditions, the nucleoporins Nup107 and gp210 were fully recruited, whereas assembly of FxFG-repeat-containing nucleoporins was blocked. Together, we define NSF- and SNARE-mediated membrane fusion events as essential steps during NE formation downstream of Nup107 recruitment, and upstream of membrane flattening and completion of NPC assembly.

Functional response of a near-surface soil microbial community to a simulated underground CO2 storage leak.

Science.gov (United States)

Morales, Sergio E; Holben, William E

2013-01-01

Understanding the impacts of leaks from geologic carbon sequestration, also known as carbon capture and storage, is key to developing effective strategies for carbon dioxide (CO2) emissions management and mitigation of potential negative effects. Here, we provide the first report on the potential effects of leaks from carbon capture and storage sites on microbial functional groups in surface and near-surface soils. Using a simulated subsurface CO2 storage leak scenario, we demonstrate how CO2 flow upward through the soil column altered both the abundance (DNA) and activity (mRNA) of microbial functional groups mediating carbon and nitrogen transformations. These microbial responses were found to be seasonally dependent and correlated to shifts in atmospheric conditions. While both DNA and mRNA levels were affected by elevated CO2, they did not react equally, suggesting two separate mechanisms for soil microbial community response to high CO2 levels. The results did not always agree with previous studies on elevated atmospheric (rather than subsurface) CO2 using FACE (Free-Air CO2 Enrichment) systems, suggesting that microbial community response to CO2 seepage from the subsurface might differ from its response to atmospheric CO2 increases.

Sorptive fractionation of organic matter and formation of organo-hydroxy-aluminum complexes during litter biodegradation in the presence of gibbsite

Science.gov (United States)

Heckman, K.; Grandy, A. S.; Gao, X.; Keiluweit, M.; Wickings, K.; Carpenter, K.; Chorover, J.; Rasmussen, C.

2013-11-01

Solid and aqueous phase Al species are recognized to affect organic matter (OM) stabilization in forest soils. However, little is known about the dynamics of formation, composition and dissolution of organo-Al hydroxide complexes in microbially-active soil systems, where plant litter is subject to microbial decomposition in close proximity to mineral weathering reactions. We incubated gibbsite-quartz mineral mixtures in the presence of forest floor material inoculated with a native microbial consortium for periods of 5, 60 and 154 days. At each time step, samples were density separated into light (2.0 g cm-3) fractions. The light fraction was mainly comprised of particulate organic matter, while the intermediate and heavy density fractions contained moderate and large amounts of Al-minerals, respectively. Multi-method interrogation of the fractions indicated the intermediate and heavy fractions differed both in mineral structure and organic compound composition. X-ray diffraction analysis and SEM/EDS of the mineral component of the intermediate fractions indicated some alteration of the original gibbsite structure into less crystalline Al hydroxide and possibly proto-imogolite species, whereas alteration of the gibbsite structure was not evident in the heavy fraction. DRIFT, Py-GC/MS and STXM/NEXAFS results all showed that intermediate fractions were composed mostly of lignin-derived compounds, phenolics, and polysaccharides. Heavy fraction organics were dominated by polysaccharides, and were enriched in proteins, N-bearing compounds, and lipids. The source of organics appeared to differ between the intermediate and heavy fractions. Heavy fractions were enriched in 13C with lower C/N ratios relative to intermediate fractions, suggesting a microbial origin. The observed differential fractionation of organics among hydroxy-Al mineral types suggests that microbial activity superimposed with abiotic mineral-surface-mediated fractionation leads to strong density

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

Science.gov (United States)

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microscale Insight into Microbial Seed Banks.

Science.gov (United States)

Locey, Kenneth J; Fisk, Melany C; Lennon, J T

2016-01-01

Microbial dormancy leads to the emergence of seed banks in environmental, engineered, and host-associated ecosystems. These seed banks act as reservoirs of diversity that allow microbes to persist under adverse conditions, including extreme limitation of resources. While microbial seed banks may be influenced by macroscale factors, such as the supply of resources, the importance of microscale encounters between organisms and resource particles is often overlooked. We hypothesized that dimensions of spatial, trophic, and resource complexity determine rates of encounter, which in turn, drive the abundance, productivity, and size of seed banks. We tested this using >10,000 stochastic individual based models (IBMs) that simulated energetic, physiological, and ecological processes across combinations of resource, spatial, and trophic complexity. These IBMs allowed realistic dynamics and the emergence of seed banks from ecological selection on random variation in species traits. Macroscale factors like the supply and concentration of resources had little effect on resource encounter rates. In contrast, encounter rates were strongly influenced by interactions between dispersal mode and spatial structure, and also by the recalcitrance of resources. In turn, encounter rates drove abundance, productivity, and seed bank dynamics. Time series revealed that energetically costly traits can lead to large seed banks and that recalcitrant resources can lead to greater stability through the formation of seed banks and the slow consumption of resources. Our findings suggest that microbial seed banks emerge from microscale dimensions of ecological complexity and their influence on resource limitation and energetic costs.

