A study of so-called hypochondriasis.

PubMed

von Scheele, C; Nordgren, L; Kempi, V; Hetta, J; Hallborg, A

1990-01-01

Twenty-four patients with unexplained somatic complaints were subjected to a thorough somatic examination. Only when the examination proved negative was the patient entered into the study. The patients were clinically appraised according to criteria given in DSM-III. Generalized anxiety disorder (GAD) was diagnosed in 12, somatization disorder (SD) in 8, and hypochondriasis in 4 patients. Seventeen of the 24 patients agreed to participate in biochemical investigations including a TRH load, a dexamethasone test, and a determination of the monoamine metabolites 5-HIAA and HVA in cerebrospinal fluid (CSF). A normal TSH increase and a normal suppression of cortisol were registered. The HVA values correlated significantly with the 5-HIAA values as well as with the alexithymia scores. Concerning alexithymia and maturity level, no difference as to social class was found. The patients filled in a Zung depression chart. The Zung scale and the 5-HIAA values were both inconsistent with depressive illness. In so-called hypochondriasis a long-term relationship, including selected somatic and biochemical examinations and thorough information, was crucial in abating the patient's distrust and thus the need for health care.

Analysis of organic compounds' degradation and electricity generation in anaerobic fluidized bed microbial fuel cell for coking wastewater treatment.

PubMed

Liu, Xinmin; Wu, Jianjun; Guo, Qingjie

2017-12-01

A single-chambered packing-type anaerobic fluidized microbial fuel cell (AFBMFC) with coking wastewater (CWW) as fuel was built to treat CWW, which not only has high treating efficiency, but also can convert organic matter in wastewater into electricity. AFBMFC was constructed by using anaerobic sludge that was domesticated as inoculation sludge, which was used to biochemically treat CWW. The organic compounds in CWW were extracted by liquid-liquid extraction step by step every day. The extraction phase was concentrated by a rotary evaporator and a nitrogen sweeping device and was analyzed by GC-MS. And the electricity-generation performances of AFBMFC were investigated. The results show that the composition of CWW was complicated, which mainly contains hydrocarbons, phenols, nitrogenous organic compounds, alcohols and aldehydes, esters and acids and so on. After a cycle of anaerobic biochemical treatment, the content of organic compounds in the effluent decreased significantly. After the treatment of AFBMFC, 99.9% phenols, 98.4% alcohol and aldehydes and 95.3% nitrogenous compounds were biodegraded. In the effluent, some new compounds (such as tricosane and dibutyl phthalate) were produced. The chemical oxygen demand (COD) of CWW decreased from 3372 to 559 mg/L in the closed-circuit microbial fuel cell, and the COD removal was 83.4 ± 1.0%. The maximum power density of AFBMFC was 2.13 ± 0.01 mW m -2 .

ON THE RELATION OF BACTERIA TO SO-CALLED "CHEMICAL PNEUMONIA"

PubMed Central

Koontz, A. R.; Allen, M. S.

1929-01-01

The question of a causal relation of the bacteria in gassed lungs to the pneumonia present cannot be regarded as decided. It may be said that: 1. The appearance of gassed lungs with pneumonia is very similar to the pneumonia of known bacterial origin. 2. In a few cases the type of pneumonia found coincides with the reported cases of so-called "chemical pneumonia," which is characterized by a preponderance of epithelial cells in the exudate. 3. Gassed lungs are not sterile but show highly varying numbers of bacteria. 4. The bacteria are not intracellular and are not present in large numbers in the majority of cases. The arguments for and against a causal relationship between the bacteria and the pneumonia may be summed up as follows: 1. Against a Causal Relationship a. The early appearance of pneumonia after gassing. b. The occurrence of pneumonia with very small numbers of bacteria present. c. The fact that very few bacteria are engulfed by leucocytes in gassed lungs, whereas large numbers are present in the non-gassed pneumonias and are conspicuously intracellular. 2. In Favor of a Causal Relationship a. The presence of bacteria in any numbers. b. The picture of broncho-pneumonia presented is similar to broncho-pneumonia of known bacterial origin. c. Pneumonias characterized by large numbers of epithelial cells in the exudate (so-called "chemical pneumonia") occur in animals that were never gassed or subjected to other irritating substances in any way. PMID:19869606

Novel anti-infective compounds from marine bacteria.

PubMed

Rahman, Hafizur; Austin, Brian; Mitchell, Wilfrid J; Morris, Peter C; Jamieson, Derek J; Adams, David R; Spragg, Andrew Mearns; Schweizer, Michael

2010-03-05

As a result of the continuous evolution of microbial pathogens towards antibiotic-resistance, there have been demands for the development of new and effective antimicrobial compounds. Since the 1960s, the scientific literature has accumulated many publications about novel pharmaceutical compounds produced by a diverse range of marine bacteria. Indeed, marine micro-organisms continue to be a productive and successful focus for natural products research, with many newly isolated compounds possessing potentially valuable pharmacological activities. In this regard, the marine environment will undoubtedly prove to be an increasingly important source of novel antimicrobial metabolites, and selective or targeted approaches are already enabling the recovery of a significant number of antibiotic-producing micro-organisms. The aim of this review is to consider advances made in the discovery of new secondary metabolites derived from marine bacteria, and in particular those effective against the so called "superbugs", including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant enterococci (VRE), which are largely responsible for the increase in numbers of hospital acquired, i.e., nosocomial, infections.

Physico-chemical parameters, bioactive compounds and microbial quality of thermo-sonicated carrot juice during storage.

PubMed

Martínez-Flores, Héctor E; Garnica-Romo, Ma Guadalupe; Bermúdez-Aguirre, Daniela; Pokhrel, Prashant Raj; Barbosa-Cánovas, Gustavo V

2015-04-01

Thermosonication has been successfully tested in food for microbial inactivation; however, changes in bioactive compounds and shelf-life of treated products have not been thoroughly investigated. Carrot juice was thermo-sonicated (24 kHz, 120 μm amplitude) at 50 °C, 54 °C and 58 °C for 10 min (acoustic power 2204.40, 2155.72, 2181.68 mW/mL, respectively). Quality parameters and microbial growth were evaluated after processing and during storage at 4 °C. Control and sonicated treatments at 50 °C and 54 °C had 10, 12 and 14 d of shelf-life, respectively. Samples sonicated at 58 °C had the best quality; microbial growth remained low at around 3-log for mesophiles, 4.5-log for yeasts and molds and 2-log for enterobacteria after 20 d of storage. Furthermore, thermo-sonicated juice at 58 °C retained >98% of carotenoids and 100% of ascorbic acid. Phenolic compounds increased in all stored, treated juices. Thermo-sonication is therefore a promising technology for preserving the quality of carrot juice by minimising the physicochemical changes during storage, retarding microbial growth and retaining the bioactive compounds. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial turnover and incorporation of organic compounds in oil sand mining reclamation sites

NASA Astrophysics Data System (ADS)

Lappé, M.; Kallmeyer, J.

2013-12-01

Microorganisms play an important role in the development of new soils and in the reclamation of disturbed landscapes. Especially in hydrocarbon-contaminated soils their ability to degrade organic matter and pollutants makes them essential to re-establish full ecosystem functionality. Microbes are also involved in the mobilization of nutrients for plant growth and in the production of greenhouse gases. Reclamation sites from oil sand mining activities in Alberta, Canada, contain residual bitumen as well as other hydrocarbons. So, these areas provide a great opportunity to study microbial degradation of residual contaminants from oil sand. To get an impression of degradation rates as well as metabolic pathways, incubation experiments were performed in the lab. We measured microbial turnover (catabolic metabolism) and incorporation (anabolic metabolism) rates of different common organic compounds in samples from differently treated reclamation sites - with plant cover and without plant cover. About 10 g of sample material was suspended in 10 mL of a solution that mimics the in-situ concentration of dissolved ions. Radioactively labelled 14C-acetate was added as a common substrate, whereas 14C-naphthenic acid was chosen to investigate the microbial community's capability to utilize a typical hydrocarbon pollutant in oil sand tailings as a nutrient source. To test for the influence of fertilizers on microbial activity, phosphate, nitrate and potassium were added to some samples in different combinations. Incubations were run over two different time periods (7 and 14 days). At the end of each incubation experiment, the amount of produced 14CO2, 14C incorporated into the cells and the remaining unreacted 14C in the slurry were measured. First results show that most of the added 14C-acetate is used for respiration as it is mostly released as 14CO2. In upper soil layers only about 3% of 14C is incorporated into cells, whereas in deeper horizons with lower cell abundances

Metabolic and Microbial Modulation of the Large Intestine Ecosystem by Non-Absorbed Diet Phenolic Compounds: A Review.

PubMed

Mosele, Juana I; Macià, Alba; Motilva, Maria-José

2015-09-18

Phenolic compounds represent a diverse group of phytochemicals whose intake is associated with a wide spectrum of health benefits. As consequence of their low bioavailability, most of them reach the large intestine where, mediated by the action of local microbiota, a series of related microbial metabolites are accumulated. In the present review, gut microbial transformations of non-absorbed phenolic compounds are summarized. Several studies have reached a general consensus that unbalanced diets are associated with undesirable changes in gut metabolism that could be detrimental to intestinal health. In terms of explaining the possible effects of non-absorbed phenolic compounds, we have also gathered information regarded their influence on the local metabolism. For this purpose, a number of issues are discussed. Firstly, we consider the possible implications of phenolic compounds in the metabolism of colonic products, such as short chain fatty acids (SCFA), sterols (cholesterol and bile acids), and microbial products of non-absorbed proteins. Due to their being recognized as affective antioxidant and anti-inflammatory agents, the ability of phenolic compounds to counteract or suppress pro-oxidant and/or pro-inflammatory responses, triggered by bowel diseases, is also presented. The modulation of gut microbiota through dietetic maneuvers including phenolic compounds is also commented on. Although the available data seems to assume positive effects in terms of gut health protection, it is still insufficient for solid conclusions to be extracted, basically due to the lack of human trials to confirm the results obtained by the in vitro and animal studies. We consider that more emphasis should be focused on the study of phenolic compounds, particularly in their microbial metabolites, and their power to influence different aspects of gut health.

[Effects of Organic and Inorganic Slow-Release Compound Fertilizer on Different Soils Microbial Community Structure].

PubMed

Wang, Fei; Yuan, Ting; Gu, Shou-kuan; Wang, Zheng-yin

2015-04-01

As a new style fertilizer, slow-control release fertilizer had been an important subject in recent years, but few researches were about soil microbial community structure diversity. Phospholipid fatty acid method was used to determined the microbial community structure diversity of acid soil and slight alkaline soil applied with slow-release compound fertilizer (SRF), chemical fertilizer (CF) and common compound fertilizer (CCF) at the 10th, 30th, 60th and 90th day under the constant temperature incubation condition. Results indicated that various bacteria (i. e 13:0, i14:0,14:0, i15:0, a15:0, i16:0, 16:12OH, 16:1w5c,16:0, i17:0, a17:0, cy17:0, 17:02OH, i18:0, 18:0 and cy19:0w8c), two actinomycetes (10Me17:0 and 10Me18:0) and only one fungus (18:1 w9c) were detected in two soils after applying slow-release compound fertilizer and other fertilizers during the whole incubation period. SRF could significantly increase the fungi PLFA content by 8.3% and 6.8% at the early stage (the 10th day and 30th day) compared with CF, as well as significantly increase by 22.7% and 17.1% at the late stage (the 60th day and 90th day) compared with CCF in acid soil. SRF significantly increased bacteria, fungi and gram positive bacteria compared with CF and CCF in incubation period (except at the 30th day) in slight alkaline soil. SRF could significantly improve the ratio of normal saturated fatty acid and monounsaturated fatty acid at the 30th day and 90th days in acid soil compared with no fertilizer (CK), CF and CCF, while as to slight alkaline soil, SRF was significantly greater than that of CK, CF and CCF only at the 60th day. SRF could significantly decrease the ratio of iso PLFA and anteiso PLFA in acid soil (in 30-90 days) and slight alkaline soil (in 10-60 days). For two soils PLFA varieties, contents and ratios of microbial community, slow-release compound fertilizer increased soil microbial PLFA varieties and contents, and decreased the influence to microbial survival

Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds.

PubMed

Schempp, Florence M; Drummond, Laura; Buchhaupt, Markus; Schrader, Jens

2018-03-14

Terpenoid flavor and fragrance compounds are of high interest to the aroma industry. Microbial production offers an alternative sustainable access to the desired terpenoids independent of natural sources. Genetically engineered microorganisms can be used to synthesize terpenoids from cheap and renewable resources. Due to its modular architecture, terpenoid biosynthesis is especially well suited for the microbial cell factory concept: a platform host engineered for a high flux toward the central C 5 prenyl diphosphate precursors enables the production of a broad range of target terpenoids just by varying the pathway modules converting the C 5 intermediates to the product of interest. In this review typical terpenoid flavor and fragrance compounds marketed or under development by biotech and aroma companies are given, and the specificities of the aroma market are discussed. The main part of this work focuses on key strategies and recent advances to engineer microbes to become efficient terpenoid producers.

Control of malodorous hydrogen sulfide compounds using microbial fuel cell.

PubMed

Eaktasang, Numfon; Min, Hyeong-Sik; Kang, Christina; Kim, Han S

2013-10-01

In this study, a microbial fuel cell (MFC) was used to control malodorous hydrogen sulfide compounds generated from domestic wastewaters. The electricity production demonstrated a distinct pattern of a two-step increase during 170 h of system run: the first maximum current density was 118.6 ± 7.2 mA m⁻² followed by a rebound of current density increase, reaching the second maximum of 176.8 ± 9.4 mA m⁻². The behaviors of the redox potential and the sulfate level in the anode compartment indicated that the microbial production of hydrogen sulfide compounds was suppressed in the first stage, and the hydrogen sulfide compounds generated from the system were removed effectively as a result of their electrochemical oxidation, which contributed to the additional electricity production in the second stage. This was also directly supported by sulfur deposits formed on the anode surface, which was confirmed by analyses on those solids using a scanning electron microscope equipped with energy dispersive X-ray spectroscopy as well as an elemental analyzer. To this end, the overall reduction efficiencies for HS⁻ and H₂S(g) were as high as 67.5 and 96.4 %, respectively. The correlations among current density, redox potential, and sulfate level supported the idea that the electricity signal generated in the MFC can be utilized as a potential indicator of malodor control for the domestic wastewater system.

Thermally stimulated luminescence studies of undoped, Cu- and Mn-doped CaSO4 compounds

NASA Astrophysics Data System (ADS)

Manam, J.; Das, S.

Thermally stimulated luminescence (TSL) of undoped and doped CaSO4 with activators such as Cu and Mn has been investigated. The polycrystalline samples of undoped and doped CaSO4 are prepared by the melting method. The formation of CaSO4 compound is confirmed by X-ray diffraction and Fourier transform infrared studies. Scanning electron microscopic studies of CaSO4 are also carried out. The TSL glow curves of undoped CaSO4, Cu- and Mn-doped CaSO4 are studied. Comparison of the thermoluminescence (TL) intensity of the most intensive glow peak of Cu-doped CaSO4 compound with that of undoped CaSO4 shows that addition of Cu impurity in CaSO4 compound enhances the TL intensity by about four times. However, the addition of Mn impurity to undoped CaSO4 increases the TL intensity by about three times when compared with that of undoped CaSO4. The TL-dose dependence of all three samples was studied and was observed to be almost linear in the studied range of irradiation time. Among the samples studied, namely undoped CaSO4 and Cu- and Mn-doped CaSO4, Cu-doped CaSO4 is found to be the most sensitive. The trap parameters, namely order of kinetics (b), activation energy (E) and frequency factor (s) associated with the most intensive glow peaks of CaSO4:Mn, CaSO4:Cu and CaSO4 phosphors were determined using the glow curve shape (Chen's) method.

Biotransformation of Furanic and Phenolic Compounds with Hydrogen Gas Production in a Microbial Electrolysis Cell.

PubMed

Zeng, Xiaofei; Borole, Abhijeet P; Pavlostathis, Spyros G

2015-11-17

Furanic and phenolic compounds are problematic byproducts resulting from the breakdown of lignocellulosic biomass during biofuel production. The capacity of a microbial electrolysis cell (MEC) to produce hydrogen gas (H2) using a mixture of two furanic (furfural, FF; 5-hydroxymethyl furfural, HMF) and three phenolic (syringic acid, SA; vanillic acid, VA; and 4-hydroxybenzoic acid, HBA) compounds as the substrate in the bioanode was assessed. The rate and extent of biotransformation of the five compounds and efficiency of H2 production, as well as the structure of the anode microbial community, were investigated. The five compounds were completely transformed within 7-day batch runs and their biotransformation rate increased with increasing initial concentration. At an initial concentration of 1200 mg/L (8.7 mM) of the mixture of the five compounds, their biotransformation rate ranged from 0.85 to 2.34 mM/d. The anode Coulombic efficiency was 44-69%, which is comparable to that of wastewater-fed MECs. The H2 yield varied from 0.26 to 0.42 g H2-COD/g COD removed in the anode, and the bioanode volume-normalized H2 production rate was 0.07-0.1 L/L-d. The biotransformation of the five compounds took place via fermentation followed by exoelectrogenesis. The major identified fermentation products that did not transform further were catechol and phenol. Acetate was the direct substrate for exoelectrogenesis. Current and H2 production were inhibited at an initial substrate concentration of 1200 mg/L, resulting in acetate accumulation at a much higher level than that measured in other batch runs conducted with a lower initial concentration of the five compounds. The anode microbial community consisted of exoelectrogens, putative degraders of the five compounds, and syntrophic partners of exoelectrogens. The MEC H2 production demonstrated in this study is an alternative to the currently used process of reforming natural gas to supply H2 needed to upgrade bio-oils to stable

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

PubMed Central

Wang, Yuanqi; Hatt, Janet K.; Tsementzi, Despina; Rodriguez-R, Luis M.; Ruiz-Pérez, Carlos A.; Kizer, Heidi; Maresca, Gina; Krishnan, Raj; Poretsky, Rachel; Spain, Jim C.

2017-01-01

ABSTRACT A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called “rare biosphere.” How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species. IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

PubMed

Wang, Yuanqi; Hatt, Janet K; Tsementzi, Despina; Rodriguez-R, Luis M; Ruiz-Pérez, Carlos A; Weigand, Michael R; Kizer, Heidi; Maresca, Gina; Krishnan, Raj; Poretsky, Rachel; Spain, Jim C; Konstantinidis, Konstantinos T

2017-04-15

A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species. IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so

Phenolic root exudate and tissue compounds vary widely among temperate forest tree species and have contrasting effects on soil microbial respiration.

PubMed

Zwetsloot, Marie J; Kessler, André; Bauerle, Taryn L

2018-04-01

Root-soil interactions fundamentally affect the terrestrial carbon (C) cycle and thereby ecosystem feedbacks to climate change. This study addressed the question of whether the secondary metabolism of different temperate forest tree species can affect soil microbial respiration. We hypothesized that phenolics can both increase and decrease respiration depending on their function as food source, mobilizer of other soil resources, signaling compound, or toxin. We analyzed the phenolic compounds from root exudates and root tissue extracts of six tree species grown in a glasshouse using high-performance liquid chromatography. We then tested the effect of individual phenolic compounds, representing the major identified phenylpropanoid compound classes, on microbial respiration through a 5-d soil incubation. Phenolic root profiles were highly species-specific. Of the eight classes identified, flavonoids were the most abundant, with flavanols being the predominating sub-class. Phenolic effects on microbial respiration ranged from a 26% decrease to a 46% increase, with reduced respiration occurring in the presence of compounds possessing a catechol ring. Tree species variation in root phenolic composition influences the magnitude and direction of root effects on microbial respiration. Our data support the hypothesis that functional group rather than biosynthetic class determines the root phenolic effect on soil C cycling. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Biotransformation of furanic and phenolic compounds with hydrogen gas production in a microbial electrolysis cell

DOE PAGES

Zeng, Xiaofei; Borole, Abhijeet P.; Pavlostathis, Spyros G.