Preliminary Evaluation of Microbial Communities Isolated from the Calcifying Fluid of Oysters

Science.gov (United States)

Banker, R.

2016-02-01

The process of biomineralization is defined as the selective uptake of elements that are incorporated into a defined mineral structure under strict biological control. For bivalve molluscs, such as clams, oysters, and mussels, the mantle is the primary organ in control of shell deposition. Alternatively, remote calcification takes place when carbonate-precipitating microbes (e.g. sulfate reducers) colonize a shell-secreting organism and enhance the ability of the host to build shell material. The oyster syndrome is a term that describes bivalves that possess an unusual shell morphology characterized by exceptionally thick valves containing numerous chambers filled with chalky calcite. Although remote calcification via microbial metabolism has been proposed as a mechanism of chalky deposit formation in oysters, this hypothesis has not yet been rigorously investigated. Here I present data on the microbial communities found in the calcifying fluid of two oyster species; Crassostrea gigas and Ostrea lurida are examples of oysters that do and do not exhibit the oyster syndrome, respectively. Comparison of the microbiomes of these two morphological end members may provide insight into the role of microbes in the formation of chalky deposits. Results indicate that the microbial community in the surrounding water is the dominant source for bacterial taxa found in the calcifying fluid of both oyster species. Also, it appears as though C. gigas maintains a microbial community that is more similar to its ambient environment than O. lurida. These results demonstrate that the ambient aquatic environment has a guiding influence on the microbiome found in the calcifying fluid of bivalve molluscs. However, the magnitude of this effect varies among organisms, even those that are closely related.

Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

Science.gov (United States)

Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

2014-01-01

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683

Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

OpenAIRE

Zhang, Jianbo; Sturla, Shana; Lacroix, Christophe; Schwab, Clarissa

2018-01-01

ABSTRACT Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrole...

Microbial CH4 and N2O consumption in acidic wetlands

Directory of Open Access Journals (Sweden)

Steffen eKolb

2012-03-01

Full Text Available Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH4, and nitrous oxide (N2O. Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH4 is consumed in sub soil by aerobic methanotrophs at anoxic–oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots. Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH4 in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH4 consumption have not been systematically evaluated. N2O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N2O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N2O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N2O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and dentrifiers that consume atmospheric CH4 and N2O in acidic wetlands.

Microbial biofilms in water-mixed metalworking fluids; Mikrobielle Biofilme in wassergemischten Kuehlschmierstoffen

Energy Technology Data Exchange (ETDEWEB)

Koch, Thomas [Wisura GmbH, Bremen (Germany)

2013-05-15

The microbial load of water-miscible metalworking fluids (MWF) as well as the hygienic aspects and the cost-related impact on the production process due to the activity of microbes is in the focus of many scientific investigations and documented in the related publications. The majority of this research work is focused on the microbiology of the water body, i.e. with the microbial life in the liquid coolant. The habitat biofilm, i.e. the three-dimensional growth of bacteria and fungi on surfaces of the coolant systems has been scarcely considered. Based on the scientific findings made in the recent years studying biofilms it can be concluded, that the relevant microbial processes for the depletion of the MWF and its recontamination takes predominantly places in biofilms. This paper gives an overview of the structure, the formation and the life in biofilms and represents their relevance in MWF systems. (orig.)

Nanoporous Mo2C functionalized 3D carbon architecture anode for boosting flavins mediated interfacial bioelectrocatalysis in microbial fuel cells

Science.gov (United States)

Zou, Long; Lu, Zhisong; Huang, Yunhong; Long, Zhong-er; Qiao, Yan

2017-08-01

An efficient microbial electrocatalysis in microbial fuel cells (MFCs) needs both high loading of microbes (biocatalysts) and robust interfacial electron transfer from microbes to electrode. Herein a nanoporous molybdenum carbide (Mo2C) functionalized carbon felt electrode with rich 3D hierarchical porous architecture is applied as MFC anode to achieve superior electrocatalytic performance. The nanoporous Mo2C functionalized anode exhibits strikingly improved microbial electrocatalysis in MFCs with 5-fold higher power density and long-term stability of electricity production. The great enhancement is attributed to the introduction of rough Mo2C nanostructural interface into macroporous carbon architecture for promoting microbial growth with great excretion of endogenous electron shuttles (flavins) and rich available nanopores for enlarging electrochemically active surface area. Importantly, the nanoporous Mo2C functionalized anode is revealed for the first time to have unique electrocatalytic activity towards redox reaction of flavins with more negative redox potential, indicating a more favourable thermodynamic driving force for anodic electron transfer. This work not only provides a promising electrode for high performance MFCs but also brings up a new insight into the effect of nanostructured materials on interfacial bioelectrocatalysis.

Spectral induced polarization and electrodic potential monitoring of microbially mediated iron sulfide transformations

Energy Technology Data Exchange (ETDEWEB)

Hubbard, Susan; Personna, Y.R.; Ntarlagiannis, D.; Slater, L.; Yee, N.; O' Brien, M.; Hubbard, S.

2008-02-15

Stimulated sulfate-reduction is a bioremediation technique utilized for the sequestration of heavy metals in the subsurface.We performed laboratory column experiments to investigate the geoelectrical response of iron sulfide transformations by Desulfo vibriovulgaris. Two geoelectrical methods, (1) spectral induced polarization (SIP), and (2) electrodic potential measurements, were investigated. Aqueous geochemistry (sulfate, lactate, sulfide, and acetate), observations of precipitates (identified from electron microscopy as iron sulfide), and electrodic potentials on bisulfide ion (HS) sensitive silver-silver chloride (Ag-AgCl) electrodes (630 mV) were diagnostic of induced transitions between an aerobic iron sulfide forming conditions and aerobic conditions promoting iron sulfide dissolution. The SIP data showed 10m rad anomalies during iron sulfide mineralization accompanying microbial activity under an anaerobic transition. These anomalies disappeared during iron sulfide dissolution under the subsequent aerobic transition. SIP model parameters based on a Cole-Cole relaxation model of the polarization at the mineral-fluid interface were converted to (1) estimated biomineral surface area to pore volume (Sp), and (2) an equivalent polarizable sphere diameter (d) controlling the relaxation time. The temporal variation in these model parameters is consistent with filling and emptying of pores by iron sulfide biofilms, as the system transitions between anaerobic (pore filling) and aerobic (pore emptying) conditions. The results suggest that combined SIP and electrodic potential measurements might be used to monitor spatiotemporal variability in microbial iron sulfide transformations in the field.

The Effects of Subsurface Bioremediation on Soil Structure, Colloid Formation, and Contaminant Transport

Science.gov (United States)

Wang, Y.; Liang, X.; Zhuang, J.; Radosevich, M.

2016-12-01

Anaerobic bioremediation is widely applied to create anaerobic subsurface conditions designed to stimulate microorganisms that degrade organic contaminants and immobilize toxic metals in situ. Anaerobic conditions that accompany such techniques also promotes microbially mediated Fe(III)-oxide mineral reduction. The reduction of Fe(III) could potentially cause soil structure breakdown, formation of clay colloids, and alternation of soil surface chemical properties. These processes could then affect bioremediation and the migration of contaminants. Column experiments were conducted to investigate the impact of anaerobic bioreduction on soil structure, hydraulic properties, colloid formation, and transport of three tracers (bromide, DFBA, and silica shelled silver nanoparticles). Columns packed with inoculated water stable soil aggregates were placed in anaerobic glovebox, and artificial groundwater media was pumped into the columns to simulate anaerobic bioreduction process for four weeks. Decent amount of soluble Fe(II) accompanied by colloids were detected in the effluent from bioreduction columns a week after initiation of bioreduction treatment, which demonstrated bioreduction of Fe(III) and formation of colloids. Transport experiments were performed in the columns before and after bioreduction process to assess the changes of hydraulic and surface chemical properties through bioreduction treatment. Earlier breakthrough of bromide and DFBA after treatment indicated alterations in flow paths (formation of preferential flow paths). Less dispersion of bromide and DFBA, and less tailing of DFBA after treatment implied breakdown of soil aggregates. Dramatically enhanced transport and early breakthrough of silica shelled silver nanoparticles after treatment supported the above conclusion of alterations in flow paths, and indicated changes of soil surface chemical properties.

Microbially influenced corrosion of copper nuclear fuel waste containers in a Canadian disposal vault

Energy Technology Data Exchange (ETDEWEB)

King, F

1996-11-01

An assessment of the potential for microbially influenced corrosion (MIC) of copper nuclear fuel waste containers in a Canadian disposal vault is presented. The assessment is based on a consideration of the microbial activity within a disposal vault, the reported cases of MIC of Cu alloys in the literature and the known corrosion behaviour of Cu. Because of the critical role of biofilms in the reported cases of MIC, their formation and properties are discussed in detail. Next, the literature on the MIC of Cu alloys is briefly reviewed. The various MIC mechanisms proposed are critically discussed and the implications for the corrosion of Cu containers considered. In the majority of literature cases, MIC depends on alternating aerated and deaerated environments, with accelerated corrosion being observed when fresh aerated water replaces stagnant water, e.g., the MIC of Cu-Ni heat exchangers in polluted seawater and the microbially influenced pitting of Cu water pipes. Finally, because of the predominance of corrosion by sulphate-reducing bacteria (SRB) in the MIC literature, the abiotic behaviour of Cu alloys in sulphide solutions is also reviewed. The effect of the evolving environment in a disposal vault on the extent and location of microbial activity is discussed. Biofilm formation on the container surface is considered unlikely throughout the container lifetime, but especially initially when the environmental conditions will be particularly aggressive. Microbial activity in areas of the vault away from the container is possible, however. Corrosion of the container could then occur if microbial metabolic by-products diffuse to the container surface. Sulphide, produced by the action of SRB are considered to be the most likely cause of container corrosion. It is concluded that the only likely form of MIC of Cu containers will result from sulphide produced by SRB diffusing to the container surface. A modelling procedure for predicting the extent of corrosion is