2015-10-27

In this study, furanic and phenolic compounds are problematic byproducts resulting from the decomposition of lignocellulosic biomass during biofuel production. This study assessed the capacity of a microbial electrolysis cell (MEC) to produce hydrogen gas (H 2) using a mixture of two furanic (furfural, FF; 5-hydroxymethyl furfural, HMF) and three phenolic (syringic acid, SA; vanillic acid, VA; and 4-hydroxybenzoic acid, HBA) compounds as the sole carbon and energy source in the bioanode. The rate and extent of biotransformation of the five compounds, efficiency of H 2 production, as well as the anode microbial community structure were investigated. The five compoundsmore » were completely transformed within 7-day batch runs and their biotransformation rate increased with increasing initial concentration. At an initial concentration of 1,200 mg/L (8.7 mM) of the mixture of the five compounds, their biotransformation rate ranged from 0.85 to 2.34 mM/d. The anode coulombic efficiency was 44-69%, which is comparable to wastewater-fed MECs. The H 2 yield varied from 0.26 to 0.42 g H 2-COD/g COD removed in the anode, and the bioanode volume-normalized H 2 production rate was 0.07-0.1 L/L-d. The major identified fermentation products that did not transform further were catechol and phenol. Acetate was the direct substrate for exoelectrogenesis. Current and H 2 production were inhibited at an initial substrate concentration of 1,200 mg/L, resulting in acetate accumulation at a much higher level than that measured in other batch runs conducted with a lower initial concentration of the five compounds. The anode microbial community consisted of exoelectrogens, putative degraders of the five compounds, and syntrophic partners of exoelectrogens. The H 2 production route demonstrated in this study has proven to be an alternative to the currently used process of reforming natural gas to supply H 2 needed to upgrade bio-oils to stable hydrocarbon fuels.« less

Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health.

PubMed

Bitas, Vasileios; Kim, Hye-Seon; Bennett, Joan W; Kang, Seogchan

2013-08-01

Secreted proteins and metabolites play diverse and critical roles in organismal and organism-environment interactions. Volatile organic compounds (VOC) can travel far from the point of production through the atmosphere, porous soils, and liquid, making them ideal info-chemicals for mediating both short- and long-distance intercellular and organismal interactions. Critical ecological roles for animal- and plant-derived VOC in directing animal behaviors and for VOC as a language for plant-to-plant communication and regulators of various physiological processes have been well documented. Similarly, microbial VOC appear to be involved in antagonism, mutualism, intra- and interspecies regulation of cellular and developmental processes, and modification of their surrounding environments. However, the available knowledge of how microbial VOC affect other organisms is very limited. Evidence supporting diverse roles of microbial VOC with the focus on their impact on plant health is reviewed here. Given the vast diversity of microbes in nature and the critical importance of microbial communities associated with plants for their ecology and fitness, systematic exploration of microbial VOC and characterization of their biological functions and ecological roles will likely uncover novel mechanisms for controlling diverse biological processes critical to plant health and will also offer tangible practical benefits in addressing agricultural and environmental problems.

Production of a High Efficiency Microbial Flocculant by Proteus mirabilis TJ-1 Using Compound Organic Wastewater

NASA Astrophysics Data System (ADS)

Zhang, Zhiqiang; Xia, Siqing; Zhang, Jiao

2010-11-01

The production of a high efficiency microbial flocculant (MBF) by Proteus mirabilis TJ-1 using compound organic wastewater was investigated. To cut down the cost of the MBF production, several nutritive organic wastewaters were selected to replace glucose and peptone as the carbon source and the nitrogen source in the optimized medium of strain TJ-1, respectively. The compound wastewater of the milk candy and the soybean milk was found to be good carbon source and nitrogen source for this strain to produce MBF. The cost-effective culture medium consists of (per liter): 800 mL wastewater of milk candy, 200 mL wastewater of soybean milk, 0.3 g MgSO4ṡ7 H2O, 5 g K2HPO4, 2 g and KH2PO4, pH 7.0. The economic cost for the MBF production can be cut down over a half by using the developed culture medium. Furthermore, the utilization of the two wastewaters in the preparation of culture medium of strain TJ-1 can not only save their big treatment cost, but also realize their resource reuse.

[Microbial denitrogenation of fuel oil].

PubMed

Li, Shan-shan; Ma, Ting; Li, Guo-qiang; Liang, Feng-lai; Liu, Ru-lin

2006-12-01

The amount of organic nitrides contained in fuel oil is smaller than the one of organic sulfur compounds, but the existence of them is enough to affect the invariability of oil product greatly , and has a big effect on the color of oil. They also contribute to catalyst poisoning during the refining of crude oil, thus reducing the catalyzing rate of the catalyst and increasing process costs. Further more, some nitrogen organic compounds possess mutagenic and toxic activities. The combustion of these contaminants form nitrogen oxides (NOx), releasing of which to the air will cause the formation of acid rain and hence to air pollution. The classical hydroprocessing methods of nitrogen removal are costly and complicated, so the scientists are more and more interested in microbial denitrogenation. The aspects as follows are introduced, including the aromatic nitrogen compounds of fuel oil, the varieties of denitrogenation techincs, the classes of microbial denitrogenation and its biochemical pathways, molecular genetics developments of carbazole-degradative genes, and our opinion of the research direction in the future.

Microbial colonization of biopolymeric thin films containing natural compounds and antibiotics fabricated by MAPLE

NASA Astrophysics Data System (ADS)

Cristescu, R.; Surdu, A. V.; Grumezescu, A. M.; Oprea, A. E.; Trusca, R.; Vasile, O.; Dorcioman, G.; Visan, A.; Socol, G.; Mihailescu, I. N.; Mihaiescu, D.; Enculescu, M.; Chifiriuc, M. C.; Boehm, R. D.; Narayan, R. J.; Chrisey, D. B.

2015-05-01

Although a great number of antibiotics are currently available, they are often rendered ineffective by the ability of microbial strains to develop genetic resistance and to grow in biofilms. Since many antimicrobial agents poorly penetrate biofilms, biofilm-associated infections often require high concentrations of antimicrobial agents for effective treatment. Among the various strategies that may be used to inhibit microbial biofilms, one strategy that has generated significant interest involves the use of bioactive surfaces that are resistant to microbial colonization. In this respect, we used matrix assisted pulsed laser evaporation (MAPLE) involving a pulsed KrF* excimer laser source (λ = 248 nm, τ = 25 ns, ν = 10 Hz) to obtain thin composite biopolymeric films containing natural (flavonoid) or synthetic (antibiotic) compounds as bioactive substances. Chemical composition and film structures were investigated by Fourier transform infrared spectroscopy and X-ray diffraction. Films morphology was studied by scanning electron microscopy and transmission electron microscopy. The antimicrobial assay of the microbial biofilms formed on these films was assessed by the viable cell counts method. The flavonoid-containing thin films showed increased resistance to microbial colonization, highlighting their potential to be used for the design of anti-biofilm surfaces.

A Novel Method for Analyzing Microbially Affiliated Volatile Organic Compounds in Soil Environments

NASA Astrophysics Data System (ADS)

Ruhs, C. V.; McNeal, K. S.

2010-12-01

A concerted, international effort by citizens, governments, industries and educational systems is necessary to address the myriad environmental issues that face us today. The authors of this paper concentrate on soil environments and, specifically, the methods currently used to characterize them. The ability to efficiently and effectively monitor and characterize various soils is desired, allows for the study, supervision, and protection of natural and cultivated ecosystems, and may assist stakeholders in meeting governmentally-imposed environmental standards. This research addresses soil characterization by a comparison of four methods that emphasize a combination of microbial community and metabolic measures: BIOLOG, fatty acid methyl-ester analysis (FAME), descriptive physical and chemical analysis (moisture content, pH, carbon content, nutrient content, and grain size), and the novel soil-microbe volatile organic compound analysis (SMVOC) presented in this work. In order to achieve the method comparison, soils were collected from three climatic regions (Bahamas, Michigan, and Mississippi), with three samples taken from niche ecosystems found at each climatic region (a total of nine sites). Of interest to the authors is whether or not an investigation of microbial communities and the volatile organic compounds (VOCs) produced by microbial communities from nine separate soil ecosystems provides useful information about soil dynamics. In essence, is analysis of soil-derived VOCs using gas chromatography-mass spectrometry (GC-MS) an effective method for characterizing microbial communities and their metabolic activity of soils rapidly and accurately compared with the other three traditional characterization methods? Preliminary results suggest that VOCs in each of these locales differ with changes in soil types, soil moisture, and bacterial community. Each niche site shows distinct patterns in both VOCs and BIOLOG readings. Results will be presented to show the

Microbial Volatile Organic Compound Emissions from Stachybotrys chartarum growing on Gypsum Wallboard and Ceiling tile

EPA Science Inventory

This study compared seven toxigenic strains of S. chartarum found in water-damaged buildings to characterize the microbial volatile organic compound (MVOC) emissions profile while growing on gypsum wallboard (W) and ceiling tile (C) coupons. The inoculated coupons with their sub...

Performance of Microbial Concrete Developed Using Bacillus Subtilus JC3

NASA Astrophysics Data System (ADS)

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.

[The diagnosis of so-called whiplash injury of the cervical vertebrae. A case report].

PubMed

Ludolph, E; Meindl, U

1990-08-01

The acceleration injury of the cervical spine (so-called whip-lash injury) is a common traumatic mechanism in traffic accident. Severe damages are possible. Scepticism is necessary, if several hours or days are symptom-free. Radiological results which seem to prove an injury should be controlled. Severe injuries are in consideration of the symptom-free course incredible. This is demonstrated with a description of a case.

Integrating microbial physiology and enzyme traits in the quality model

NASA Astrophysics Data System (ADS)

Sainte-Marie, Julien; Barrandon, Matthieu; Martin, Francis; Saint-André, Laurent; Derrien, Delphine

2017-04-01

Microbe activity plays an undisputable role in soil carbon storage and there have been many calls to integrate microbial ecology in soil carbon (C) models. With regard to this challenge, a few trait-based microbial models of C dynamics have emerged during the past decade. They parameterize specific traits related to decomposer physiology (substrate use efficiency, growth and mortality rates...) and enzyme properties (enzyme production rate, catalytic properties of enzymes…). But these models are built on the premise that organic matter (OM) can be represented as one single entity or are divided into a few pools, while organic matter exists as a continuum of many different compounds spanning from intact plant molecules to highly oxidised microbial metabolites. In addition, a given molecule may also exist in different forms, depending on its stage of polymerization or on its interactions with other organic compounds or mineral phases of the soil. Here we develop a general theoretical model relating the evolution of soil organic matter, as a continuum of progressively decomposing compounds, with decomposer activity and enzyme traits. The model is based on the notion of quality developed by Agren and Bosatta (1998), which is a measure of molecule accessibility to degradation. The model integrates three major processes: OM depolymerisation by enzyme action, OM assimilation and OM biotransformation. For any enzyme, the model reports the quality range where this enzyme selectively operates and how the initial quality distribution of the OM subset evolves into another distribution of qualities under the enzyme action. The model also defines the quality range where the OM can be uptaken and assimilated by microbes. It finally describes how the quality of the assimilated molecules is transformed into another quality distribution, corresponding to the decomposer metabolites signature. Upon decomposer death, these metabolites return to the substrate. We explore here the how

Microbial use of gas phase organic compounds in the surface ocean

NASA Astrophysics Data System (ADS)

Arrieta, Jesus M.; Duarte, Carlos M.; Monserrat Sala, M.; Dachs, Jordi

2016-04-01

Large diffusive air-sea fluxes of gas-phase organic carbon (GOC) have been identified, indicating that the ocean may be a major sink for these compounds. However, little is known about the fate of these GOC compounds entering the surface ocean. We report efficient use of atmospheric GOC by marine prokaryotes at different locations in the NE Subtropical Atlantic Ocean, the Arctic Ocean and the Mediterranean Sea. Our results indicate that between 2 to 27% of the prokaryotic carbon demand was supported by GOC. Between 1 and 94% of the GOC entering the ocean was consumed by prokaryotes depending on locations, thus sustaining a disequilibrium, which drives the transfer of GOC from the atmosphere into the ocean. The magnitude of this, previously unnoticed, microbial GOC utilization stresses the need for incorporating the oceanic uptake of gaseous organic carbon into the global carbon budget.

Exposure to grain dust and microbial components in the Norwegian grain and compound feed industry.

PubMed

Halstensen, Anne Straumfors; Heldal, Kari Kulvik; Wouters, Inge M; Skogstad, Marit; Ellingsen, Dag G; Eduard, Wijnand

2013-11-01

The aim of this study was to extensively characterize grain workers' personal exposure during work in Norwegian grain elevators and compound feed mills, to identify differences in exposures between the workplaces and seasons, and to study the correlations between different microbial components. Samples of airborne dust (n = 166) were collected by full-shift personal sampling during work in 20 grain elevators and compound feed mills during one autumn season and two winter seasons. The personal exposure to grain dust, endotoxins, β-1→3-glucans, bacteria, and fungal spores was quantified. Correlations between dust and microbial components and differences between workplaces and seasons were investigated. Determinants of endotoxin and β-1→3-glucan exposure were evaluated by linear mixed-effect regression modeling. The workers were exposed to an overall geometric mean of 1.0mg m(-3) inhalable grain dust [geometric standard deviation (GSD) = 3.7], 628 endotoxin units m(-3) (GSD = 5.9), 7.4 µg m(-3) of β-1→3-glucan (GSD = 5.6), 21 × 10(4) bacteria m(-3) (GSD = 7.9) and 3.6 × 10(4) fungal spores m(-3) (GSD = 3.4). The grain dust exposure levels were similar across workplaces and seasons, but the microbial content of the grain dust varied substantially between workplaces. Exposure levels of all microbial components were significantly higher in grain elevators compared with all other workplaces. The grain dust exposure was significantly correlated (Pearson's r) with endotoxin (rp = 0.65), β-1→3-glucan (rp = 0.72), bacteria (rp = 0.44) and fungal spore (rp = 0.48) exposure, whereas the explained variances were strongly dependent on the workplace. Bacteria, grain dust, and workplace were important determinants for endotoxin exposure, whereas fungal spores, grain dust, and workplace were important determinants for β-1→3-glucan exposure. Although the workers were exposed to a relatively low mean dust level, the microbial exposure was high. Furthermore, the

Microbial production of volatile sulphur compounds in the large intestine of pigs fed two different diets

USDA-ARS?s Scientific Manuscript database

Only little is known about the microbial production of volatile sulphur compounds (VSC) in the 18 gastrointestinal tract, the dietary influence, and the magnitude of this production. To investigate intestinal VSC production in more detail, pigs were fed diets based on either wheat and barley (CONTRO...

ADAPTATION OF AQUIFER MICROBIAL COMMUNITIES TO THE BIODEGRADATION OF XENOBIOTIC COMPOUNDS: INFLUENCE OF SUBSTRATE CONCENTRATION AND PREEXPOSURE

EPA Science Inventory

Studies were conducted to examine the adaptation response of aquifer microbial communities to xenobiotic compounds and the influence of chemical preexposure in the laboratory and in situ on adaptation. Adaptation and biodegradation were assessed as mineralization and cellular inc...

[Social and legal problems in the so-called poriomania, with special reference to desertion and AWOL].

PubMed

Dieckhöfer, K; Vogel, T

1974-01-01

Following a synopsis of the main bibliography and a number of own cases it could be pointed out that the so-called poriomania is accompanied with punishable acts in about one-third of all cases. An analysis of the different delicts yielded as result a clear preponderance of larcency of money, fraud and embezzlement - in comparison with desertion and absence without official leave. Only 20% of all cases with punishable acts were denounced. In former times, up to the first world war, about a percentage of 74 of all criminal cases in connection with poriomania was exonerated on the erroneous assumption that the behaviour of the so-called poriomania would be caused by epilepsy. About one third of all persons with poriomania are feebleminded. There is a high inclination to fraud, pseudologia, abuse of alcohol and prostitution. An enlarged inclination (15%) to suicide is also remarkable. A familiar accumulation of poriomania does not justify the supposition of an endogenous factor. Therefore criminal acts in connection with poriomania connot be exonerated. The personality of men with poriomania is characterised by unsteadiness, unstableness and velleity.

Incredibly Versatile Microbial Fuel Cells Innovative Ideas at HES-SO Valais-Wallis for Solving Topical Problems.

PubMed

Heinzelmann, Elsbeth

2016-01-01

At HES-SO Valais-Wallis, Prof. Fabian Fischer is specialized in microbial fuel cells for novel applications that meet the challenge of producing renewable energies. He and his team possess a unique expertise in bioelectric energy vector generation, phosphate extraction (CHIMIA 2015, 69, 296) and the testing of antimicrobial surfaces. Let's take a look behind the scenes of the Institute of Life Technologies in Sion.

Removal and fate of trace organic compounds in microbial fuel cells.

PubMed

Wang, Heming; Heil, Dean; Ren, Zhiyong Jason; Xu, Pei

2015-04-01

This study focused on understanding and characterizing the removal of trace organic compounds (TOrCs) in microbial fuel cells (MFC). 26 TOrCs with broad physicochemical properties were spiked in synthetic wastewater. Single-chamber air-cathode MFC (SMFC) and double-chamber air-cathode MFC (DMFC) were constructed to provide combined or separated oxidation/reduction environments for TOrCs removal. The study showed that TOrCs removal processes involved both sorption and biodegradation. For neutral TOrCs, the removal efficiency was affected primarily by the biodegradability probability and hydrophobicity of the compounds, while electrostatic interactions played an additional role in the MFCs as the removal of positively charged TOrCs was generally higher than negatively charged TOrCs. The presence of TOrCs showed negligible impact on MFC power generation, likewise the operation of MFCs had marginal effect on TOrCs removal, except longer residence time in MFCs improved biological removal performance. Copyright © 2014 Elsevier Ltd. All rights reserved.

Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review

PubMed Central

Zou, Wei; Zhao, Changqing; Luo, Huibo

2018-01-01

Strong flavor baijiu (SFB), also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected. PMID:29686656

Microbial Electrosynthesis: Feeding Microbes Electricity To Convert Carbon Dioxide and Water to Multicarbon Extracellular Organic Compounds

PubMed Central

Nevin, Kelly P.; Woodard, Trevor L.; Franks, Ashley E.; Summers, Zarath M.; Lovley, Derek R.