Microbially influenced corrosion of copper nuclear fuel waste containers in a Canadian disposal vault

International Nuclear Information System (INIS)

King, F.

1996-11-01

An assessment of the potential for microbially influenced corrosion (MIC) of copper nuclear fuel waste containers in a Canadian disposal vault is presented. The assessment is based on a consideration of the microbial activity within a disposal vault, the reported cases of MIC of Cu alloys in the literature and the known corrosion behaviour of Cu. Because of the critical role of biofilms in the reported cases of MIC, their formation and properties are discussed in detail. Next, the literature on the MIC of Cu alloys is briefly reviewed. The various MIC mechanisms proposed are critically discussed and the implications for the corrosion of Cu containers considered. In the majority of literature cases, MIC depends on alternating aerated and deaerated environments, with accelerated corrosion being observed when fresh aerated water replaces stagnant water, e.g., the MIC of Cu-Ni heat exchangers in polluted seawater and the microbially influenced pitting of Cu water pipes. Finally, because of the predominance of corrosion by sulphate-reducing bacteria (SRB) in the MIC literature, the abiotic behaviour of Cu alloys in sulphide solutions is also reviewed. The effect of the evolving environment in a disposal vault on the extent and location of microbial activity is discussed. Biofilm formation on the container surface is considered unlikely throughout the container lifetime, but especially initially when the environmental conditions will be particularly aggressive. Microbial activity in areas of the vault away from the container is possible, however. Corrosion of the container could then occur if microbial metabolic by-products diffuse to the container surface. Sulphide, produced by the action of SRB are considered to be the most likely cause of container corrosion. It is concluded that the only likely form of MIC of Cu containers will result from sulphide produced by SRB diffusing to the container surface. A modelling procedure for predicting the extent of corrosion is

Microbial mediation of radionuclide transport -significance for the nuclear fuel waste management program

International Nuclear Information System (INIS)

Champ, D.R.

1984-08-01

The role that microbially catalyzed processes may play in determining, or altering, radionuclide migration is an unresolved question in the Nuclear Fuel Waste Management Program. This report documents the results of a review of the available information on the existence and biochemical capabilities of micro-organisms and the potential for their involvement in processes affecting the migration of radionuclides of interest. The potential was judged sufficient to warrant conducting experiments to assess their role. The outline of an experimental program to address the role of micro-organisms is presented

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, Ruud A.; Rothballer, Michael; Strik, David P. B. T. B.; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode–rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Hydroxyl Radical-Mediated Novel Modification of Peptides: N-Terminal Cyclization through the Formation of α-Ketoamide.

Science.gov (United States)

Lee, Seon Hwa; Kyung, Hyunsook; Yokota, Ryo; Goto, Takaaki; Oe, Tomoyuki

2015-01-20

The hydroxyl radical-mediated oxidation of peptides and proteins constitutes a large group of post-translational modifications that can result in structural and functional changes. These oxidations can lead to hydroxylation, sulfoxidation, or carbonylation of certain amino acid residues and cleavage of peptide bonds. In addition, hydroxyl radicals can convert the N-terminus of peptides to an α-ketoamide via abstraction of the N-terminal α-hydrogen and hydrolysis of the ketimine intermediate. In the present study, we identified N-terminal cyclization as a novel modification mediated by a hydroxyl radical. The reaction of angiotensin (Ang) II (DRVYIHPF) and the hydroxyl radical generated by the Cu(II)/ascorbic acid (AA) system or UV/hydrogen peroxide system produced N-terminal cyclized-Ang II (Ang C) and pyruvamide-Ang II (Ang P, CH3COCONH-RVYIHPF). The structure of Ang C was confirmed by mass spectrometry and comparison to an authentic standard. The subsequent incubation of isolated Ang P in the presence of Cu(II)/AA revealed that Ang P was the direct precursor of Ang C. The proposed mechanism involves the formation of a nitrogen-centered (aminyl) radical, which cyclizes to form a five-membered ring containing the alkoxy radical. The subsequent β-scission reaction of the alkoxyl radical results in the cleavage of the terminal CH3CO group. The initial aminyl radical can be stabilized by chelation to the Cu(II) ions. The affinity of Ang C toward the Ang II type 1 receptor was significantly lower than that of Ang II or Ang P. Ang C was not further metabolized by aminopeptidase A, which converts Ang II to Ang III. Hydroxyl radical-mediated N-terminal cyclization was also observed in other Ang peptides containing N-terminal alanine, arginine, valine, and amyloid β 1-11 (DAEFRHDSGYE).

Nitric oxide mediates strigolactone signaling in auxin and ethylene-sensitive lateral root formation in sunflower seedlings.

Science.gov (United States)

Bharti, Niharika; Bhatla, Satish C

2015-01-01

Strigolactones (SLs) play significant role in shaping root architecture whereby auxin-SL crosstalk has been observed in SL-mediated responses of primary root elongation, lateral root formation and adventitious root (AR) initiation. Whereas GR24 (a synthetic strigolactone) inhibits LR and AR formation, the effect of SL biosynthesis inhibitor (fluridone) is just the opposite (root proliferation). Naphthylphthalamic acid (NPA) leads to LR proliferation but completely inhibits AR development. The diffusive distribution of PIN1 in the provascular cells in the differentiating zone of the roots in response to GR24, fluridone or NPA treatments further indicates the involvement of localized auxin accumulation in LR development responses. Inhibition of LR formation by GR24 treatment coincides with inhibition of ACC synthase activity. Profuse LR development by fluridone and NPA treatments correlates with enhanced [Ca(2+)]cyt in the apical region and differentiating zones of LR, indicating a critical role of [Ca(2+)] in LR development in response to the coordinated action of auxins, ethylene and SLs. Significant enhancement of carotenoid cleavage dioxygenase (CCD) activity (enzyme responsible for SL biosynthesis) in tissue homogenates in presence of cPTIO (NO scavenger) indicates the role of endogenous NO as a negative modulator of CCD activity. Differences in the spatial distribution of NO in the primary and lateral roots further highlight the involvement of NO in SL-modulated root morphogenesis in sunflower seedlings. Present work provides new report on the negative modulation of SL biosynthesis through modulation of CCD activity by endogenous nitric oxide during SL-modulated LR development.

Power output of microbial fuel cell emphasizing interaction of anodic binder with bacteria

Science.gov (United States)

Li, Hongying; Liao, Bo; Xiong, Juan; Zhou, Xingwang; Zhi, Huozhen; Liu, Xiang; Li, Xiaoping; Li, Weishan

2018-03-01

Electrochemically active biofilm is necessary for the electron transfer between bacteria and anodic electrode in microbial fuel cells and selecting the type of anodic electrode material that favours formation of electrochemically active biofilm is crucial for the microbial fuel cell operation. We report a new finding that the interaction of anodic binder with bacteria plays more important role than its hydrophilicity for forming an electrochemically active biofilm, which is emphasized by applying poly(bisphenol A-co-epichorohydrin) as an anodic binder of the microbial fuel cell based on carbon nanotubes as anodic electrode and Escherichia coli as bacterium. The physical characterizations and electrochemical measurements demonstrate that poly(bisphenol A-co-epichorohydrin) exhibits a strong interaction with bacteria and thus provides the microbial fuel cell with excellent power density output. The MFC using poly(bisphenol A-co-epichorohydrin) reaches a maximum power density output of 3.8 W m-2. This value is larger than that of the MFCs using polytetrafluoroethylene that has poorer hydrophilicity, or polyvinyl alcohol that has better hydrophilicity but exhibits weaker interaction with bacteria than poly(bisphenol A-co-epichorohydrin).

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

Science.gov (United States)

Zomorrodi, Ali R; Segrè, Daniel

2017-11-16

Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.

Microbial activities in soil near natural gas leaks

Energy Technology Data Exchange (ETDEWEB)

Adamse, A D; Hoeks, J; de Bont, J A.M.; van Kessel, J F

1972-01-01

From the present experiments it may be concluded that in the surroundings of natural gas leaks, methane, ethane and possibly some other components of the natural gas are oxidized by microbial activities as long as oxygen is available. This is demonstrated by an increased oxygen consumption and carbon dioxide production, as well as by increased numbers of different types of bacteria. The resulting deficiency of oxygen, the excess of carbon dioxide, and perhaps the formation of inhibitory amounts of ethylene, are considered to be mainly responsible for the death of trees near natural gas leaks. Also the long period of time needed by the soil to recover, may be due to prolonged microbial activities, as well as to the presence of e.g. ethylene. The present experiments suggest that especially methane-oxidizing bacteria of the Methylosinus trichosporium type were present in predominating numbers and consequently have mainly been responsible for the increased oxygen consumption. However, some fungi oxidizing components of natural gas, including methane and ethane may also have contributed to the increased microbial activities in the soil. The same will be true of a possible secondary microflora on products derived from microorganisms oxidizing natural gas components. 12 references, 9 figures, 7 tables.

Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns.

Directory of Open Access Journals (Sweden)

David J Esteban

Full Text Available Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67-72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil

Environmental controls on microbial communities in continental serpentinite fluids

Directory of Open Access Journals (Sweden)

Melitza eCrespo-Medina

2014-11-01

Full Text Available Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate and formate, with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the three month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

Mechanistic Understanding of Microbial Plugging for Improved Sweep Efficiency

Energy Technology Data Exchange (ETDEWEB)

Steven Bryant; Larry Britton

2008-09-30

Microbial plugging has been proposed as an effective low cost method of permeability reduction. Yet there is a dearth of information on the fundamental processes of microbial growth in porous media, and there are no suitable data to model the process of microbial plugging as it relates to sweep efficiency. To optimize the field implementation, better mechanistic and volumetric understanding of biofilm growth within a porous medium is needed. In particular, the engineering design hinges upon a quantitative relationship between amount of nutrient consumption, amount of growth, and degree of permeability reduction. In this project experiments were conducted to obtain new data to elucidate this relationship. Experiments in heterogeneous (layered) beadpacks showed that microbes could grow preferentially in the high permeability layer. Ultimately this caused flow to be equally divided between high and low permeability layers, precisely the behavior needed for MEOR. Remarkably, classical models of microbial nutrient uptake in batch experiments do not explain the nutrient consumption by the same microbes in flow experiments. We propose a simple extension of classical kinetics to account for the self-limiting consumption of nutrient observed in our experiments, and we outline a modeling approach based on architecture and behavior of biofilms. Such a model would account for the changing trend of nutrient consumption by bacteria with the increasing biomass and the onset of biofilm formation. However no existing model can explain the microbial preference for growth in high permeability regions, nor is there any obvious extension of the model for this observation. An attractive conjecture is that quorum sensing is involved in the heterogeneous bead packs.

Soil biochar amendment shapes the composition of N_2O-reducing microbial communities

International Nuclear Information System (INIS)

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H.; Kappler, Andreas; Behrens, Sebastian

2016-01-01

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N_2O) emissions. N_2O is a potent greenhouse gas. The main sources of N_2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N_2O emission mitigation and the abundance and activity of N_2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N_2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N_2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N_2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N_2O-reducing microbial taxa. • Taxonomic shifts among N_2O-reducing microbes might explain lower N_2O emissions.

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

Science.gov (United States)

Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

2015-06-15

Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Endogenous leukotriene formation during anaphylactic shock

International Nuclear Information System (INIS)

Keppler, A.; Oerning, L.; Bernstroem, K.; Hammarstroem, S.

1987-01-01

Leukotriene (LT)C 4 is a biologically active substance, presumed to play major roles as a mediator of allergic and anaphylactic reactions. It is formed e.g. by basophilic and eosinophilic leukocytes, monocytes, macrophages, and mast cells. In cells having IgE receptors, bridging of these by divalent anti-IgE-receptor antibodies or by interaction between receptor-bound IgE and anti-IgE will induce LTC 4 formation. Leukotriene formation has also been demonstrated in other in vitro models of immediate hypersensivity. The biological actions of LTC 4 , comprise induction of airway obstruction, constriction of coronary arteries, hypotension, and plasma extravasation. Leukotriene formation in vivo may mediate anaphylactic shock symptoms and cause the death of an animal. In order to prove the presumed mediator role of this substance in anaphylactic reactions, it is necessary to demonstrate its endogenous formation during shock. Studies on the metabolism of LTC 4 have revealed rapid catabolism by various transformations of the peptide substituent. Recently, three metabolites were demonstrated to be excreted as end-products in man (LTE 4 ,) and the rat (N-acetyl LTE 4 and N-acetyl 11-trans LTE 4 ). By monitoring biliary N-acetyl LTE 4 levels, endogenous leukotriene formation in the rat was demonstrated in vivo after tissue trauma and endotoxin shock. We now wish to report evidence for endogenous leukotriene C 4 production during anaphylactic shock in guinea pigs. 37 refs. (author)

Microbial Ecology of Soil Aggregation in Agroecosystems

Science.gov (United States)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences

Biological Superoxide In Manganese Oxide Formation

Science.gov (United States)

Hansel, C.; Learman, D.; Zeiner, C.; Santelli, C. M.