2010-01-01

The possibility of providing the acetogenic microorganism Sporomusa ovata with electrons delivered directly to the cells with a graphite electrode for the reduction of carbon dioxide to organic compounds was investigated. Biofilms of S. ovata growing on graphite cathode surfaces consumed electrons with the reduction of carbon dioxide to acetate and small amounts of 2-oxobutyrate. Electrons appearing in these products accounted for over 85% of the electrons consumed. These results demonstrate that microbial production of multicarbon organic compounds from carbon dioxide and water with electricity as the energy source is feasible. PMID:20714445

Effects of furan derivatives and phenolic compounds on electricity generation in microbial fuel cells

NASA Astrophysics Data System (ADS)

Catal, Tunc; Fan, Yanzhen; Li, Kaichang; Bermek, Hakan; Liu, Hong

Lignocellulosic biomass is an attractive fuel source for MFCs due to its renewable nature and ready availability. Furan derivatives and phenolic compounds could be potentially formed during the pre-treatment process of lignocellulosic biomass. In this study, voltage generation from these compounds and the effects of these compounds on voltage generation from glucose in air-cathode microbial fuel cells (MFCs) were examined. Except for 5-hydroxymethyl furfural (5-HMF), all the other compounds tested were unable to be utilized directly for electricity production in MFCs in the absence of other electron donors. One furan derivate, 5-HMF and two phenolic compounds, trans-cinnamic acid and 3,5-dimethoxy-4-hydroxy-cinnamic acid did not affect electricity generation from glucose at a concentration up to 10 mM. Four phenolic compounds, including syringaldeyhde, vanillin, trans-4-hydroxy-3-methoxy, and 4-hydroxy cinnamic acids inhibited electricity generation at concentrations above 5 mM. Other compounds, including 2-furaldehyde, benzyl alcohol and acetophenone, inhibited the electricity generation even at concentrations less than 0.2 mM. This study suggests that effective electricity generation from the hydrolysates of lignocellulosic biomass in MFCs may require the employment of the hydrolysis methods with low furan derivatives and phenolic compounds production, or the removal of some strong inhibitors prior to the MFC operation, or the improvement of bacterial tolerance against these compounds through the enrichment of new bacterial cultures or genetic modification of the bacterial strains.

[Technical information: The 'so called' Camille Bernard lower lip reconstruction: An eponymous confusion clarified].

PubMed

Marck, K W; Martin, D

2017-12-01

The use of eponyms honours those who have contributed to the development of medicine and facilitates communication between colleagues. Eponyms are based on historical knowledge to know who was the first to use a given technique. In the previous century, two different operative procedures have been attached to the 'so called' Bernard lower lip reconstruction. This historical literature on lip reconstruction with a focus on the years 1853-1855 elucidates the roles of Bernard, Saeman, Desgranges and Burow, and gives suggestions for eponyms that do justice to the innovating surgeons Bernard, Burow and Desgranges. Copyright © 2017. Published by Elsevier Masson SAS.

Microbial denitrogenation of fossil fuels.

PubMed

Benedik, M J; Gibbs, P R; Riddle, R R; Willson, R C

1998-09-01

The microbial degradation of nitrogen compounds from fossil fuels is important because of the contribution these contaminants make to the formation of nitrogen oxides (NOx) and hence to air pollution and acid rain. They also contribute to catalyst poisoning during the refining of crude oil, thus reducing process yields. We review the current status of microbial degradation of aromatic nitrogen compounds and discuss the potential of microbial processes to alleviate these problems.

Screening of Microbial Extracts for Anticancer Compounds Using Streptomyces Kinase Inhibitor Assay.

PubMed

Shanbhag, Prashant; Bhave, Sarita; Vartak, Ashwini; Kulkarni-Almeida, Asha; Mahajan, Girish; Villanueva, Ivan; Davies, Julian

2015-07-01

Eukaryotic kinases are known to play an important role in signal transduction pathways by phosphorylating their respective substrates. Abnormal phosphorylations by these kinases have resulted in diseases. Hence inhibitors of kinases are of considerable pharmaceutical interest for a wide variety of disease targets, especially cancers. A number of reports have been published which indicate that eukaryotic-like kinases may complement two-component kinase systems in several bacteria. In Streptomyces sp. such kinases have been found to have a role in formation of aerial hyphae, spores, pigmentation & even in antibiotic production in some strains. Eukaryotic kinase inhibitors are seen to inhibit formation of aerial mycelia in Streptomyces without inhibiting vegetative mycelia. This property has been used to design an assay to screen for eukaryotic kinase inhibitors. The assay involves testing of compounds against Streptomyces 85E ATCC 55824 using agar well diffusion method. Inhibitors of kinases give rise to "bald" colonies where aerial mycelia and sporulation inhibition is seen. The assay has been standardized using known eukaryotic protein kinase inhibiting anticancer agents like AG-490, AG-1295, AG-1478, Flavopiridol and Imatinib as positive controls, at a concentration ranging from 10 μg/well to 100 μg/well. Anti-infective compounds which are not reported to inhibit eukaryotic protein kinases were used as negative controls. A number of microbial cultures have been screened for novel eukaryotic protein kinase inhibitors. Further these microbial extracts were tested in various cancer cell lines like Panel, HCT116, Calul, ACHN and H460 at a concentration of 10 μg/mL/ well. The anticancer data was seen correlating well with the Streptomyces kinase assay thus validating the assay.

What Plurals and Compounds Reveal about Constraints in Word Formation

ERIC Educational Resources Information Center

Jaensch, Carol; Heyer, Vera; Gordon, Peter; Clahsen, Harald

2014-01-01

Morphological systems are constrained in how they interact with each other. One case that has been widely studied in the psycholinguistic literature is the avoidance of plurals inside compounds (e.g. *"rats eater" vs. "rat eater") in English and other languages, the so-called "plurals-in-compounds effect." Several…

The So-Called 'Face on Mars' in Infrared

NASA Technical Reports Server (NTRS)

2002-01-01

[figure removed for brevity, see original site] (Released 24 July 2002) This set of THEMIS infrared images shows the so-called 'face on Mars' landform located in the northern plains of Mars near 40o N, 10o W (350 o E). The 'face' is located near the center of the image approximately 1/6 of the way down from the top, and is one of a large number of knobs, mesas, hills, and buttes that are visible in this THEMIS image. The THEMIS infrared camera has ten different filters between 6.2 and 15 micrometers - nine view the surface and one views the CO₂ atmosphere. The calibrated and geometrically projected data from all of the nine surface-viewing filters are shown in this figure. The major differences seen in this region are due to temperature effects -- sunlit slopes are warm (bright), whereas those in shadow are cold (dark), The temperature in this scene ranges from 50 oC (darkest) to 15 oC (brightest). The major differences between the different filters are due to the expected variation in the amount of energy emitted from the surface at different wavelengths. Minor spectral differences (infrared 'color') also exist between the different filters, but these differences are small in this region due to the uniform composition of the rocks and soils exposed at the surface. The THEMIS infrared camera provides an excellent regional view of Mars - this image covers an area 32 kilometers (20 miles) by approximately 200 kilometers (125 miles) at a resolution of 100 meters per picture element ('pixel'). This image provides a broad perspective of the landscape and geology of the Cydonia region, showing numerous knobs and hills that have been eroded into a remarkable array of different shapes. In this 'big picture' view the Cydonia region is seen to be covered with dozens of interesting knobs and mesas that are similar in many ways to the knob named the 'face' - so many in fact that it requires care to discover the 'face' among this jumble of knobs and hills. The 3-km

[Chronic mucosynechial pemphigoid: so-called ocular pemphigus].

PubMed

Zingirian, M

1976-01-01

The so-called ocular pemphigus is an oculocutaneomucosal disease, the clinical manifestations of which have been recognized for over a century while its recognition as a nosological and histopathological unit is quite recent. The clinical picture in the eye consists essentially of progressive scar contraction which, preceded by a transient bullous phase, leads to symblepharon, entropion and trichiasis. Corneal complications, such as bullous eruption, erosions, proliferation of vasculoconnective tissue, supervene later. The final appearance is that of complete xerosis with total symblepharon producing a typical 'statute eye'. This local process may be accompanied by bullous lesions of the skin and mucous membranes but the general condition of the patient invariably remains good. In the advanced stages of the disease the appearance is described as 'pemphigoid facies'. The nosological place of ocular pemphigus has been a matter of debate. At various times it has been identified with pemphigus vulgaris, dermatitis herpetiformis of Duhring-Brocq, erythema multiforme of Hebra, Stevens-Johnson syndrome, syphilitic dermatitis bullosa and other bullous dermatoses. At present the condition is universally recognized as a clinical entity, referred to as chronic mucosynechial pemphigoid (CMSP). The anatomopathological picture is quite peculiar. The elementary lesion is a sub-epidermic bulla, hence easily distinguished from that of pemphigus vulgaris, which is situated in the Malpighian layer. This difference applies to the lesions of the skin as well as to those of the mucous membranes including the conjuctiva. In the conjunctiva, epithelial changes suggestive of its epidermization were demonstrated. The Malpighian layer shows a high glycogen and DNA content with overall reduction in enzyme activity. The dermis shows infiltration by lymphocytes, histiocytes and plasma cells, and a considerable increase in hyaluronic acid content. There are many areas of dermoepidermal

The ternary system K2SO4MgSO4CaSO4

USGS Publications Warehouse

Rowe, J.J.; Morey, G.W.; Silber, C.C.

1967-01-01

Melting and subsolidus relations in the system K2SO4MgSO4CaSO4 were studied using heating-cooling curves, differential thermal analysis, optics, X-ray diffraction at room and high temperatures and by quenching techniques. Previous investigators were unable to study the binary MgSO4CaSO4 system and the adjacent area in the ternary system because of the decomposition of MgSO4 and CaSO4 at high temperatures. This problem was partly overcome by a novel sealed-tube quenching method, by hydrothermal synthesis, and by long-time heating in the solidus. As a result of this study, we found: (1) a new compound, CaSO4??3MgSO4 (m.p. 1201??C) with a field extending into the ternary system; (2) a high temperature form of MgSO4 with a sluggishly reversible inversion. An X-ray diffraction pattern for this polymorphic form is given; (3) the inversion of ??-CaSO4 (anhydrite) to ??-CaSO4 at 1195??C, in agreement with grahmann; (1) (4) the melting point of MgSO4 is 1136??C and that of CaSO4 is 1462??C (using sealed tube methods to prevent decomposition of the sulphates); (5) calcium langbeinite (K2SO4??2CaSO4) is the only compound in the K2SO4CaSO4 binary system. This resolved discrepancies in the results of previous investigators; (6) a continuous solid solution series between congruently melting K2SOP4??2MgSO4 (langbeinite) and incongruently melting K2SO4??2CaSO4 (calcium langbeinite); (7) the liquidus in the ternary system consists of primary phase fields of K2SO4, MgSO4, CaSO4, langbeinite-calcium langbeinite solid solution, and CaSO4??3MgSO4. The CaSO4 field extends over a large portion of the system. Previously reported fields for the compounds (K2SO4??MgSO4??nCaSO4), K2SO4??3CaSO4 and K2SO4??CaSO4 were not found; (8) a minimum in the ternary system at: 740??C, 25% MgSO4, 6% CaSO4, 69% K2SO4; and ternary eutectics at 882??C, 49% MgSO4, 19% CaSO4, 32% K2SO4; and 880??, 67??5% MgSO4, 5% CaSO4, 27??5% K2SO4. ?? 1967.

Using So-Called Mind-Body Practices to Promote Youths' Well-Being: Reflections on Therapeutic Outcomes, Strategies, and Processes

ERIC Educational Resources Information Center

Renshaw, Tyler L.

2016-01-01

The present article provides commentary on this pioneering special issue covering the usefulness of so-called mind-body practices with youth and in schools. I begin by addressing the way we talk about this approach to practice, describing a few undesirable consequences that can follow from using the mind-body moniker adopted from the world of…

Characterization of microbial communities in subsurface nuclear blast cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P; Czerwinski, Ken; Russell, Charles E

2010-07-13

This US Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Effects of ethanol-based fuel contamination: microbial community changes, production of regulated compounds, and methane generation.

PubMed

Nelson, Denice K; Lapara, Timothy M; Novak, Paige J

2010-06-15

Ethanol-based fuels are becoming more heavily used, increasing the likelihood of ethanol-based fuel spills during transportation and storage. Although ethanol is well-known to be readily biodegradable, very little is known about the effects that such a spill might have on an indigenous microbial community. Of particular concern is that ethanol contamination could stimulate the growth of organisms that can generate regulated compounds and/or produce explosive quantities of methane gas. A column-based study was performed to elucidate the potential impacts of ethanol-based fuel (E85) on the indigenous microbial community during a simulated fuel spill. A continuous dilute supply of E85 resulted in profound shifts in both the bacterial and archaeal communities. The shift was accompanied by the production of high concentrations of volatile fatty acids and butanol, a compound that is regulated in groundwater by some states. Results also indicated that a continuous feed of dilute E85 generated explosive levels of methane within one month of column operation. Quantitative PCR data showed a statistically significant increase in methanogenic populations when compared to a control column. The elevated population numbers correlated to areas of the column receiving a sustained carbon load. Toxicity data indicated that microbial growth was completely inhibited (as evidenced by absence of ethanol breakdown products) at ethanol levels above 6% (v/v). These data suggest that ethanol from ethanol-based fuel can be readily degraded, but can also produce metabolic products that are regulated as well as explosive levels of methane. The core of an E85 spill may serve as a long-term source of contamination as it cannot be degraded until significant dilution has occurred.

Contribution of microbial carbon to soil fractions: significance of diverse microbial group biochemistry

NASA Astrophysics Data System (ADS)

Throckmorton, H.; Bird, J. A.; Dane, L.; Firestone, M. K.; Horwath, W. R.

2011-12-01

The importance of diverse microbial groups to soil C maintenance is still a matter of debate. This study follows the turnover of 13C labeled nonliving residues from diverse microbial groups into soil physical fractions in situ in a temperate forest in California (CA) and a tropical forest in Puerto Rico (PR), during 5 sampling points per site- over a 3 and 2 year period, respectively. Microbial groups include fungi, actinomycetes, Gm(+) bacteria, and Gm(-) bacteria, isolated from CA and PR soils to obtain temperate and tropical isolates composited of 3-4 species per group. The selected density fractionation approach isolated: a "light fraction" (LF), non-mineral aggregate "occluded fraction" (OF), and a "mineral bound fraction" (MF). Pyrolysis gas chromatography mass spectrometry (Py-GC-MS) was employed to characterize microbial group isolates, whole soils, and fractions. Microbial isolates contained unique biochemical fingerprints: temperate and tropical fungi and tropical Gm(-) were characterized by a low abundance of phenol, benzene, and N-compounds compared with other microbial group isolates. Py-GC-MS revealed compositional differences among soil fractions at both sites, likely attributed to differences in the decomposition stage and C source material (ie. plant vs. microbial). For both sites, benzene and N-compounds were greatest in the MF; lignin and phenol compounds were greatest in the LF; and lipids were greatest in the OF. The trend for polysaccharides differed between sites, with the greatest concentration in the CA OF; and for PR with the lowest concentration in the OF, and similar concentrations in the LF and MF. SOM chemistry was most similar between sites in the LF, compared with the OF and MF, suggesting that differences in SOM chemistry between sites may be more attributed to differential decomposition processes than unique litter quality inputs. A substantial portion of microbial C moved from the LF into the OF, and the MF by the first sampling

Microbial electrosynthetic cells

DOEpatents

May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

2018-01-30

Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

Inhibitory Effect of Furanic and Phenolic Compounds on Exoelectrogenesis in a Microbial Electrolysis Cell Bioanode

DOE PAGES

Zeng, Xiaofei; Borole, Abhijeet P.; Pavlostathis, Spyros G.

2016-09-09

Furanic and phenolic compounds are 20 lignocellulose-derived compounds known to inhibit to H2- and ethanol- producing microorganisms in dark fermentation. Bioelectrochemical conversion of furanic and phenolic compounds to electricity or H2 has recently been demonstrated as a productive method to use these compounds. However, potential inhibitory effect of furanic and phenolic compounds on exoelectrogenesis in bioelectrochemical systems is not well understood. This study systematically investigated the inhibitory effect of furfural (FF), 5-hydroxymethylfurfural (HMF), syringic acid (SA), vanillic acid (VA), and 4-hydroxybenzoic acid (HBA) on exoelectrogenesis in the bioanode of a microbial electrolysis cell. A mixture of these five compounds atmore » an increasing initial total concentration from 0.8 to 8.0 g/L resulted in current decrease up to 91%. The observed inhibition primarily affected exoelectrogenesis, instead of non-exoelectrogenic biotransformation pathways (e.g., fermentation) of the five compounds. Furthermore, the parent compounds at a high concentration, as opposed to their biotransformation products, were responsible for the observed inhibition. Tests with individual compounds show that all five parent compounds contributed to the observed inhibition by the mixture. The IC50 (concentration resulting in 50% current decrease) was estimated as 2.7 g/L for FF, 3.0 g/L for HMF, 1.9 g/L for SA, 2.1 g/L for VA and 2.0 g/L for HBA. Nevertheless, these compounds below their non-inhibitory concentrations jointly resulted in significant inhibition as a mixture. Catechol and phenol, which were persistent biotransformation products of the mixture, inhibited exoelectrogens at high concentrations, but to a lesser extent than the parent compounds. Recovery of exoelectrogenesis from inhibition by all compounds was observed, except for catechol, which resulted in irreversible inhibition. The reversibility of inhibition, as well as the observed difference in recovery

Use of natural compounds to improve the microbial stability of Amaranth-based homemade fresh pasta.

PubMed

Del Nobile, M A; Di Benedetto, N; Suriano, N; Conte, A; Lamacchia, C; Corbo, M R; Sinigaglia, M

2009-04-01

A study on the use of natural antimicrobial compounds to improve the microbiological stability of refrigerated amaranth-based homemade fresh pasta is presented in this work. In particular, the antimicrobial activity of thymol, lemon extract, chitosan and grapefruit seed extract (GFSE) has been tested against mesophilic and psychrotrophic bacteria, total coliforms, Staphylococcus spp., yeasts and moulds. A sensory analysis on both fresh and cooked pasta was also run. Results suggest that chitosan and GFSE strongly increase the microbial acceptability limit of the investigated spoilage microorganisms, being the former the most effective. Thymol efficiently reduces the growth of mesophilic bacteria, psychrotrophic bacteria and Staphylococcus spp., whereas it does not affect, substantially, the growth cycle of total coliforms. Lemon extract is the less effective in preventing microbial growth. In fact, it is able to delay only total mesophilic and psychrotrophic bacterial evolution. From a sensorial point of view no significant differences were recorded between the control samples and all the types of loaded amaranth-based pasta.

The So-Called 'Face on Mars'

NASA Technical Reports Server (NTRS)

2002-01-01

(Released 13 April 2002) The Science The so called 'Face on Mars' can be seen slightly above center and to the right in this THEMIS visible image. This 3-km long knob, located near 10o N, 40o W (320o E), was first imaged by the Viking spacecraft in the 1970's and was seen by some to resemble a face carved into the rocks of Mars. Since that time the Mars Orbiter Camera on the Mars Global Surveyor spacecraft has provided detailed views of this hill that clearly show that it is a normal geologic feature with slopes and ridges carved by eons of wind and downslope motion due to gravity. A similar-size hill in Phoenix, Arizona resembles a camel lying on the ground, and Phoenicians whimsically refer to it as Camelback Mountain. Like the hills and knobs of Mars, however, Camelback Mountain was carved into its unusual shape by thousands of years of erosion. The THEMIS image provides a broad perspective of the landscape in this region, showing numerous knobs and hills that have been eroded into a remarkable array of different shapes. Many of these knobs, including the 'Face', have several flat ledges partway up the hill slopes. These ledges are made of more resistant layers of rock and are the last remnants of layers that once were continuous across this entire region. Erosion has completely removed these layers in most places, leaving behind only the small isolated hills and knobs seen today. Many of the hills and ridges in this area also show unusual deposits of material that occur preferentially on the cold, north-facing slopes. It has been suggested that these deposits were 'pasted' on the slopes, with the distinct, rounded boundary on their upslope edges being the highest remaining point of this pasted-on layer. In several locations, such as in the large knob directly south of the 'Face', these deposits occur at several different heights on the hill. This observation suggests the layer once draped the entire knob and has since been removed from all but the north

Microbial toxicity of the insensitive munitions compound, 2,4-dinitroanisole (DNAN), and its aromatic amine metabolites.