2011-12-01

Manganese (Mn) oxides are among the strongest sorbents and oxidants within the environment, controlling the fate and transport of numerous elements and the degradation of recalcitrant carbon. Both bacteria and fungi mediate the oxidation of Mn(II) to Mn(III/IV) oxides but the genetic and biochemical mechanisms responsible remain poorly understood. Furthermore, the physiological basis for microbial Mn(II) oxidation remains an enigma. We have recently reported that a common marine bacterium (Roseobacter sp. AzwK-3b) oxidizes Mn(II) via reaction with extracellular superoxide (O2-) produced during exponential growth. Here we expand this superoxide-mediated Mn(II) oxidation pathway to fungi, introducing a surprising homology between prokaryotic and eukaryotic metal redox processes. For instance, Stibella aciculosa, a common soil Ascomycete filamentous fungus, precipitates Mn oxides at the base of asexual reproductive structures (synnemata) used to support conidia (Figure 1). This distribution is a consequence of localized production of superoxide (and it's dismutation product hydrogen peroxide, H2O2), leading to abiotic oxidation of Mn(II) by superoxide. Disruption of NADPH oxidase activity using the oxidoreductase inhibitor DPI leads to diminished cell differentiation and subsequent Mn(II) oxidation inhibition. Addition of Cu(II) (an effective superoxide scavenger) leads to a concentration dependent decrease in Mn oxide formation. We predict that due to the widespread production of extracellular superoxide within the fungal and likely bacterial kingdoms, biological superoxide may be an important contributor to the cycling of Mn, as well as other metals (e.g., Hg, Fe). Current and future explorations of the genes and proteins involved in superoxide production and Mn(II) oxidation will ideally lend insight into the physiological and biochemical basis for these processes.

Proceedings of the 8. International Symposium on Microbial Ecology : microbial biosystems : new frontiers

International Nuclear Information System (INIS)

Bell, C.R.; Brylinsky, M.; Johnson-Green, P.

2000-01-01

A wide range of disciplines were presented at this conference which reflected the importance of microbial ecology and provided an understanding of the factors that determine the growth and activities of microorganisms. The conference attracted 1444 delegates from 54 countries. The research emerging from the rapidly expanding frontier of microbial ecosystems was presented in 62 oral presentation and 817 poster presentations. The two volumes of these proceedings presented a total of 27 areas in microbial ecology, some of which included terrestrial biosystems, aquatic, estuarine, surface and subsurface microbial ecology. Other topics included bioremediation, microbial ecology in industry and microbial ecology of oil fields. Some of the papers highlighted the research that is underway to determine the feasibility of using microorganisms for enhanced oil recovery (EOR). Research has shown that microbial EOR can increase production at lower costs than conventional oil recovery. The use of bacteria has also proven to be a feasible treatment method in the biodegradation of hydrocarbons associated with oil spills. refs., tabs., figs

Microbial consortia involved in the anaerobic degradation of hydrocarbons.

Science.gov (United States)

Zwolinski; Harris, R F; Hickey, W J

2000-01-01

In this review, we examine the energetics of well-characterized biodegradation pathways and explore the possibilities for these to support growth of multiple organisms interacting in consortia. The relevant phenotypic and/or phylogenetic characteristics of isolates and consortia mediating hydrocarbon degradation coupled with different terminal electron-accepting processes (TEAP) are also reviewed. While the information on metabolic pathways has been gained from the analysis of individual isolates, the energetic framework presented here demonstrates that microbial consortia could be readily postulated for hydrocarbon degradation coupled to any TEAP. Several specialized reactions occur within these pathways, and the organisms mediating these are likely to play a key role in defining the hydrocarbon degradation characteristics of the community under a given TEAP. Comparing these processes within and between TEAPs reveals biological unity in that divergent phylotypes display similar degradation mechanisms and biological diversity in that hydrocarbon-degraders closely related as phylotypes differ in the type and variety of hydrocarbon degradation pathways they possess. Analysis of microcosms and of field samples suggests that we have only begun to reveal the diversity of organisms mediating anaerobic hydrocarbon degradation. Advancements in the understanding of how hydrocarbon-degrading communities function will be significantly affected by the extent to which organisms mediating specialized reactions can be identified, and tools developed to allow their study in situ.

Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System

Directory of Open Access Journals (Sweden)

Konstanze T. Schiessl

2017-10-01

Full Text Available A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.

Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System.

Science.gov (United States)

Schiessl, Konstanze T; Janssen, Elisabeth M-L; Kraemer, Stephan M; McNeill, Kristopher; Ackermann, Martin

2017-01-01

A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils.

Science.gov (United States)

Wagner, Robert; Zona, Donatella; Oechel, Walter; Lipson, David

2017-08-01

While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP. Interestingly, α-diversity of the methanogens was positively correlated with PMP, while β-diversity was unrelated to PMP. The β-diversity of the entire microbial community, however, was related to PMP. Shannon diversity was a better correlate of PMP than Simpson diversity across analyses, while rarefied species richness was a weak correlate of PMP. These results demonstrate the following: first, soil pH and microbial community structure both probably control methane production in Arctic soils. Second, there may be high functional redundancy in the methanogens with regard to methane production. Third, iron-reducing bacteria co-occur with methanogens in Arctic soils, and iron-reduction-mediated effects on methanogenesis may be controlled by α- and β-diversity. And finally, species evenness and rare species abundances may be driving relationships between microbial groups, influencing Arctic methane production. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

[Characterization and microbial community shifts of rice strawdegrading microbial consortia].