PubMed

Liang, Jidong; Olivares, Christopher; Field, Jim A; Sierra-Alvarez, Reyes

2013-11-15

2,4-Dinitroanisole (DNAN) is an insensitive munitions compound considered to replace conventional explosives such as 2,4,6-trinitrotoluene (TNT). DNAN undergoes facile microbial reduction to 2-methoxy-5-nitroaniline (MENA) and 2,4-diaminoanisole (DAAN). This study investigated the inhibitory effect of DNAN, MENA, and DAAN toward various microbial targets in anaerobic (acetoclastic methanogens) and aerobic (heterotrophs and nitrifiers) sludge, and the bioluminescent bacterium, Aliivibrio fischeri, used in the Microtox assay. Aerobic heterotrophic and nitrifying batch experiments with DAAN could not be performed because the compound underwent extensive autooxidation in these assays. DNAN severely inhibited methanogens, nitrifying bacteria, and A. fischeri (50% inhibitory concentrations (IC50) ranging 41-57μM), but was notably less inhibitory to aerobic heterotrophs (IC50>390 μM). Reduction of DNAN to MENA and DAAN lead to a marked decrease in methanogenic inhibition (i.e., DNAN>MENA≈DAAN). Reduction of all nitro groups in DNAN also resulted in partial detoxification in assays with A. fischeri. In contrast, reduction of a single nitro group did not alter the inhibitory impact of DNAN toward A. fischeri and nitrifying bacteria given the similar IC50 values determined for MENA and DNAN in these assays. These results indicate that reductive biotransformation could reduce the inhibitory potential of DNAN. Copyright © 2013 Elsevier B.V. All rights reserved.

Lipid Biomarkers for a Hypersaline Microbial Mat Community

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

2003-01-01

The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

The Neuro-endocrinological Role of Microbial Glutamate and GABA Signaling

PubMed Central

Mazzoli, Roberto; Pessione, Enrica

2016-01-01

Gut microbiota provides the host with multiple functions (e.g., by contributing to food digestion, vitamin supplementation, and defense against pathogenic strains) and interacts with the host organism through both direct contact (e.g., through surface antigens) and soluble molecules, which are produced by the microbial metabolism. The existence of the so-called gut–brain axis of bi-directional communication between the gastrointestinal tract and the central nervous system (CNS) also supports a communication pathway between the gut microbiota and neural circuits of the host, including the CNS. An increasing body of evidence has shown that gut microbiota is able to modulate gut and brain functions, including the mood, cognitive functions, and behavior of humans. Nonetheless, given the extreme complexity of this communication network, its comprehension is still at its early stage. The present contribution will attempt to provide a state-of-the art description of the mechanisms by which gut microbiota can affect the gut–brain axis and the multiple cellular and molecular communication circuits (i.e., neural, immune, and humoral). In this context, special attention will be paid to the microbial strains that produce bioactive compounds and display ascertained or potential probiotic activity. Several neuroactive molecules (e.g., catecholamines, histamine, serotonin, and trace amines) will be considered, with special focus on Glu and GABA circuits, receptors, and signaling. From the basic science viewpoint, “microbial endocrinology” deals with those theories in which neurochemicals, produced by both multicellular organisms and prokaryotes (e.g., serotonin, GABA, glutamate), are considered as a common shared language that enables interkingdom communication. With regards to its application, research in this area opens the way toward the possibility of the future use of neuroactive molecule-producing probiotics as therapeutic agents for the treatment of

The Neuro-endocrinological Role of Microbial Glutamate and GABA Signaling.

PubMed

Mazzoli, Roberto; Pessione, Enrica

2016-01-01

Gut microbiota provides the host with multiple functions (e.g., by contributing to food digestion, vitamin supplementation, and defense against pathogenic strains) and interacts with the host organism through both direct contact (e.g., through surface antigens) and soluble molecules, which are produced by the microbial metabolism. The existence of the so-called gut-brain axis of bi-directional communication between the gastrointestinal tract and the central nervous system (CNS) also supports a communication pathway between the gut microbiota and neural circuits of the host, including the CNS. An increasing body of evidence has shown that gut microbiota is able to modulate gut and brain functions, including the mood, cognitive functions, and behavior of humans. Nonetheless, given the extreme complexity of this communication network, its comprehension is still at its early stage. The present contribution will attempt to provide a state-of-the art description of the mechanisms by which gut microbiota can affect the gut-brain axis and the multiple cellular and molecular communication circuits (i.e., neural, immune, and humoral). In this context, special attention will be paid to the microbial strains that produce bioactive compounds and display ascertained or potential probiotic activity. Several neuroactive molecules (e.g., catecholamines, histamine, serotonin, and trace amines) will be considered, with special focus on Glu and GABA circuits, receptors, and signaling. From the basic science viewpoint, "microbial endocrinology" deals with those theories in which neurochemicals, produced by both multicellular organisms and prokaryotes (e.g., serotonin, GABA, glutamate), are considered as a common shared language that enables interkingdom communication. With regards to its application, research in this area opens the way toward the possibility of the future use of neuroactive molecule-producing probiotics as therapeutic agents for the treatment of neurogastroenteric and

Tracing C Fluxes From Leaf Litter To Microbial Respired CO2 And Specific Soil Compounds

NASA Astrophysics Data System (ADS)

Rubino, M.; Lubritto, C.; D'Onofrio, A.; Gleixner, G.; Terrasi, F.; Cotrufo, F. M.

2004-12-01

Despite litter decomposition is one of the major process controlling soil C stores and nutrient cycling, yet C dynamics during litter decay are poorly understood and quantified. Here we report the results of a laboratory experiment where 13C depleted leaf litter was incubated on a 13C enriched soil with the aims to: i) partition the C loss during litter decay into microbial respired-CO2 and C input into the soil; ii) identify the soil compounds where litter derived C is retained; iii) assess whether litter quality is a determinant of both the above processes. Three 13C-depleted leaf litter(delta13C ca. -43), differing in their degradability, were incubated on C4 soil (delta13C ca. -18) under laboratory controlled conditions for 8 months, with litter respiration and delta13C-CO2 being measured at regular intervals. At harvest, Compound Specific Isotope Analyses was performed on soil and litter samples in order to follow the fate of litter-derived C compounds in the various pools of SOMƒn The delta13C of soils carbohydrates, alkanes and Phospho Lipids Fatty Acids (PLFA) were measured, and the mixing model approach used to quantify the contribution of litter derived C to the specific compounds.

Study on the synergic effect of natural compounds on the microbial quality decay of packed fish hamburger.

PubMed

Corbo, M R; Speranza, B; Filippone, A; Granatiero, S; Conte, A; Sinigaglia, M; Del Nobile, M A

2008-10-31

The effectiveness of natural compounds in slowing down the microbial quality decay of refrigerated fish hamburger is addressed in this study. In particular, the control of the microbiological spoilage by combined use of three antimicrobials, and the determination of their optimal composition to extend the fish hamburger Microbiological Stability Limit (MAL) are the main objectives of this work. Thymol, grapefruit seed extract (GFSE) and lemon extract were tested for monitoring the cell growth of the main fish spoilage microorganisms (Pseudomonas fluorescens, Photobacterium phosphoreum and Shewanella putrefaciens), inoculated in fish hamburgers, and the growth of mesophilic and psychrotrophic bacteria. A Central Composite Design (CCD) was developed to highlight a possible synergic effect of the above natural compounds. Results showed an increase in the MAL value for hamburgers mixed with the antimicrobial compounds, compared to the control sample. The optimal antimicrobial compound composition, which corresponds to the maximal MAL value determined in this study, is: 110 mgL(-1) of thymol, 100 mgL(-1) of GFSE and 120 mgL(-1) of lemon extract. The presence of the natural compounds delay the sensorial quality decay without compromising the flavor of the fish hamburgers.

Detecting volatile compounds from Kraft lignin degradation in the headspace of microbial cultures by selected ion flow tube mass spectrometry (SIFT-MS).

PubMed

Gibson, Andrew; Malek, Lada; Dekker, Robert F H; Ross, Brian

2015-05-01

Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) was used to quantify methanol and other volatile compounds in the headspace of one bacterial and 12 fungal lignin-degrading microbial cultures. Cultures were grown in 250 mL Erlenmeyer flasks capped with aluminum foil containing 40 mL of nutrient media using Kraft lignin (0.3% w/v) as the sole carbon source. Analysis was done using SIFT-MS with H3O(+) and NO(+) precursors. Product ions were identified with multiple ion mode (MIM). Full scan (FS) mode was used to identify other compounds of interest. Absidia cylindrospora, Ischnoderma resinosum and Pholiota aurivella increased headspace methanol concentration by 136 ppb, 1196 ppb and 278 ppb, respectively, while Flammulina velutipes and Laetiporus sulphureus decreased concentration below ambient levels. F. velutipes and L. sulphureus were found to produce products of methanol oxidation (formaldehyde and formic acid) and were likely metabolizing methanol. Some additional unidentified compounds generated by the fungal cultures are intriguing and will require further study. SIFT-MS can be used to quantify methanol and other volatile compounds in the headspace of microbial cultures and has the potential to be a rapid, sensitive, non-invasive tool useful in elucidating the mechanisms of lignin degradative pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

DOE PAGES

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; ...

2016-07-26

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

PubMed Central

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

2016-01-01

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure

Characterization of microbial and chemical composition of shuttle wet waste with permanent gas and volatile organic compound analyses

NASA Astrophysics Data System (ADS)

Peterson, B. V.; Hummerick, M.; Roberts, M. S.; Krumins, V.; Kish, A. L.; Garland, J. L.; Maxwell, S.; Mills, A.

2004-01-01

Solid-waste treatment in space for Advanced Life Support, ALS, applications requires that the material can be safely processed and stored in a confined environment. Many solid-wastes are not stable because they are wet (40-90% moisture) and contain levels of soluble organic compounds that can contribute to the growth of undesirable microorganisms with concomitant production of noxious odors. In the absence of integrated Advanced Life Support systems on orbit, permanent gas, trace volatile organic and microbiological analyses were performed on crew refuse returned from the volume F "wet" trash of three consecutive Shuttle missions (STS-105, 109, and 110). These analyses were designed to characterize the short-term biological stability of the material and assess potential crew risks resulting from microbial decay processes during storage. Waste samples were collected post-orbiter landing and sorted into packaging material, food waste, toilet waste, and bulk liquid fractions deposited during flight in the volume F container. Aerobic and anaerobic microbial loads were determined in each fraction by cultivation on R2A and by acridine orange direct count (AODC). Dry and ash weights were performed to determine both water and organic content of the materials. Experiments to determine the aerobic and anaerobic biostability of refuse stored for varying periods of time were performed by on-line monitoring of CO 2 and laboratory analysis for production of hydrogen sulfide and methane. Volatile organic compounds and permanent gases were analyzed using EPA Method TO15 by USEPA et al. [EPA Method TO15, The Determination of Volatile Organic Compounds (VOCs) in Ambient Air using SUMMA, Passivated Canister Sampling and Gas Chromatographic Analysis, 1999] with gas chromatography/mass spectrometry and by gas chromatography with selective detectors. These baseline measures of waste stream content, labile organics, and microbial load in the volume F Shuttle trash provide data for waste

Characterization of microbial and chemical composition of shuttle wet waste with permanent gas and volatile organic compound analyses

NASA Technical Reports Server (NTRS)

Peterson, B. V.; Hummerick, M.; Roberts, M. S.; Krumins, V.; Kish, A. L.; Garland, J. L.; Maxwell, S.; Mills, A.

2004-01-01

Solid-waste treatment in space for Advanced Life Support, ALS, applications requires that the material can be safely processed and stored in a confined environment. Many solid-wastes are not stable because they are wet (40-90% moisture) and contain levels of soluble organic compounds that can contribute to the growth of undesirable microorganisms with concomitant production of noxious odors. In the absence of integrated Advanced Life Support systems on orbit, permanent gas, trace volatile organic and microbiological analyses were performed on crew refuse returned from the volume F "wet" trash of three consecutive Shuttle missions (STS-105, 109, and 110). These analyses were designed to characterize the short-term biological stability of the material and assess potential crew risks resulting from microbial decay processes during storage. Waste samples were collected post-orbiter landing and sorted into packaging material, food waste, toilet waste, and bulk liquid fractions deposited during flight in the volume F container. Aerobic and anaerobic microbial loads were determined in each fraction by cultivation on R2A and by acridine orange direct count (AODC). Dry and ash weights were performed to determine both water and organic content of the materials. Experiments to determine the aerobic and anaerobic biostability of refuse stored for varying periods of time were performed by on-line monitoring of CO2 and laboratory analysis for production of hydrogen sulfide and methane. Volatile organic compounds and permanent gases were analyzed using EPA Method TO15 by USEPA et al. [EPA Method TO15, The Determination of Volatile Organic Compounds (VOCs) in Ambient Air using SUMMA, Passivated Canister Sampling and Gas Chromatographic Analysis,1999] with gas chromatography/mass spectrometry and by gas chromatography with selective detectors. These baseline measures of waste stream content, labile organics, and microbial load in the volume F Shuttle trash provide data for waste

Characterization of microbial and chemical composition of shuttle wet waste with permanent gas and volatile organic compound analyses.

PubMed

Peterson, B V; Hummerick, M; Roberts, M S; Krumins, V; Kish, A L; Garland, J L; Maxwell, S; Mills, A

2004-01-01

Solid-waste treatment in space for Advanced Life Support, ALS, applications requires that the material can be safely processed and stored in a confined environment. Many solid-wastes are not stable because they are wet (40-90% moisture) and contain levels of soluble organic compounds that can contribute to the growth of undesirable microorganisms with concomitant production of noxious odors. In the absence of integrated Advanced Life Support systems on orbit, permanent gas, trace volatile organic and microbiological analyses were performed on crew refuse returned from the volume F "wet" trash of three consecutive Shuttle missions (STS-105, 109, and 110). These analyses were designed to characterize the short-term biological stability of the material and assess potential crew risks resulting from microbial decay processes during storage. Waste samples were collected post-orbiter landing and sorted into packaging material, food waste, toilet waste, and bulk liquid fractions deposited during flight in the volume F container. Aerobic and anaerobic microbial loads were determined in each fraction by cultivation on R2A and by acridine orange direct count (AODC). Dry and ash weights were performed to determine both water and organic content of the materials. Experiments to determine the aerobic and anaerobic biostability of refuse stored for varying periods of time were performed by on-line monitoring of CO2 and laboratory analysis for production of hydrogen sulfide and methane. Volatile organic compounds and permanent gases were analyzed using EPA Method TO15 by USEPA et al. [EPA Method TO15, The Determination of Volatile Organic Compounds (VOCs) in Ambient Air using SUMMA, Passivated Canister Sampling and Gas Chromatographic Analysis,1999] with gas chromatography/mass spectrometry and by gas chromatography with selective detectors. These baseline measures of waste stream content, labile organics, and microbial load in the volume F Shuttle trash provide data for waste

Possibilities for the detection of microbial life on extrasolar planets.

PubMed

Knacke, Roger F

2003-01-01

We consider possibilities for the remote detection of microbial life on extrasolar planets. The Darwin/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes. Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms. Satellites in Earth orbit routinely monitor colonies of terrestrial algae in oceans and lakes by analysis of reflected ocean light in the visible region of the spectrum. These remote sensing techniques suggest strategies for extrasolar searches for signatures of chlorophylls and related photosynthetic compounds associated with life. However, identification of such life-related compounds on extrasolar planets would require observations through strong, interfering absorptions and scattering radiances from the remote atmospheres and landmasses. Techniques for removal of interfering radiances have been extensively developed for remote sensing from Earth orbit. Comparable techniques would have to be developed for extrasolar planet observations also, but doing so would be challenging for a remote planet. Darwin/TPF coronagraph concepts operating in the visible seem to be best suited for searches for extrasolar microbial life forms with instruments that can be projected for the 2010-2020 decades, although resolution and signal-to-noise ratio constraints severely limit detection possibilities on terrestrial-type planets. The generation of telescopes with large apertures and extremely high spatial resolutions that will follow Darwin/TPF could offer striking possibilities for the direct detection of extrasolar microbial life.

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead.

PubMed

Blunt, Susanna M; Sackett, Joshua D; Rosen, Michael R; Benotti, Mark J; Trenholm, Rebecca A; Vanderford, Brett J; Hedlund, Brian P; Moser, Duane P

2018-05-01

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead

USGS Publications Warehouse

Blunt, Susanna M.; Sackett, Joshua D.; Rosen, Michael R.; Benotti, Mark J.; Trenholm, Rebecca A.; Vanderford, Brett J.; Hedlund, Brian P.; Moser, Duane P.

2018-01-01

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine

Is the glass half empty or half full? A novel "philosophical" approach to the "mystery" of the so-called ferrule effect.

PubMed

Stavridakis, Minos; Brokos, Yiannis; Krejci, Ivo

2018-06-01

The prognosis of endodontically treated teeth has traditionally been associated with the presence of the so-called ferrule effect that is generally related with the presence of a minimum of 1-2 mm of sound tooth structure at the cervical area of parallel axial walls that totally encircle the tooth. Even though all of these factors are well desired, one should question if their absence should condemn a tooth and compel extraction as the only logical treatment plan option. For this reason an hypothesis is being formed that associates the aforementioned factors not with the presence of the so-called ferrule effect, but rather with the resistance form of the preparation that is being provided by the sound tooth structure at the cervical area of the tooth. When the desired resistance form is provided by sound tooth structure of endodontically treated teeth, then less lateral forces are being transferred to the post & core and subsequently to the root of the teeth, thus minimizing the chances of decementation of the post & core or worst fracture of the root. Even more important, if this hypothesis may be further entertained, then even when the so-called ferrule effect is not present, the teeth may not be extracted, but alternative strategies for post & core restorations may be investigated, such a more flexible carbon- or glass-fiber posts & core build ups made from flowable resin composite that may accommodate for the increased lateral forced exerted to the post & core complex during function. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbial Resources and Enological Significance: Opportunities and Benefits

PubMed Central

Petruzzi, Leonardo; Capozzi, Vittorio; Berbegal, Carmen; Corbo, Maria R.; Bevilacqua, Antonio; Spano, Giuseppe; Sinigaglia, Milena

2017-01-01

Among the innovative trends in the wine sector, the continuous exploration of enological properties associated with wine microbial resources represents a cornerstone driver of quality improvement. Since the advent of starter cultures technology, the attention has been focused on intraspecific biodiversity within the primary species responsible for alcoholic fermentation (Saccharomyces cerevisiae) and, subsequently, for the so-called ‘malolactic fermentation’ (Oenococcus oeni). However, in the last decade, a relevant number of studies proposed the enological exploitation of an increasing number of species (e.g., non-Saccharomyces yeasts) associated with spontaneous fermentation in wine. These new species/strains may provide technological solutions to specific problems and/or improve sensory characteristics, such as complexity, mouth-feel and flavors. This review offers an overview of the available information on the enological/protechnological significance of microbial resources associated with winemaking, summarizing the opportunities and the benefits associated with the enological exploitation of this microbial potential. We discuss proposed solutions to improve quality and safety of wines (e.g., alternative starter cultures, multistrains starter cultures) and future perspectives. PMID:28642742

Microbial reduction of uranium

USGS Publications Warehouse

Lovley, D.R.; Phillips, E.J.P.; Gorby, Y.A.; Landa, E.R.

1991-01-01

REDUCTION of the soluble, oxidized form of uranium, U(VI), to insoluble U(IV) is an important mechanism for the immobilization of uranium in aquatic sediments and for the formation of some uranium ores1-10. U(VI) reduction has generally been regarded as an abiological reaction in which sulphide, molecular hydrogen or organic compounds function as the reductant1,2,5,11. Microbial involvement in U(VI) reduction has been considered to be limited to indirect effects, such as microbial metabolism providing the reduced compounds for abiological U(VI) reduction and microbial cell walls providing a surface to stimulate abiological U(VI) reduction1,12,13. We report here, however, that dissimilatory Fe(III)-reducing microorganisms can obtain energy for growth by electron transport to U(VI). This novel form of microbial metabolism can be much faster than commonly cited abiological mechanisms for U(VI) reduction. Not only do these findings expand the known potential terminal electron acceptors for microbial energy transduction, they offer a likely explanation for the deposition of uranium in aquatic sediments and aquifers, and suggest a method for biological remediation of environments contaminated with uranium.

Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P.; Bruckner, Jim; Fisher, Jen

2010-09-01

This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program’s Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

New interpretation of the so-called Nubian strata in northeast Africa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klitzsch, E.H.; Squyres, C.H.

1988-08-01

Stratigraphical interpretation of the so-called Nubian Sandstone of Egypt and northern Sudan have led to new ideas on the structural and paleogeographical development of northeast Africa. The strata formerly comprised under the term Nubian Sandstone include sediments from Cambrian to Paleocene age. Based on field work and paleontological investigations during the last 10 years, these strata can be subdivided into three major cycles, each characterizing a certain structural situation of northeast Africa. The first or Paleozoic cycle comprises strata of Cambrian to Early Carboniferous age. These strata were deposited during a period of generally northern dip of northeast Africa; continentalmore » sediments transported northward interfinger with marine strata resulting from southward transgressions. Sediments of the second cycle were deposited during and after Gondwana and northern continents collided, which caused updoming of large areas of Egypt and bordering areas to the west and east. As a result, most of Egypt became subject to erosion; transgressions remained near the present northern edge of the continent, and purely continental deposition took place in northern Sudan and bordering areas in Chad and Libya. The resulting strata are similar to the Karroo of East Africa. Strata of the third cycle were deposited after Pangea began to disintegrate. Northeast Africa now had a generally northern dip again, and consequently deposition was controlled - as during the first cycle - by northward drainage and southward transgressions. This last cycle began during Late Jurassic time.« less

In silico identification and construction of microbial gene clusters associated with biodegradation of xenobiotic compounds.

PubMed

Awasthi, Garima; Kumari, Anjani; Pant, Aditya Bhushan; Srivastava, Prachi

2018-01-01

Chemical substances not showing any importance in existence of biological systems and causing serious health hazards may be designated as Xenobiotic compound. Elimination or degradation of these unwanted substances is a major issue of concern for current time research. Process of biodegradation is a very important aspect of current research as discussed in current manuscript. Current study focuses on the detailed mining of data for the construction of microbial consortia for wide range of xenobiotics compounds. Intensive literature search was done for the construction of this library. Desired data was retrieved from NCBI in fasta format. Data was analysed through homology approaches by using BLAST. This homology based searched enriched with a great vision that not only bacterial population but many other cheap and potential sources are available for different xenobiotic degradation. Though it was focused that bacterial population covers a major part of biodegradation which is near about 90.6% but algae and fungi are also showing promising future in degradation of some important xenobiotic compounds. Analysis of data reveals that Pseudomonas putida has potential for degrading maximum compounds. Establishment of correlation through cluster analysis signifies that Pseudomonas putida, Aspergillus niger and Skeletonema costatum can have combined traits that can be used in finding out actual evolutionary relationship between these species. These findings may also givea new outcome in terms of much cheaper and eco-friendly source in the area of biodegradation of specified xenobiotic compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bioactive compounds synthesized by non-ribosomal peptide synthetases and type-I polyketide synthases discovered through genome-mining and metagenomics.

PubMed

Nikolouli, Katerina; Mossialos, Dimitris

2012-08-01

Non-ribosomal peptide synthetases (NRPS) and type-I polyketide synthases (PKS-I) are multimodular enzymes involved in biosynthesis of oligopeptide and polyketide secondary metabolites produced by microorganisms such as bacteria and fungi. New findings regarding the mechanisms underlying NRPS and PKS-I evolution illustrate how microorganisms expand their metabolic potential. During the last decade rapid development of bioinformatics tools as well as improved sequencing and annotation of microbial genomes led to discovery of novel bioactive compounds synthesized by NRPS and PKS-I through genome-mining. Taking advantage of these technological developments metagenomics is a fast growing research field which directly studies microbial genomes or specific gene groups and their products. Discovery of novel bioactive compounds synthesized by NRPS and PKS-I will certainly be accelerated through metagenomics, allowing the exploitation of so far untapped microbial resources in biotechnology and medicine.

The Extent of Fermentative Transformation of Phenolic Compounds in the Bioanode Controls Exoelectrogenic Activity in a Microbial Electrolysis Cell

DOE PAGES

Zeng, Xiaofei; Collins, Maya; Borole, Abhijeet P.; ...

2016-11-27

Phenolic compounds in hydrolysate/pyrolysate and wastewater streams produced during the pretreatment of lignocellulosic biomass for biofuel production present a significant challenge in downstream processes. Bioelectrochemical systems are increasingly recognized as an alternative technology to handle biomass-derived streams and to promote water reuse in biofuel production. Thus, a thorough understanding of the fate of phenolic compounds in bioanodes is urgently needed. The present study investigated the biotransformation of three structurally similar phenolic compounds (syringic acid, SA; vanillic acid, VA; 4-hydroxybenzoic acid, HBA), and their individual contribution to exoelectrogenesis in a microbial electrolysis cell (MEC) bioanode. Fermentation of SA resulted in themore » highest exoelectrogenic activity among the three compounds tested, with 50% of the electron equivalents converted to current, compared to 12 and 9% for VA and HBA, respectively. The biotransformation of SA, VA and HBA was initiated by demethylation and decarboxylation reactions common to all three compounds, resulting in their corresponding hydroxylated analogs. SA was transformed to pyrogallol (1,2,3-trihydroxybenzene), whose aromatic ring was then cleaved via a phloroglucinol pathway, resulting in acetate production, which was then used in exoelectrogenesis. In contrast, more than 80% of VA and HBA was converted to catechol (1,2-dihydroxybenzene) and phenol (hydroxybenzene) as their respective dead-end products. The persistence of catechol and phenol is explained by the fact that the phloroglucinol pathway does not apply to di- or mono-hydroxylated benzenes. Previously reported, alternative ring-cleaving pathways were either absent in the bioanode microbial community or unfavorable due to high energy-demand reactions. With the exception of acetate oxidation, all biotransformation steps in the bioanode occurred via fermentation, independently of exoelectrogenesis. Therefore, the observed

Microbial Transformation of Esters of Chlorinated Carboxylic Acids

PubMed Central

Paris, D. F.; Wolfe, N. L.; Steen, W. C.

1984-01-01

Two groups of compounds were selected for microbial transformation studies. In the first group were carboxylic acid esters having a fixed aromatic moiety and an increasing length of the alkyl component. Ethyl esters of chlorine-substituted carboxylic acids were in the second group. Microorganisms from environmental waters and a pure culture of Pseudomonas putida U were used. The bacterial populations were monitored by plate counts, and disappearance of the parent compound was followed by gas-liquid chromatography as a function of time. The products of microbial hydrolysis were the respective carboxylic acids. Octanol-water partition coefficients (Kow) for the compounds were measured. These values spanned three orders of magnitude, whereas microbial transformation rate constants (kb) varied only 50-fold. The microbial rate constants of the carboxylic acid esters with a fixed aromatic moiety increased with an increasing length of alkyl substituents. The regression coefficient for the linear relationships between log kb and log Kow was high for group 1 compounds, indicating that these parameters correlated well. The regression coefficient for the linear relationships for group 2 compounds, however, was low, indicating that these parameters correlated poorly. PMID:16346459

Exploring Marine Cyanobacteria for Lead Compounds of Pharmaceutical Importance

PubMed Central

Uzair, Bushra; Tabassum, Sobia; Rasheed, Madiha; Rehman, Saima Firdous

2012-01-01

The Ocean, which is called the “mother of origin of life,” is also the source of structurally unique natural products that are mainly accumulated in living organisms. Cyanobacteria are photosynthetic prokaryotes used as food by humans. They are excellent source of vitamins and proteins vital for life. Several of these compounds show pharmacological activities and are helpful for the invention and discovery of bioactive compounds, primarily for deadly diseases like cancer, acquired immunodeficiency syndrome (AIDS), arthritis, and so forth, while other compounds have been developed as analgesics or to treat inflammation, and so forth. They produce a large variety of bioactive compounds, including substances with anticancer and antiviral activity, UV protectants, specific inhibitors of enzymes, and potent hepatotoxins and neurotoxins. Many cyanobacteria produce compounds with potent biological activities. This paper aims to showcase the structural diversity of marine cyanobacterial secondary metabolites with a comprehensive coverage of alkaloids and other applications of cyanobacteria. PMID:22545008

Pb4(BO3)2(SO4) and Pb2[(BO2)(OH)](SO4): New lead(II) borate-sulfate mixed-anion compounds with two types of 3D network structures

NASA Astrophysics Data System (ADS)

Ruan, Ting-Ting; Wang, Wen-Wen; Hu, Chun-Li; Xu, Xiang; Mao, Jiang-Gao

2018-04-01

Two new lead(II) borate-sulfate mixed-anion compounds, namely, Pb4(BO3)2(SO4) and Pb2[(BO2)(OH)](SO4), have been prepared by using high-temperature melt method or hydrothermal reaction. These compounds exhibit two different types of 3D structures composed of the same anionic units of BO3 triangles and SO4 tetrahedra which are interconnected by lead(II) cations. In Pb4(BO3)2(SO4), the lead(II) ions are bridged by borate anions into 3D [Pb4(BO3)2]2+ architectures with 1D tunnels of 8-member rings along the a-axis, which are filled by the sulfate anions. In Pb2[(BO2)(OH)](SO4), the lead(II) ions are interconnected by borate and sulfate anions into 2D Pb-B-O and Pb-S-O layers parallel to the ab plane, respectively, and these layers are further condensed into the 3D lead(II) borate-sulfate framework. TGA and DSC studies indicate that Pb4(BO3)2(SO4) is congruently melting with a melting point of 689 °C whereas Pb2[(BO2)(OH)](SO4) decomposes at approximately 335 °C. UV/Vis/NIR optical diffuse reflectance spectrum measurements reveal the optical band gaps of 4.03 and 4.08 eV for Pb4(BO3)2(SO4) and Pb2[(BO2)(OH)](SO4), respectively. Furthermore, the electronic structures of Pb4(BO3)2(SO4) have also been calculated.

Missing SO2 oxidant in the coastal atmosphere? - observations from high-resolution measurements of OH and atmospheric sulfur compounds

NASA Astrophysics Data System (ADS)

Berresheim, H.; Adam, M.; Monahan, C.; O'Dowd, C.; Plane, J. M. C.; Bohn, B.; Rohrer, F.

2014-11-01

Diurnal and seasonal variations of gaseous sulfuric acid (H2SO4) and methane sulfonic acid (MSA) were measured in NE Atlantic air at the Mace Head atmospheric research station during the years 2010 and 2011. The measurements utilized selected-ion chemical ionization mass spectrometry (SI/CIMS) with a detection limit for both compounds of 4.3 × 104 cm-3 at 5 min signal integration. The H2SO4 and MSA gas-phase concentrations were analyzed in conjunction with the condensational sink for both compounds derived from 3 nm to 10 μm (aerodynamic diameter) aerosol size distributions. Accommodation coefficients of 1.0 for H2SO4 and 0.12 for MSA were assumed, leading to estimated atmospheric lifetimes on the order of 7 and 25 min, respectively. With the SI/CIMS instrument in OH measurement mode alternating between OH signal and background (non-OH) signal, evidence was obtained for the presence of one or more unknown oxidants of SO2 in addition to OH. Depending on the nature of the oxidant(s), its ambient concentration may be enhanced in the CIMS inlet system by additional production. The apparent unknown SO2 oxidant was additionally confirmed by direct measurements of SO2 in conjunction with calculated H2SO4 concentrations. The calculated H2SO4 concentrations were consistently lower than the measured concentrations by a factor of 4.7 ± 2.4 when considering the oxidation of SO2 by OH as the only source of H2SO4. Both the OH and the background signal were also observed to increase significantly during daytime aerosol nucleation events, independent of the ozone photolysis frequency, J(O1D), and were followed by peaks in both H2SO4 and MSA concentrations. This suggests a strong relation between the unknown oxidant(s), OH chemistry, and the atmospheric photolysis and photooxidation of biogenic iodine compounds. As to the identity of the atmospheric SO2 oxidant(s), we have been able to exclude ClO, BrO, IO, and OIO as possible candidates based on {ab initio} calculations

Rates and cycles of microbial sulfate reduction in the hyper-saline Dead Sea over the last 200 kyrs from sedimentary d34S and d18O(SO4)

NASA Astrophysics Data System (ADS)

Torfstein, Adi; Turchyn, Alexandra V.

2017-08-01

We report the d34S and d18O(SO4) values measured in gypsum, pyrite, and elemental sulfur through a 456-m thick sediment core from the center of the Dead Sea, representing the last 200 kyrs, as well as from the exposed glacial outcrops of the Masada M1 section located on the margins of the modern Dead Sea. The results are used to explore and quantify the evolution of sulfur microbial metabolism in the Dead Sea and to reconstruct the lake’s water column configuration during the late Quaternary. Layers and laminae of primary gypsum, the main sulfur-bearing mineral in the sedimentary column, display the highest d34S and d18O(SO4) in the range of 13-28‰ and 13-30‰, respectively. Within this group, gypsum layers deposited during interglacials have lower d34S and d18O(SO4) relative to those associated with glacial or deglacial stages. The reduced sulfur phases, including chromium reducible sulfur, and secondary gypsum crystals are characterized by extremely low d34S in the range of -27 to +7‰. The d18O(SO4) of the secondary gypsum in the M1 outcrop ranges from 8 to 14‰. The relationship between d34S and d18O(SO4) of primary gypsum suggests that the rate of microbial sulfate reduction was lower during glacial relative to interglacial times. This suggests that the freshening of the lake during glacial wet intervals, and the subsequent rise in sulfate concentrations, slowed the rate of microbial metabolism. Alternatively, this could imply that sulfate-driven anaerobic methane oxidation, the dominant sulfur microbial metabolism today, is a feature of the hypersalinity in the modern Dead Sea. Sedimentary sulfides are quantitatively oxidized during epigenetic exposure, retaining the lower d34S signature; the d18O(SO4) of this secondary gypsum is controlled by oxygen atoms derived equally from atmospheric oxygen and from water, which is likely a unique feature in this hyperarid environment.

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.

PubMed

Rashid, Mamoon; Stingl, Ulrich

2015-12-01

Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology. Copyright © 2015 Elsevier Inc. All rights reserved.

Tensile Bond Strength of So-called Universal Primers and Universal Multimode Adhesives to Zirconia and Lithium Disilicate Ceramics.

PubMed

Elsayed, Adham; Younes, Feras; Lehmann, Frank; Kern, Matthias

2017-01-01

To test the bond strength and durability after artificial aging of so-called universal primers and universal multimode adhesives to lithium disilicate or zirconia ceramics. A total of 240 ceramic plates, divided into two groups, were produced and conditioned: 120 acid-etched lithium disilicate plates (IPS e.max CAD) and 120 air-abraded zirconia plates (Zenostar T). Each group was divided into five subgroups (n = 24), and a universal restorative primer or multimode universal adhesive was used for each subgroup to bond plexiglas tubes filled with a composite resin to the ceramic plate. The specimens were stored in water at 37°C for 3 days without thermal cycling, or for 30 or 150 days with 7500 or 37,500 thermal cycles between 5°C and 55°C, respectively. All specimens then underwent tensile bond strength testing. Initially, all bonding systems exhibited high TBS, but some showed a significant reduction after 30 and 150 days of storage. After 3, 30, and 150 days, Monobond Plus, which contains silane and phosphate monomer, showed significantly higher bond strengths than the other universal primer and adhesive systems. The bond strength to lithium disilicate and zirconia ceramic is significantly affected by the bonding system used. Using a separate primer containg silane and phosphate monomer provides more durable bonding than do silanes incorporated in universal multimode adhesives. Only one of five so-called universal primers and adhesives provided durable bonding to lithium disilicate and zirconia ceramic.

Pathological aspects of so called "hilar cholangiocarcinoma"

PubMed Central

Castellano-Megías, Víctor M; Ibarrola-de Andrés, Carolina; Colina-Ruizdelgado, Francisco

2013-01-01

Cholangiocarcinoma (CC) arising from the large intrahepatic bile ducts and extrahepatic hilar bile ducts share clinicopathological features and have been called hilar and perihilar CC as a group. However, “hilar and perihilar CC” are also used to refer exclusively to the intrahepatic hilar type CC or, more commonly, the extrahepatic hilar CC. Grossly, a major distinction can be made between papillary and non-papillary tumors. Histologically, most hilar CCs are well to moderately differentiated conventional type (biliary) carcinomas. Immunohistochemically, CK7, CK20, CEA and MUC1 are normally expressed, being MUC2 positive in less than 50% of cases. Two main premalignant lesions are known: biliary intraepithelial neoplasia (BilIN) and intraductal papillary neoplasm of the biliary tract (IPNB). IPNB includes the lesions previously named biliary papillomatosis and papillary carcinoma. A series of 29 resected hilar CC from our archives is reviewed. Most (82.8%) were conventional type adenocarcinomas, mostly well to moderately differentiated, although with a broad morphological spectrum; three cases exhibited a poorly differentiated cell component resembling signet ring cells. IPNB was observed in 5 (17.2%), four of them with an associated invasive carcinoma. A clear cell type carcinoma, an adenosquamous carcinoma and two gastric foveolar type carcinomas were observed. PMID:23919110

Pathological aspects of so called "hilar cholangiocarcinoma".

PubMed

Castellano-Megías, Víctor M; Ibarrola-de Andrés, Carolina; Colina-Ruizdelgado, Francisco

2013-07-15

Cholangiocarcinoma (CC) arising from the large intrahepatic bile ducts and extrahepatic hilar bile ducts share clinicopathological features and have been called hilar and perihilar CC as a group. However, "hilar and perihilar CC" are also used to refer exclusively to the intrahepatic hilar type CC or, more commonly, the extrahepatic hilar CC. Grossly, a major distinction can be made between papillary and non-papillary tumors. Histologically, most hilar CCs are well to moderately differentiated conventional type (biliary) carcinomas. Immunohistochemically, CK7, CK20, CEA and MUC1 are normally expressed, being MUC2 positive in less than 50% of cases. Two main premalignant lesions are known: biliary intraepithelial neoplasia (BilIN) and intraductal papillary neoplasm of the biliary tract (IPNB). IPNB includes the lesions previously named biliary papillomatosis and papillary carcinoma. A series of 29 resected hilar CC from our archives is reviewed. Most (82.8%) were conventional type adenocarcinomas, mostly well to moderately differentiated, although with a broad morphological spectrum; three cases exhibited a poorly differentiated cell component resembling signet ring cells. IPNB was observed in 5 (17.2%), four of them with an associated invasive carcinoma. A clear cell type carcinoma, an adenosquamous carcinoma and two gastric foveolar type carcinomas were observed.