Science.gov (United States)

Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

2016-12-04

To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

Sialic Acid on the Glycosylphosphatidylinositol Anchor Regulates PrP-mediated Cell Signaling and Prion Formation.

Science.gov (United States)

Bate, Clive; Nolan, William; Williams, Alun

2016-01-01

The prion diseases occur following the conversion of the cellular prion protein (PrP(C)) into disease-related isoforms (PrP(Sc)). In this study, the role of the glycosylphosphatidylinositol (GPI) anchor attached to PrP(C) in prion formation was examined using a cell painting technique. PrP(Sc) formation in two prion-infected neuronal cell lines (ScGT1 and ScN2a cells) and in scrapie-infected primary cortical neurons was increased following the introduction of PrP(C). In contrast, PrP(C) containing a GPI anchor from which the sialic acid had been removed (desialylated PrP(C)) was not converted to PrP(Sc). Furthermore, the presence of desialylated PrP(C) inhibited the production of PrP(Sc) within prion-infected cortical neurons and ScGT1 and ScN2a cells. The membrane rafts surrounding desialylated PrP(C) contained greater amounts of sialylated gangliosides and cholesterol than membrane rafts surrounding PrP(C). Desialylated PrP(C) was less sensitive to cholesterol depletion than PrP(C) and was not released from cells by treatment with glimepiride. The presence of desialylated PrP(C) in neurons caused the dissociation of cytoplasmic phospholipase A2 from PrP-containing membrane rafts and reduced the activation of cytoplasmic phospholipase A2. These findings show that the sialic acid moiety of the GPI attached to PrP(C) modifies local membrane microenvironments that are important in PrP-mediated cell signaling and PrP(Sc) formation. These results suggest that pharmacological modification of GPI glycosylation might constitute a novel therapeutic approach to prion diseases. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Potential impact of Andrassy bentonite microbial diversity in the long-term performance of a deep nuclear waste repository

Science.gov (United States)

Tadza, M. Y. Mohd; Tadza, M. A. Mohd; Bag, R.; Harith, N. S. H.

2018-01-01

Copper and steel canning and bentonite buffer are normally forseen as the primary containment component of a deep nuclear waste repository. Distribution of microbes in subsurface environments have been found to be extensive and directly or indirectly may exert influence on waste canister corrosion and the mobility of radionuclides. The understanding of clays and microbial interaction with radionuclides will be useful in predicting the microbial impacts on the performance of the waste repositories. The present work characterizes the culture-dependent microbial diversity of Andrassy bentonite recovered from Tawau clay deposits. The evaluation of microbial populations shows the presence of a number of cultivable microbes (e.g. Staphylococcus, Micrococcus, Achromobacter, Bacillus, Paecilomyces, Trichoderma, and Fusarium). Additionally, a pigmented yeast strain Rhodotorula mucilaginosa was also recovered from the formation. Both Bacillus and Rhodotorula mucilaginosa have high tolerance towards U radiation and toxicity. The presence of Rhodotorula mucilaginosa in Andrassy bentonite might be able to change the speciation of radionuclides (e.g. uranium) in a future deep repository. However, concern over the presence of Fe (III) reduction microbes such as Bacillus also found in the formation could lead to corrosion of copper steel canister and affect the overall performance of the containment system.

Mutation of the Streptococcus gordonii Thiol-Disulfide Oxidoreductase SdbA Leads to Enhanced Biofilm Formation Mediated by the CiaRH Two-Component Signaling System.

Directory of Open Access Journals (Sweden)

Lauren Davey

Full Text Available Streptococcus gordonii is a commensal inhabitant of human oral biofilms. Previously, we identified an enzyme called SdbA that played an important role in biofilm formation by S. gordonii. SdbA is thiol-disulfide oxidoreductase that catalyzes disulfide bonds in secreted proteins. Surprisingly, inactivation of SdbA results in enhanced biofilm formation. In this study we investigated the basis for biofilm formation by the ΔsdbA mutant. The results revealed that biofilm formation was mediated by the interaction between the CiaRH and ComDE two-component signalling systems. Although it did not affect biofilm formation by the S. gordonii parent strain, CiaRH was upregulated in the ΔsdbA mutant and it was essential for the enhanced biofilm phenotype. The biofilm phenotype was reversed by inactivation of CiaRH or by the addition of competence stimulating peptide, the production of which is blocked by CiaRH activity. Competition assays showed that the enhanced biofilm phenotype also corresponded to increased oral colonization in mice. Thus, the interaction between SdbA, CiaRH and ComDE affects biofilm formation both in vitro and in vivo.