Fabrication of a Microbial Biosensor Based on QD-MWNT Supports by a One-Step Radiation Reaction and Detection of Phenolic Compounds in Red Wines

PubMed Central

Kim, Seul-Ki; Kwen, Hai-Doo; Choi, Seong-Ho

2011-01-01

An Acaligense sp.-immobilized biosensor was fabricated based on QD-MWNT composites as an electron transfer mediator and a microbe immobilization support by a one-step radiation reaction and used for sensing phenolic compounds in commercial red wines. First, a quantum dot-modified multi-wall carbon nanotube (QD-MWNT) composite was prepared in the presence of MWNT by a one-step radiation reaction in an aqueous solution at room temperature. The successful preparation of the QD-MWNT composite was confirmed by XPS, TEM, and elemental analysis. Second, the microbial biosensor was fabricated by immobilization of Acaligense sp. on the surface of the composite thin film of a glassy carbon (GC) electrode, which was prepared by a hand casting method with a mixture of the previously obtained composite and Nafion solution. The sensing ranges of the microbial biosensor based on CdS-MWNT and Cu2S-MWNT supports were 0.5–5.0 mM and 0.7–10 mM for phenol in a phosphate buffer solution, respectively. Total concentration of phenolic compounds contained in commercial red wines was also determined using the prepared microbial immobilized biosensor. PMID:22319395

Impact of Microbial Composition of Cambodian Traditional Dried Starters (Dombea) on Flavor Compounds of Rice Wine: Combining Amplicon Sequencing With HP-SPME-GCMS.

PubMed

Ly, Sokny; Mith, Hasika; Tarayre, Cédric; Taminiau, Bernard; Daube, Georges; Fauconnier, Marie-Laure; Delvigne, Frank

2018-01-01

Dombae is a traditional ferment starter which has been used for starchy based wine production in Cambodia. However, the production technology of rice wine in Cambodia is not optimized. The current study aimed to investigate the microbiota associated in five ferment starters and the effect of a traditional fermentation process using a metagenomics sequencing analysis and HS-SPME-GCMS for the characterization of the aromatic profiles at the end of fermentation. Most of bacteria identified in this study were lactic acid bacteria including Weissella cibaria, Pediococcus sp. MMZ60A, Lactobacillus fermentum , and Lactobacillus plantarum . Saccharomyces cerevisiae and Saccharomycopsis fibuligera were found to be abundant yeasts while the only amylolytic filamentous fungus was Rhizopus oryzae . A total of 25 aromatic compounds were detected and identified as esters, alcohols, acids, ketones and aldehydes. The alcohol group was dominant in each rice wine. Significant changes were observed at the level of microbial communities during fermentation, suggesting microbial succession for the assimilation of starch and subsequently assimilation of fermentation by-products leading to the production of flavor compounds. At this level, the presence of Weissella, Pediococcus , and Lactobacillus genus was strongly correlated with most of the flavor compounds detected.

Impact of Microbial Composition of Cambodian Traditional Dried Starters (Dombea) on Flavor Compounds of Rice Wine: Combining Amplicon Sequencing With HP-SPME-GCMS

PubMed Central

Ly, Sokny; Mith, Hasika; Tarayre, Cédric; Taminiau, Bernard; Daube, Georges; Fauconnier, Marie-Laure; Delvigne, Frank

2018-01-01

Dombae is a traditional ferment starter which has been used for starchy based wine production in Cambodia. However, the production technology of rice wine in Cambodia is not optimized. The current study aimed to investigate the microbiota associated in five ferment starters and the effect of a traditional fermentation process using a metagenomics sequencing analysis and HS-SPME-GCMS for the characterization of the aromatic profiles at the end of fermentation. Most of bacteria identified in this study were lactic acid bacteria including Weissella cibaria, Pediococcus sp. MMZ60A, Lactobacillus fermentum, and Lactobacillus plantarum. Saccharomyces cerevisiae and Saccharomycopsis fibuligera were found to be abundant yeasts while the only amylolytic filamentous fungus was Rhizopus oryzae. A total of 25 aromatic compounds were detected and identified as esters, alcohols, acids, ketones and aldehydes. The alcohol group was dominant in each rice wine. Significant changes were observed at the level of microbial communities during fermentation, suggesting microbial succession for the assimilation of starch and subsequently assimilation of fermentation by-products leading to the production of flavor compounds. At this level, the presence of Weissella, Pediococcus, and Lactobacillus genus was strongly correlated with most of the flavor compounds detected. PMID:29867806

Effect of two sweating simulation methods on clothing evaporative resistance in a so-called isothermal condition.

PubMed

Lu, Yehu; Wang, Faming; Peng, Hui

2016-07-01

The effect of sweating simulation methods on clothing evaporative resistance was investigated in a so-called isothermal condition (T manikin  = T a  = T r ). Two sweating simulation methods, namely, the pre-wetted fabric "skin" (PW) and the water supplied sweating (WS), were applied to determine clothing evaporative resistance on a "Newton" thermal manikin. Results indicated that the clothing evaporative resistance determined by the WS method was significantly lower than that measured by the PW method. In addition, the evaporative resistances measured by the two methods were correlated and exhibited a linear relationship. Validation experiments demonstrated that the empirical regression equation showed highly acceptable estimations. The study contributes to improving the accuracy of measurements of clothing evaporative resistance by means of a sweating manikin.

Microbial Biotransformation to Obtain New Antifungals

PubMed Central

Bianchini, Luiz F.; Arruda, Maria F. C.; Vieira, Sergio R.; Campelo, Patrícia M. S.; Grégio, Ana M. T.; Rosa, Edvaldo A. R.

2015-01-01

Antifungal drugs belong to few chemical groups and such low diversity limits the therapeutic choices. The urgent need of innovative options has pushed researchers to search new bioactive molecules. Literature regarding the last 15 years reveals that different research groups have used different approaches to achieve such goal. However, the discovery of molecules with different mechanisms of action still demands considerable time and efforts. This review was conceived to present how Pharmaceutical Biotechnology might contribute to the discovery of molecules with antifungal properties by microbial biotransformation procedures. Authors present some aspects of (1) microbial biotransformation of herbal medicines and food; (2) possibility of major and minor molecular amendments in existing molecules by biocatalysis; (3) methodological improvements in processes involving whole cells and immobilized enzymes; (4) potential of endophytic fungi to produce antimicrobials by bioconversions; and (5) in silico research driving to the improvement of molecules. All these issues belong to a new conception of transformation procedures, so-called “green chemistry,” which aims the highest possible efficiency with reduced production of waste and the smallest environmental impact. PMID:26733974

Inhibitors of calling behavior of Plodia interpunctella.

PubMed

Hirashima, Akinori; Shigeta, Yoko; Eiraku, Tomohiko; Kuwano, Eiichi

2003-01-01

Some octopamine agonists were found to suppress the calling behavior of the stored product Indian meal moth, Plodia interpunctella. Compounds were screened using a calling behavior bioassay using female P. interpunctella. Four active derivatives, with inhibitory activity at the nanomolar range, were identified in order of decreasing activity: 2-(1-phenylethylamino)-2-oxazoline > 2-(2-ethyl,6-methylanilino)oxazolidine > 2-(2-methyl benzylamino)-2-thiazoline > 2-(2,6-diethylanilino)thiazolidine. Three-dimensional pharmacophore hypotheses were built from a set of 15 compounds. Among the ten common-featured models generated by the program Catalyst/HipHop, a hypothesis including a hydrogen-bond acceptor lipid, a hydrophobic aromatic and two hydrophobic aliphatic features was considered to be essential for inhibitory activity in the calling behavior. Active compounds mapped well onto all the hydrogen-bond acceptor lipid, hydrophobic aromatic and hydrophobic aliphatic features of the hypothesis. On the other hand, less active compounds were shown not to achieve the energetically favorable conformation that is found in the active molecules in order to fit the 3D common-feature pharmacophore models. The present studies demonstrate that inhibition of calling behavior is via an octopamine receptor.

Biotechnological Aspects of Microbial Extracellular Electron Transfer

PubMed Central

Kato, Souichiro

2015-01-01

Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

Insights from intercomparison of microbial and conventional soil models

NASA Astrophysics Data System (ADS)

Allison, S. D.; Li, J.; Luo, Y.; Mayes, M. A.; Wang, G.

2014-12-01

Changing the structure of soil biogeochemical models to represent coupling between microbial biomass and carbon substrate pools could improve predictions of carbon-climate feedbacks. So-called "microbial models" with this structure make very different predictions from conventional models based on first-order decay of carbon substrate pools. Still, the value of microbial models is uncertain because microbial physiological parameters are poorly constrained and model behaviors have not been fully explored. To address these issues, we developed an approach for inter-comparing microbial and conventional models. We initially focused on soil carbon responses to microbial carbon use efficiency (CUE) and temperature. Three scenarios were implemented in all models at a common reference temperature (20°C): constant CUE (held at 0.31), varied CUE (-0.016°C-1), and 50% acclimated CUE (-0.008°C-1). Whereas the conventional model always showed soil carbon losses with increasing temperature, the microbial models each predicted a temperature threshold above which warming led to soil carbon gain. The location of this threshold depended on CUE scenario, with higher temperature thresholds under the acclimated and constant scenarios. This result suggests that the temperature sensitivity of CUE and the structure of the soil carbon model together regulate the long-term soil carbon response to warming. Compared to the conventional model, all microbial models showed oscillatory behavior in response to perturbations and were much less sensitive to changing inputs. Oscillations were weakest in the most complex model with explicit enzyme pools, suggesting that multi-pool coupling might be a more realistic representation of the soil system. This study suggests that model structure and CUE parameterization should be carefully evaluated when scaling up microbial models to ecosystems and the globe.

Microbial methods of reducing technetium

DOEpatents

Wildung, Raymond E [Richland, WA; Garland, Thomas R [Greybull, WY; Gorby, Yuri A [Richland, WA; Hess, Nancy J [Benton City, WA; Li, Shu-Mei W [Richland, WA; Plymale, Andrew E [Richland, WA

2001-01-01

The present invention is directed toward a method for microbial reduction of a technetium compound to form other compounds of value in medical imaging. The technetium compound is combined in a mixture with non-growing microbial cells which contain a technetium-reducing enzyme system, a stabilizing agent and an electron donor in a saline solution under anaerobic conditions. The mixture is substantially free of an inorganic technetium reducing agent and its reduction products. The resulting product is Tc of lower oxidation states, the form of which can be partially controlled by the stabilizing agent. It has been discovered that the microorganisms Shewanella alga, strain Bry and Shewanelia putrifacians, strain CN-32 contain the necessary enzyme systems for technetium reduction and can form both mono nuclear and polynuclear reduced Tc species depending on the stabilizing agent.

[Patient education and the use of the so called complementary or alternative medicine].

PubMed

Binetti, P

2005-01-01

Modern cultural trends are inclined to recognise to all human beings an always more ample right to become involved directly in choices affecting them. This even when health is concerned thus requiring expertise not always accessible to all. Informed consent to often gets reduced to a mere formality, having a mostly defensive purpose for the physician. Patients' education is becoming an ever more pressing issue in order to safeguard decision rights and the effective knowledge of the implications of every decision simultaneously. Patients' education has serious ethical implications which can't be eluded nor referred outside as happens when we let mass media inform on the advantages and disadvantages of various therapies. One of the major fields were this misinformed choice right is expressed is the so called complementary and alternative medicine. Nowadays physicians have to get back their therapeutical leadership once again, with renewed responsibility and through education as well. Information as such is a necessary and not sufficient condition. A sheer education involving the physician in a deeper as well as in an extended therapeutical alliance is needed. The challenge of taking care involves the whole human being: his/her sick body, his/her wounded feelings as well as intelligence which has to understand what is happening clearly.

Top-Down Prioritization of Salient Items May Produce the So-Called Stimulus-Driven Capture

PubMed Central

Benoni, Hanna

2018-01-01

The current study proposes that top-down attentional prioritization of salient items may produce the so-called stimulus-driven capture. To test this proposal, the “expectation-based paradigm” was designed on the basis of a visual search task. In Experiment 1, a task-irrelevant singleton frame was presented at the same location in 70% of the trials. The target was either presented at chance level within the singleton location, or away from it. In line with the singleton capture phenomenon, participants were faster in identifying the target when it appeared in the singleton location compared to non-singleton locations. However, leaving out the singleton frame in 30% of the trials led to a similar effect; participants were faster in identifying the target when it appeared in the expected singleton location compared to expected non-singletons locations (a “quasi-capture” effect). These results suggest that the participants allocated their attention to the expected singleton location, rather than that the singleton itself captured attention. In Experiment 2, the same task-irrelevant color singleton was presented in a random position in 70% of the trials. This color frame was shown as a non-singleton in all of the 30% singleton-absent multicolored trials. A similar facilitation effect was obtained when the target appeared in the expected singleton color frame compared to other frames, in singleton-absent trials as in singleton-present trials. These results further support the idea that instances of singleton capture can be explained by top-down attentional shifts toward singleton items. Theoretical implications of these results are discussed. Mostly, the study calls to consider the possibility that all sources of attentional control may be represented by a continuous variable of top-down control, including the category of “physical salience.” PMID:29599731

Pellitorine, a potential anti-cancer lead compound against HL6 and MCT-7 cell lines and microbial transformation of piperine from Piper Nigrum.

PubMed

Ee, Gwendoline Cheng Lian; Lim, Chyi Meei; Rahmani, Mawardi; Shaari, Khozirah; Bong, Choon Fah Joseph

2010-04-05

Pellitorine (1), which was isolated from the roots of Piper nigrum, showed strong cytotoxic activities against HL60 and MCT-7 cell lines. Microbial transformation of piperine (2) gave a new compound 5-[3,4-(methylenedioxy)phenyl]-pent-2-ene piperidine (3). Two other alkaloids were also found from Piper nigrum. They are (E)-1-[3',4'-(methylenedioxy)cinnamoyl]piperidine (4) and 2,4-tetradecadienoic acid isobutyl amide (5). These compounds were isolated using chromatographic methods and their structures were elucidated using MS, IR and NMR techniques.

Variation in the pattern of omissions and substitutions of grammatical morphemes in the spontaneous speech of so-called agrammatic patients.

PubMed

Miceli, G; Silveri, M C; Romani, C; Caramazza, A

1989-04-01

We describe the patterns of omissions (and substitutions) of freestanding grammatical morphemes and the patterns of substitutions of bound grammatical morphemes in 20 so-called agrammatic patients. Extreme variation was observed in the patterns of omissions and substitutions of grammatical morphemes, both in terms of the distribution of errors for different grammatical morphemes as well as in terms of the distribution of omissions versus substitutions. Results are discussed in the context of current debates concerning the possibility of a theoretically motivated distinction between the clinical categories of agrammatism and paragrammatism and, more generally, concerning the theoretical usefulness of any clinical category. The conclusion is reached that the observed heterogeneity in the production of grammatical morphemes among putatively agrammatic patients renders the clinical category of agrammatism, and by extension all other clinical categories from the classical classification scheme (e.g., Broca's aphasia, Wernicke's aphasia, and so forth) to more recent classificatory attempts (e.g., surface dyslexia, deep dysgraphia, and so forth), theoretically useless.

Volatile affairs in microbial interactions

PubMed Central

Schmidt, Ruth; Cordovez, Viviane; de Boer, Wietse; Raaijmakers, Jos; Garbeva, Paolina

2015-01-01

Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe–microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance. PMID:26023873

Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

PubMed

Larsen, Peter; Hamada, Yuki; Gilbert, Jack

2012-07-31

Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science. Copyright © 2012 Elsevier B.V. All rights reserved.

JEM Spotlight: Fungi, mycotoxins and microbial volatile organic compounds in mouldy interiors from water-damaged buildings.

PubMed

Polizzi, Viviana; Delmulle, Barbara; Adams, An; Moretti, Antonio; Susca, Antonia; Picco, Anna Maria; Rosseel, Yves; Kindt, Ruben't; Van Bocxlaer, Jan; De Kimpe, Norbert; Van Peteghem, Carlos; De Saeger, Sarah

2009-10-01

Concerns have been raised about exposure to mycotoxin producing fungi and the microbial volatile organic compounds (MVOCs) they produce in indoor environments. Therefore, the presence of fungi and mycotoxins was investigated in 99 samples (air, dust, wallpaper, mycelium or silicone) collected in the mouldy interiors of seven water-damaged buildings. In addition, volatile organic compounds (VOCs) were sampled. The mycotoxins were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) (20 target mycotoxins) and quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS). Morphological and molecular identifications of fungi were performed. Of the 99 samples analysed, the presence of one or more mycotoxins was shown in 62 samples by means of LC-MS/MS analysis. The mycotoxins found were mainly roquefortine C, chaetoglobosin A and sterigmatocystin but also roridin E, ochratoxin A, aflatoxin B(1) and aflatoxin B(2) were detected. Q-TOF-MS analysis elucidated the possible occurrence of another 42 different fungal metabolites. In general, the fungi identified matched well with the mycotoxins detected. The most common fungal species found were Penicillium chrysogenum, Aspergillus versicolor (group), Chaetomium spp. and Cladosporium spp. In addition, one hundred and seventeen (M)VOCs were identified, especially linear alkanes (C(9)-C(17)), aldehydes, aromatic compounds and monoterpenes.

Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

USDA-ARS?s Scientific Manuscript database

Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that el...

Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

USDA-ARS?s Scientific Manuscript database

Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that eli...

Antimicrobial compounds from seaweeds-associated bacteria and fungi.

PubMed

Singh, Ravindra Pal; Kumari, Puja; Reddy, C R K

2015-02-01

In recent decade, seaweeds-associated microbial communities have been significantly evaluated for functional and chemical analyses. Such analyses let to conclude that seaweeds-associated microbial communities are highly diverse and rich sources of bioactive compounds of exceptional molecular structure. Extracting bioactive compounds from seaweed-associated microbial communities have been recently increased due to their broad-spectrum antimicrobial activities including antibacterial, antifungal, antiviral, anti-settlement, antiprotozoan, antiparasitic, and antitumor. These allelochemicals not only provide protection to host from other surrounding pelagic microorganisms, but also ensure their association with the host. Antimicrobial compounds from marine sources are promising and priority targets of biotechnological and pharmaceutical applications. This review describes the bioactive metabolites reported from seaweed-associated bacterial and fungal communities and illustrates their bioactivities. Biotechnological application of metagenomic approach for identifying novel bioactive metabolites is also dealt, in view of their future development as a strong tool to discover novel drug targets from seaweed-associated microbial communities.

Modes of action of microbially-produced phytotoxins.

PubMed

Duke, Stephen O; Dayan, Franck E

2011-08-01

Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin.

Preliminary assessment of microbial communities and biodegradation of chlorinated volatile organic compounds in wetlands at Cluster 13, Lauderick Creek area, Aberdeen Proving Ground, Maryland

USGS Publications Warehouse

Lorah, Michelle M.; Voytek, Mary A.; Spencer, Tracey A.

2003-01-01

A preliminary assessment of the microbial communities and biodegradation processes for chlorinated volatile organic compounds was con-ducted by the U.S. Geological Survey in wetlands at the Cluster 13, Lauderick Creek area at Aberdeen Proving Ground, Maryland. The U.S. Geological Survey collected wetland sediment samples from 11 sites in the Lauderick Creek area for microbial analyses, and used existing data to evaluate biodegradation processes and rates. The bacterial and methanogen communities in the Lauderick Creek wetland sediments were similar to those observed in a previous U.S. Geological Survey study at the West Branch Canal Creek wet-land area, Aberdeen Proving Ground. Evaluation of the degradation rate of 1,1,2,2-tetrachloroethane and the daughter compounds produced also showed similar results for the two wetlands. How-ever, a vertical profile of contaminant concentra-tions in the wetlands was available at only one site in the Lauderick Creek area, and flow velocities in the wetland sediment are unknown. To better evaluate natural attenuation processes and rates in the wetland sediments at Lauderick Creek, chemi-cal and hydrologic measurements are needed along ground-water flowpaths in the wetland at additional sites and during different seasons. Nat-ural attenuation in the wetlands, enhanced biore-mediation, and constructed wetlands could be feasible remediation methods for the chlorinated volatile organic compounds discharging in the Lauderick Creek area. The similarities in the microbial communities and biodegradation pro-cesses at the Lauderick Creek and West Branch Canal Creek areas indicate that enhanced bioreme-diation techniques currently being developed for the West Branch Canal Creek wetland area would be transferable to this area.

The fauna of the so-called Dakota formation of northern central Colorado and its equivalent in southeastern Wyoming

USGS Publications Warehouse

Reeside, John B.

1923-01-01

This paper describes a small fauna from beds in northern central Colorado that have long been designated the Dakota formation, often with doubt that all the beds so named were really equivalent to the typical Dakota sandstone of eastern Nebraska. The upper part of the equivalent beds in southeastern Wyoming was referred by some writers to the Benton Shale and the lower part of the Cloverly formation. This so-called Dakota formation of northern central Colorado and its equivalent in southeastern Wyoming consist of cherty conglomerate, brown quartzose sandstone, and dark shale. The conglomerate is usually at the base of the series and at many localities is overlain by a single shale unit and that in turn by a sandstone. At other localities, however, there are several alternations of sandstone and shale above the basal conglomeratic layer. The fossil described in this paper, except one specimen, were obtained from the shales of the middle part of the formation. The single specimen, an ammonite, came from the uppermost sandstone.

Modes of Action of Microbially-Produced Phytotoxins

PubMed Central

Duke, Stephen O.; Dayan, Franck E.

2011-01-01

Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin. PMID:22069756

Microbial syntrophy: interaction for the common good.

PubMed

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.

Microbial factories for recombinant pharmaceuticals

PubMed Central

Ferrer-Miralles, Neus; Domingo-Espín, Joan; Corchero, José Luis; Vázquez, Esther; Villaverde, Antonio

2009-01-01

Most of the hosts used to produce the 151 recombinant pharmaceuticals so far approved for human use by the Food and Drug Administration (FDA) and/or by the European Medicines Agency (EMEA) are microbial cells, either bacteria or yeast. This fact indicates that despite the diverse bottlenecks and obstacles that microbial systems pose to the efficient production of functional mammalian proteins, namely lack or unconventional post-translational modifications, proteolytic instability, poor solubility and activation of cell stress responses, among others, they represent convenient and powerful tools for recombinant protein production. The entering into the market of a progressively increasing number of protein drugs produced in non-microbial systems has not impaired the development of products obtained in microbial cells, proving the robustness of the microbial set of cellular systems (so far Escherichia coli and Saccharomyces cerevisae) developed for protein drug production. We summarize here the nature, properties and applications of all those pharmaceuticals and the relevant features of the current and potential producing hosts, in a comparative way. PMID:19317892

Microbial biosurfactants with their high-value functional properties

USDA-ARS?s Scientific Manuscript database

Microbial world is a rich source for finding valuable industrial chemicals and ingredients. Specifically, many microbial metabolites are surface-active compounds that can be developed into bio-based surfactants, detergents, and emulsifiers. Techno-economic analyses for the production of bio-based ...

On the so-called membrane coating granules in keratinized lichen planus lesions of the buccal mucosa.

PubMed

El-Labban, N G; Wood, R D

1982-11-01

Serial sections of the so-called membrane-coating granules have been examined in keratinized oral epithelium of lichen planus lesions. As with 'granules' apparent in non-keratinized epithelium, it is found they do not represent specialized intra-cytoplasmic organelles, but are the result of sectioning at different areas, levels and planes through the plasma membrane of interdigitating cell processes. Such 'granules' appear mostly in the superficial, but not deep, part of the cytoplasm of the upper prickle cells. This is considered to be due to topographic differences between the upper and under surfaces of these cells and the presence of narrower intercellular spaces than those between deeper epithelial cells. Such arrangement often results in cell processes in sections appearing free in the superficial part of the cell below. The appearance of 'granules' arises when the plane of section is not at right angles to the two plasma membranes surrounding these processes.

The impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate.

PubMed

Batista, Nádia Nara; Ramos, Cíntia Lacerda; Dias, Disney Ribeiro; Pinheiro, Ana Carla Marques; Schwan, Rosane Freitas

2016-02-01

Theobroma cacao seeds are the main raw material for chocolate production. During their fermentation, a succession of microorganisms are responsible for the physicochemical changes occurring in the pulp and inside the beans. The aim of this study was to investigate the effects of yeast inoculation (Saccharomyces cerevisiae UFLA CA11, Pichia kluivery CCMA0237, and Hanseniaspora uvarum CCMA0236) on the profile of the volatile compounds and microbial communities in cocoa fermentation. The resulting chocolate was also evaluated by temporal dominance of sensations (TDS) analyses. The dominant microorganisms during spontaneous fermentation were S. cerevisiae, H. uvarum, H. guilliermondii, Lactobacillus fermentum, Pediococcus sp., and Acetobacter pasteurianus. Similarly, S. cerevisiae, P. kluyveri, Candida sp., Pediococcus sp., and A. pasteurianus were the predominant microorganisms assessed by Denaturing Gradient Gel Electrophoresis (DGGE) in inoculated fermentation. Sixty-seven volatile compounds were detected and quantified by gas chromatography/mass spectrometry (GC/MS) at the end of fermentation and chocolates. The main group of volatile compound found after the inoculated and spontaneous fermentations was esters (41 and 39 %, respectively). In the chocolates, the main group was acids (73 and 44 % from the inoculated and spontaneous fermentations, respectively). The TDS analyses showed a dominance of bitter and cocoa attributes in both chocolates. However, in the inoculated chocolate, lingering fruity notes were more intense, while the chocolate produced by spontaneous fermentation was more astringent. Thus, the inoculation of yeast influenced the microbial profile, which likely affected the volatile compounds that affect sensory characteristics, resulting in chocolate with dominant bitter, cocoa, and fruity attributes.

Salient lesions in domestic ruminants infected with the emerging so-called Schmallenberg virus in Germany.

PubMed

Herder, V; Wohlsein, P; Peters, M; Hansmann, F; Baumgärtner, W

2012-07-01

The so-called Schmallenberg virus (SBV), first detected in a German town of the same name in October 2011, is a novel emerging orthobunyavirus in Europe causing malformations and severe economic loss in ruminants. This report describes lesions in 40 sheep, 2 goats, and 16 cattle naturally infected with SBV as determined by real-time quantitative reverse transcription polymerase chain reaction. The most common macroscopic changes were arthrogryposis, vertebral malformations, brachygnathia inferior, and malformations of the central nervous system, including hydranencephaly, porencephaly, hydrocephalus, cerebellar hypoplasia, and micromyelia. Histologic lesions included lymphohistiocytic meningoencephalomyelitis in some cases, glial nodules mainly in the mesencephalon and hippocampus of lambs and goats, and neuronal degeneration and necrosis mainly in the brain stem of calves. Micromyelia was characterized by a loss of gray and white matter, with few neurons remaining in the ventral horn in calves. The skeletal muscles had myofibrillar hypoplasia in lambs and calves. The lesions of SBV-associated abortion and perinatal death are similar to those attributed to Akabane virus and other viruses in the Simbu group of bunyaviruses.

The perils and promises of microbial abundance: novel natures and model ecosystems, from artisanal cheese to alien seas.

PubMed

Paxson, Heather; Helmreich, Stefan

2014-04-01

Microbial life has been much in the news. From outbreaks of Escherichia coli to discussions of the benefits of raw and fermented foods to recent reports of life forms capable of living in extreme environments, the modest microbe has become a figure for thinking through the presents and possible futures of nature, writ large as well as small. Noting that dominant representations of microbial life have shifted from an idiom of peril to one of promise, we argue that microbes--especially when thriving as microbial communities--are being upheld as model ecosystems in a prescriptive sense, as tokens of how organisms and human ecological relations with them could, should, or might be. We do so in reference to two case studies: the regulatory politics of artisanal cheese and the speculative research of astrobiology. To think of and with microbial communities as model ecosystems offers a corrective to the scientific determinisms we detect in some recent calls to attend to the materiality of scientific objects.

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

Treesearch

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...

A Canadian Working Group report on fecal microbial therapy: Microbial ecosystems therapeutics

PubMed Central

Allen-Vercoe, Emma; Reid, Gregor; Viner, Norman; Gloor, Gregory B; Hota, Susy; Kim, Peter; Lee, Christine; O’Doherty, Kieran C; Vanner, Stephen J; Weese, J Scott; Petrof, Elaine O

2012-01-01

A working group from across Canada comprised of clinician and basic scientists, epidemiologists, ethicists, Health Canada regulatory authorities and representatives of major funding agencies (Canadian Institutes of Health Research and the Crohn’s and Colitis Foundation of Canada) met to review the current experience with fecal microbial therapy and to identify the key areas of study required to move this field forward. The report highlights the promise of fecal microbial therapy and related synthetic stool therapy (together called ‘microbial ecosystems therapeutics’) for the treatment of Clostridium difficile colitis and, possibly, other disorders. It identifies pressing clinical issues that need to be addressed as well as social, ethical and regulatory barriers to the use of these important therapies. PMID:22803022

A microbial perspective of human developmental biology.

PubMed

Charbonneau, Mark R; Blanton, Laura V; DiGiulio, Daniel B; Relman, David A; Lebrilla, Carlito B; Mills, David A; Gordon, Jeffrey I

2016-07-07

When most people think of human development, they tend to consider only human cells and organs. Yet there is another facet that involves human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy prenatal and postnatal growth and to develop innovative strategies for disease prevention and treatment. Given the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for the establishment of 'human microbial observatories' designed to examine microbial community development in birth cohorts representing populations with diverse anthropological characteristics, including those undergoing rapid change.

Gravitropism in Phycomyces: violation of the so-called resultant law - evidence for two response components.

PubMed

Göttig, M; Galland, P

2014-01-01

We investigated gravitropic bending of sporangiophores of the zygomycete fungus Phycomyces blakesleeanus in response to centrifugal accelerations to test the so-called resultant law of gravitropism ('Resultantengesetz'; Jahrbuch der wissenschaftlichen Botanik, 71, 325, 1929; Der Geotropismus der Pflanzen, Gustav Fischer, Jena, Germany, 1932), which predicts that gravitropic organs orient in a centrifuge rotor parallel to the stimulus vector resulting from the centrifugal acceleration and gravity. Sporangiophores of wild-type strain C171 carAcarR and of several gravitropism mutants were subjected for 7 h to centrifugal accelerations in a dynamic range between 0.01 and 3 × g. The stimulus-response curves that were obtained for C171 carA carR, C2 carA geo and C148 carA geo madC were complex and displayed two response components: a low-acceleration component between 0.01 and 0.5 × g and a high-acceleration component above 0.5 × g. The low acceleration component is characterised by bending angles exceeding those predicted by the resultant law and kinetics faster than that of the second component; in contrast, the high-acceleration component is characterised by bending slightly below the predicted level and kinetics slower than that of the first component. Sporangiophores of the wild-type C171 centrifuged horizontally displayed the opposite behaviour, i.e. low accelerations diminished and high accelerations slightly enhanced bending. Further proof for the existence of the two response components was provided by the phenotype of gravitropism mutants that either lacked the first response component or which caused its overexpression. The tropism mutant C148 with defective madC gene, which codes for a RasGap protein (Fungal Genetics Reports, 60 (Suppl.), Abstract # 211, 2013), displayed hypergravitropism and concomitant deviations from the resultant law that were twice as high as in the wild-type C171. Gravitropism mutants with defects in the genes madF, madG and

The so-called "Spanish model" - tobacco industry strategies and its impact in Europe and Latin America.

PubMed

Schneider, Nick K; Sebrié, Ernesto M; Fernández, Esteve

2011-12-07

To demonstrate the tobacco industry rationale behind the "Spanish model" on non-smokers' protection in hospitality venues and the impact it had on some European and Latin American countries between 2006 and 2011. Tobacco industry documents research triangulated against news and media reports. As an alternative to the successful implementation of 100% smoke-free policies, several European and Latin American countries introduced partial smoking bans based on the so-called "Spanish model", a legal framework widely advocated by parts of the hospitality industry with striking similarities to "accommodation programmes" promoted by the tobacco industry in the late 1990s. These developments started with the implementation of the Spanish tobacco control law (Ley 28/2005) in 2006 and have increased since then. The Spanish experience demonstrates that partial smoking bans often resemble tobacco industry strategies and are used to spread a failed approach on international level. Researchers, advocates and policy makers should be aware of this ineffective policy.

The so-called "Spanish model" - Tobacco industry strategies and its impact in Europe and Latin America

PubMed Central

2011-01-01

Background To demonstrate the tobacco industry rationale behind the "Spanish model" on non-smokers' protection in hospitality venues and the impact it had on some European and Latin American countries between 2006 and 2011. Methods Tobacco industry documents research triangulated against news and media reports. Results As an alternative to the successful implementation of 100% smoke-free policies, several European and Latin American countries introduced partial smoking bans based on the so-called "Spanish model", a legal framework widely advocated by parts of the hospitality industry with striking similarities to "accommodation programmes" promoted by the tobacco industry in the late 1990s. These developments started with the implementation of the Spanish tobacco control law (Ley 28/2005) in 2006 and have increased since then. Conclusion The Spanish experience demonstrates that partial smoking bans often resemble tobacco industry strategies and are used to spread a failed approach on international level. Researchers, advocates and policy makers should be aware of this ineffective policy. PMID:22151884

Dreams of death: Von Weizsäcker's Dreams in so-called endogenic anorexia: a research note.

PubMed

Jackson, C; Beumont, P J; Thornton, C; Lennerts, W

1993-04-01

Viktor Von Weizsäcker's paper "Dreams in so-called endogenic Magersucht (anorexia," first published in the Deutsche Medizinische Wochenschrift in 1937 (translation in M. Kaufman & M. Heiman [1964]. Evolution of psychosomatic concepts: Anorexia nervosa: A paradigm (pp. 181-197), New York: International Universities Press, has been described as a noteworthy and historically important contribution to the recognition of anorexia nervosa as a psychosomatic illness. Von Weizsäcker analyzed the dreams of patients he was treating for "endogenous anorexia" (magersucht). He claimed that in the bulimic phase his patients experienced nightmares dealing with themes of death, but that in the anorectic phases of restricted eating more pleasant dreams dealt with themes of blissful contentment. The authors draw current attention to his work as another early example of the treatment of the theme of death and death symbolism in the literature on eating disorders, and suggest some reappraisal of von Weizsäcker's interpretations of his own material.

Growth-altering microbial interactions are responsive to chemical context

PubMed Central

2017-01-01

Microbial interactions are ubiquitous in nature, and are equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. We present a novel workflow for inferring microbial interactions that integrates semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving throughput and reproducibility of colony interaction assays. We apply our approach to infer interactions among bacterial species associated with the normal lung microbiome, and how those interactions are altered by the presence of benzo[a]pyrene, a carcinogenic compound found in cigarettes. We found that the presence of this single compound changed the interaction network, demonstrating that microbial interactions are indeed dynamic and responsive to local chemical context. PMID:28319121

Bioremediation of PAH-contamined soils: Consequences on formation and degradation of polar-polycyclic aromatic compounds and microbial community abundance.

PubMed

Biache, Coralie; Ouali, Salma; Cébron, Aurélie; Lorgeoux, Catherine; Colombano, Stéfan; Faure, Pierre

2017-05-05

A bioslurry batch experiment was carried out over five months on three polycyclic aromatic compound (PAC) contaminated soils to study the PAC (PAH and polar-PAC) behavior during soil incubation and to evaluate the impact of PAC contamination on the abundance of microbial communities and functional PAH-degrading populations. Organic matter characteristics and reactivity, assessed through solvent extractable organic matter and PAC contents, and soil organic matter mineralization were monitored during 5 months. Total bacteria and fungi, and PAH-ring hydroxylating dioxygenase genes were quantified. Results showed that PAHs and polar-PACs were degraded with different degradation dynamics. Differences in degradation rates were observed among the three soils depending on PAH distribution and availability. Overall, low molecular weight compounds were preferentially degraded. Degradation selectivity between isomers and structurally similar compounds was observed which could be used to check the efficiency of bioremediation processes. Bacterial communities were dominant over fungi and were most likely responsible for PAC degradation. Abundance of PAH-degrading bacteria increased during incubations, but their proportion in the bacterial communities tended to decrease. The accumulation of some oxygenated-PACs during the bioslurry experiment underlines the necessity to monitor these compounds during application of remediation treatment on PAH contaminated soils. Copyright © 2017 Elsevier B.V. All rights reserved.

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

PubMed Central

Olson, Nathan D.; Lund, Steven P.; Colman, Rebecca E.; Foster, Jeffrey T.; Sahl, Jason W.; Schupp, James M.; Keim, Paul; Morrow, Jayne B.; Salit, Marc L.; Zook, Justin M.

2015-01-01

Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing platforms requires careful attention to detail for robust results. Thus far, much of the scientific Communit’s focus for use in bacterial genomics has been on evaluating genome assembly algorithms and rigorously validating assembly program performance. Missing, however, is a focus on critical evaluation of variant callers for these genomes. Variant calling is essential for comparative genomics as it yields insights into nucleotide-level organismal differences. Variant calling is a multistep process with a host of potential error sources that may lead to incorrect variant calls. Identifying and resolving these incorrect calls is critical for bacterial genomics to advance. The goal of this review is to provide guidance on validating algorithms and pipelines used in variant calling for bacterial genomics. First, we will provide an overview of the variant calling procedures and the potential sources of error associated with the methods. We will then identify appropriate datasets for use in evaluating algorithms and describe statistical methods for evaluating algorithm performance. As variant calling moves from basic research to the applied setting, standardized methods for performance evaluation and reporting are required; it is our hope that this review provides the groundwork for the development of these standards. PMID:26217378

Microbial enhanced oil recovery research. [Peptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, M.M.; Georgiou, G.

1992-01-01

The surface active lipopeptide produced by Bacillus licheniformis JF-2 was isolated to near apparent homogeneity. NMR experiments revealed that this compound consists of a heptapeptide with an amino acid sequence similar to surfactin and a heterogeneous fatty acid consisting of the normal-, anteiso-, and iso- branched isomers. The surface activity of the B. licheniformis JF-2 surfactant was shown to depend on the presence of fermentation products and is strongly affected by the pH. Under conditions of optimal salinity and pH the interfacial tension against decane was 6 [times] 10[sup 3] mN/m which is one of the lowest values ever obtainedmore » with a microbial surfactant. Microbial compounds which exhibit particularly high surface activity are classified as biosurfactants. Microbial biosurfactants include a wide variety of surface and interfacially active compounds, such as glycolipids, lipopeptides polysaccharideprotein complexes, phospholipids, fatty acids and neutral lipids. Biosurfactants are easily biodegradable and thus are particularly suited for environmental applications such as bioremediation and the dispersion of oil spills. Bacillus licheniformis strain JF-2 has been shown to be able to grow and produce a very effective biosurfactant under both aerobic and anaerobic conditions and in the presence of high salt concentrations. The production of biosurfactants in anaerobic, high salt environments is potentially important for a variety of in situ applications such as microbial enhanced oil recovery. As a first step towards evaluating the commercial utility of the B. licheniformis JF-2 surfactant, we isolated t-he active. compound from the culture supernatant, characterized its chemical structure and investigated its phase behavior. We found that the surface activity of the surfactant is strongly dependent on the pH of the aqueous. phase. This may be important for the biological function of the surfactant and is of interest for several applications in

From nestling calls to fledgling silence: adaptive timing of change in response to aerial alarm calls.

PubMed

Magrath, Robert D; Platzen, Dirk; Kondo, Junko

2006-09-22

Young birds and mammals are extremely vulnerable to predators and so should benefit from responding to parental alarm calls warning of danger. However, young often respond differently from adults. This difference may reflect: (i) an imperfect stage in the gradual development of adult behaviour or (ii) an adaptation to different vulnerability. Altricial birds provide an excellent model to test for adaptive changes with age in response to alarm calls, because fledglings are vulnerable to a different range of predators than nestlings. For example, a flying hawk is irrelevant to a nestling in a enclosed nest, but is dangerous to that individual once it has left the nest, so we predict that young develop a response to aerial alarm calls to coincide with fledging. Supporting our prediction, recently fledged white-browed scrubwrens, Sericornis frontalis, fell silent immediately after playback of their parents' aerial alarm call, whereas nestlings continued to calling despite hearing the playback. Young scrubwrens are therefore exquisitely adapted to the changing risks faced during development.

Acute liver failure following recreational use of psychotropic "head shop" compounds.

PubMed

Fröhlich, S; Lambe, E; O'Dea, J

2011-03-01

The recreational use of the so-called "legal-highs" has been in both the medical and political arena over the last year as a result of the appearance of "head shops" in many towns in Ireland. These shops specialized in selling new psychotropic compounds that circumvented established drug legislation. Little is known about the potentially harmful effects of these substances but case reports suggest a plethora of harmful psychological and physical effects. Our case describes for the first time acute liver failure associated with the ingestion of two of these amphetamine type compounds.

Exploring anaerobic environments for cyanide and cyano-derivatives microbial degradation.

PubMed

Luque-Almagro, Víctor M; Cabello, Purificación; Sáez, Lara P; Olaya-Abril, Alfonso; Moreno-Vivián, Conrado; Roldán, María Dolores

2018-02-01

Cyanide is one of the most toxic chemicals for living organisms described so far. Its toxicity is mainly based on the high affinity that cyanide presents toward metals, provoking inhibition of essential metalloenzymes. Cyanide and its cyano-derivatives are produced in a large scale by many industrial activities related to recovering of precious metals in mining and jewelry, coke production, steel hardening, synthesis of organic chemicals, and food processing industries. As consequence, cyanide-containing wastes are accumulated in the environment becoming a risk to human health and ecosystems. Cyanide and related compounds, like nitriles and thiocyanate, are degraded aerobically by numerous bacteria, and therefore, biodegradation has been offered as a clean and cheap strategy to deal with these industrial wastes. Anaerobic biological treatments are often preferred options for wastewater biodegradation. However, at present very little is known about anaerobic degradation of these hazardous compounds. This review is focused on microbial degradation of cyanide and related compounds under anaerobiosis, exploring their potential application in bioremediation of industrial cyanide-containing wastes.

A Call for Expanding Inclusive Student Engagement in SoTL

ERIC Educational Resources Information Center

Felton, Peter; Bagg, Julianne; Bumbry, Michael; Hill, Jennifer; Hornsby, Karen; Pratt, Maria; Weller, Saranne

2013-01-01

Scholars in higher education increasingly recognize the transformative potential of student-faculty partnerships focused on inquiry into teaching and learning. However, some students tend to be privileged in SoTL initiatives while others are discouraged, implicitly or explicitly, from engaging in this work. In this paper, we consider why certain…

Rapid evaluation technique to differentiate mushroom disease-related moulds by detecting microbial volatile organic compounds using HS-SPME-GC-MS.

PubMed

Radványi, Dalma; Gere, Attila; Jókai, Zsuzsa; Fodor, Péter

2015-01-01

Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) was used to analyse microbial volatile organic compounds (MVOCs) of mushroom disease-related microorganisms. Mycogone perniciosa, Lecanicillum fungicola var. fungicola, and Trichoderma aggressivum f. europaeum species, which are typically harmful in mushroom cultivation, were examined, and Agaricus bisporus (bisporic button mushroom) was also examined as a control. For internal standard, a mixture of alkanes was used; these were introduced as the memory effect of primed septa in the vial seal. Several different marker compounds were found in each sample, which enabled us to distinguish the different moulds and the mushroom mycelium from each other. Monitoring of marker compounds enabled us to investigate the behaviour of moulds. The records of the temporal pattern changes were used to produce partial least squares regression (PLS-R) models that enabled determination of the exact time of contamination (the infection time of the media). Using these evaluation techniques, the presence of mushroom disease-related fungi can be easily detected and monitored via their emitted MVOCs.

Comparative Toxicities of Salts on Microbial Processes in Soil

PubMed Central

Maheshwari, Arpita; Bengtson, Per; Rousk, Johannes

2016-01-01

Soil salinization is a growing threat to global agriculture and carbon sequestration, but to date it remains unclear how microbial processes will respond. We studied the acute response to salt exposure of a range of anabolic and catabolic microbial processes, including bacterial (leucine incorporation) and fungal (acetate incorporation into ergosterol) growth rates, respiration, and gross N mineralization and nitrification rates. To distinguish effects of specific ions from those of overall ionic strength, we compared the addition of four salts frequently associated with soil salinization (NaCl, KCl, Na2SO4, and K2SO4) to a nonsaline soil. To compare the tolerance of different microbial processes to salt and to interrelate the toxicity of different salts, concentration-response relationships were established. Growth-based measurements revealed that fungi were more resistant to salt exposure than bacteria. Effects by salt on C and N mineralization were indistinguishable, and in contrast to previous studies, nitrification was not found to be more sensitive to salt exposure than other microbial processes. The ion-specific toxicity of certain salts could be observed only for respiration, which was less inhibited by salts containing SO42− than Cl− salts, in contrast to the microbial growth assessments. This suggested that the inhibition of microbial growth was explained solely by total ionic strength, while ion-specific toxicity also should be considered for effects on microbial decomposition. This difference resulted in an apparent reduction of microbial growth efficiency in response to exposure to SO42− salts but not to Cl− salts; no evidence was found to distinguish K+ and Na+ salts. PMID:26801570

Human developmental biology viewed from a microbial perspective

PubMed Central

Charbonneau, Mark R.; Blanton, Laura V.; DiGiulio, Daniel B.; Relman, David A.; Lebrilla, Carlito B.; Mills, David A.; Gordon, Jeffrey I.

2017-01-01

Preface Most people think of human development only in terms of ‘human’ cells and organs. Here, we discuss another facet involving human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy pre- and postnatal growth and to develop new strategies for disease prevention and treatment. Considering the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for human microbial observatory programs designed to examine microbial community development in birth cohorts representing populations with diverse anthropologic characteristics, including those undergoing rapid change. PMID:27383979

Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges.

PubMed

Kennedy, Jonathan; Marchesi, Julian R; Dobson, Alan D W

2007-05-01

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.

Unique pioneer microbial communities exposed to volcanic sulfur dioxide

PubMed Central

Fujimura, Reiko; Kim, Seok-Won; Sato, Yoshinori; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

2016-01-01

Newly exposed volcanic substrates contain negligible amounts of organic materials. Heterotrophic organisms in newly formed ecosystems require bioavailable carbon and nitrogen that are provided from CO2 and N2 fixation by pioneer microbes. However, the knowledge of initial ecosystem developmental mechanisms, especially the association between microbial succession and environmental change, is still limited. This study reports the unique process of microbial succession in fresh basaltic ash, which was affected by long-term exposure to volcanic sulfur dioxide (SO2). Here we compared the microbial ecosystems among deposits affected by SO2 exposure at different levels. The results of metagenomic analysis suggested the importance of autotrophic iron-oxidizing bacteria, particularly those involved in CO2 and N2 fixation, in the heavily SO2 affected site. Changes in the chemical properties of the deposits after the decline of the SO2 impact led to an apparent decrease in the iron-oxidizer abundance and a possible shift in the microbial community structure. Furthermore, the community structure of the deposits that had experienced lower SO2 gas levels showed higher similarity with that of the control forest soil. Our results implied that the effect of SO2 exposure exerted a selective pressure on the pioneer community structure by changing the surrounding environment of the microbes. PMID:26791101

A new strategy of glucose supply in a microbial fermentation model

NASA Astrophysics Data System (ADS)

Kasbawati, Gunawan, A. Y.; Sidarto, K. A.; Hertadi, R.

2015-09-01

Strategy of glucose supply to achieve an optimal productivity of ethanol production of a yeast cell is one of the main features in a microbial fermentation process. Beside a known continuous glucose supply, in this study we consider a new supply strategy so called the on-off supply. An optimal control theory is applied to the fermentation system to find the optimal rate of glucose supply and time of supply. The optimization problem is solved numerically using Differential Evolutionary algorithm. We find two alternative solutions that we can choose to get the similar result: either long period process with low supply or short period process with high glucose supply.

Performance evaluation of a continuous-flow bioanode microbial electrolysis cell fed with furanic and phenolic compounds

DOE PAGES

Zeng, Xiaofei; Borole, Abhijeet P.; Pavlostathis, Spyros G.

2016-07-04

Furanic and phenolic compounds, formed during the pretreatment of lignocellulosic biomass, are problematic byproducts in down-stream biofuel processes. A microbial electrolysis cell (MEC) is an alternative technology to handle furanic and phenolic compounds and produce renewable hydrogen (H 2). In this study, we evaluated the performance of a continuous-flow bioanode MEC fed with furanic and phenolic compounds at different operating conditions. All hydraulic retention times (HRTs) tested (6-24 h) resulted in complete transformation of the parent compounds at an organic loading rate (OLR) of 0.2g L -1 per d and applied voltage of 0.6 V. Increasing the OLR to 0.8more » g L -1 per d at an HRT of 6h resulted in an increased H 2 production rate from 0.07 to 0.14 L L anode 1 per d, but an OLR of 3.2 g L -1 per d did not lead to a higher H 2 production rate. Significant methane production was observed at an OLR of 3.2 g L -1 per d. The lack of increased H 2 production at the highest OLR tested was due to a limited rate of exoelectrogenesis but not fermentation, evidenced by the accumulation of high acetate levels and higher growth of fermenters and methanogens over exoelectrogens. Increasing applied voltage from 0.6 to 1.0V at an OLR of 3.2 g L -1 per d and HRT of 6h enhanced exoelectrogenesis and resulted in a 1.7-fold increase of H 2 production. Under all operating conditions, more than 90% of the biomass was biofilm-associated. Lastly, the present study provides new insights into the performance of continuous-flow bioelectrochemical systems fed with complex waste streams resulting from the pretreatment of lignocellulosic biomass.« less

Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds

PubMed Central

Dhakal, Dipesh; Pokhrel, Anaya Raj; Shrestha, Biplav; Sohng, Jae Kyung

2017-01-01

Actinobacteria are prolific producers of thousands of biologically active natural compounds with diverse activities. More than half of these bioactive compounds have been isolated from members belonging to actinobacteria. Recently, rare actinobacteria existing at different environmental settings such as high altitudes, volcanic areas, and marine environment have attracted attention. It has been speculated that physiological or biochemical pressures under such harsh environmental conditions can lead to the production of diversified natural compounds. Hence, marine environment has been focused for the discovery of novel natural products with biological potency. Many novel and promising bioactive compounds with versatile medicinal, industrial, or agricultural uses have been isolated and characterized. The natural compounds cannot be directly used as drug or other purposes, so they are structurally modified and diversified to ameliorate their biological or chemical properties. Versatile synthetic biological tools, metabolic engineering techniques, and chemical synthesis platform can be used to assist such structural modification. This review summarizes the latest studies on marine rare actinobacteria and their natural products with focus on recent approaches for structural and functional diversification of such microbial chemicals for attaining better applications. PMID:28663748

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

PubMed

Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

2017-05-01

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

Control of Boreal Forest Soil Microbial Communities and Processes by Plant Secondary Compounds

NASA Astrophysics Data System (ADS)

Leewis, M. C.; Leigh, M. B.

2016-12-01

Plants release an array of secondary plant metabolites (SPMEs), which vary widely between plant species/progenies and may drive shifts in soil microbial community structure and function. We hypothesize that SPMEs released through litterfall and root turnover in the boreal forest control ecosystem carbon cycling by inhibiting microbial decomposition processes, which are overcome partially by increased aromatic biodegradation of microbial communities that also fortuitously prime soils for accelerated biodegradation of contaminants. Soils and litter (stems, roots, senescing leaves) were collected from 3 different birch progenies from Iceland, Finland, and Siberia that have been reported to contain different SPME content (low, medium, high, respectively) due to differences in herbivory pressure over their natural history, as well as black spruce, all growing in a long-term common tree garden at the Kevo Subarctic Field Research Institute, Finland. We characterized the SPME content of these plant progenies and used a variety of traditional microbiological techniques (e.g., enzyme assays, litter decomposition and contaminant biodegradation rates) and molecular techniques (e.g., high-throughput amplicon sequencing for bacteria and fungi) to assess how different levels of SPMEs may correlate to shifts in microbial community structure and function. Microbial communities (bacterial and fungal) significantly varied in composition as well as leaf litter and diesel biodegradation rates, in accordance with the phytochemistry of the trees present. This study offers novel, fundamental information about phytochemical controls on ecosystem processes, resilience to contaminants, and microbial decomposition processes.

Genome engineering for microbial natural product discovery.

PubMed

Choi, Si-Sun; Katsuyama, Yohei; Bai, Linquan; Deng, Zixin; Ohnishi, Yasuo; Kim, Eung-Soo

2018-03-03

The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design. Copyright © 2018 Elsevier Ltd. All rights reserved.

Soil microbial diversity and activity as terroir elements of Sangiovese vineyards in the Chianti Classico region (Italy)

NASA Astrophysics Data System (ADS)

Fabiani, Arturo; Mocali, Stefano; Priori, Simone; Valboa, Giuseppe; Vignozzi, Nadia; Pellegrini, Sergio; Storchi, Paolo; Perria, Rita; Costantini, Edoardo

2016-04-01

Linking the uniqueness and quality of grapes and wine to the environment they are produced, based on the terroir concept, have recently become popular in many parts of world. The natural components of terroir are actually a set of processes, which together create a delicate equilibrium and regulation of its effect on products in both space and time. Climate, geology, geomorphology and soil are therefore the main environmental factors which make up the terroir effect on different scales. However, information on the impact of soil microbial communities on soil functions, grapevine plants and wine quality is still lacking. Thus, four of the most suitable areas (so called "cru") for the production of Sangiovese wine were chosen within the Barone Ricasoli farm of Brolio, the largest winery in the Chianti Classico area in central Italy: Fattoio, Miniera, Ceni and Colli-Agresto. Based on previous pedological and sensing technologies surveys, each area was further divided into two distinct homogeneous areas of about 1.5 ha called Basic Terroir Unit (UTB), which were monitored over 3 years (2012-2014) for the soil the chemical-physical variability (moisture, organic matter, nitrogen, potassium), the vineyard physiological status (water stress, grape production, characteristics of the grapes and wine) and the structure and activity of soil microbial communities (determined through DGGE, soil respiration and microbial biomass, respectively). The aim of the work was to assess the relationships among soil parameters and vine quality at intra- and inter- UTB level and, in particular, the potential impact of microbial composition and/or function on the terroir concept. The overall results highlighted a microbial community structure specific for each cru area and, in particular, associated to each UTB. Furthermore, microbial activity in Miniera and Ceni appeared to be positively related to Sangiovese quality, as determined through the Sangiovese Performance Index. However, except

Hydrogen Ordering in Hexagonal Intermetallic AB5 Type Compounds

NASA Astrophysics Data System (ADS)

Sikora, W.; Kuna, A.

2008-04-01

Intermetallic compounds AB5 type (A = rare-earth atoms, B = transition metal) are known to store reversibly large amounts of hydrogen and as that are discussed in this work. It was shown that the alloy cycling stability can be significantly improved by employing the so-called non-stoichiometric compounds AB5+x and that is why analysis of change of structure turned out to be interesting. A tendency for ordering of hydrogen atoms is one of the most intriguing problems for the unsaturated hydrides. The symmetry analysis method in the frame of the theory of space group and their representation gives opportunity to find all possible transformations of the parent structure. In this work symmetry analysis method was applied for AB5+x structure type (P6/mmm parent symmetry space group). There were investigated all possible ordering types and accompanying atom displacements in positions 1a, 2c, 3g (fully occupied in stoichiometric compounds AB5), in positions 2e, 6l (where atom B could appear in non-stoichiometric compounds) and also 4h, 6m, 6k, 12n, 12o, which could be partly occupied by hydrogen as a result of hydrides. An analysis was carried out of all possible structures of lower symmetry, following from P6/mmm for we k=(0, 0, 0). Also the way of getting the structure described by the P63mc space group with double cell along the z-axiswe k=(0, 0, 0.5), as it is suggested in the work of Latroche et al. is discussed by the symmetry analysis. The analysis was obtained by computer program MODY. The program calculates the so-called basis vectors of irreducible representations of a given symmetry group, which can be used for calculation of possible ordering modes.

The So-called 'Face on Mars' at Night

NASA Technical Reports Server (NTRS)

2003-01-01

[figure removed for brevity, see original site]

This pair of THEMIS infrared images shows the so-called 'face on Mars' landform viewed during both the day and night. The nighttime THEMIS IR image was acquired on Oct. 24, 2002; the daytime image was originally released on July 24, 2002. Both images are of THEMIS's 9th IR band (12.57 microns), and they have been geometrically projected for image registration. The 'face on Mars' is located in the northern plains of Mars near 40o N, 10o W (350 o E). This knob can be seen in the daytime image because of the temperature differences between the sunlit (warm and bright) and shadowed (cold and dark) slopes. The temperature in the daytime scene ranges from -50 oC (darkest) to -15 oC (brightest). At night many of the hills and knobs in this region are difficult to detect because the effects of heating and shadowing on the slopes are no longer present. The temperatures at night vary from approximately -90 oC (darkest) to -75 oC (warmest). The nighttime temperature differences are due primarily to differences in the abundance of rocky materials that retain their heat at night and stay warm. Fine grained dust and sand cools of more rapidly at night. The circular rims and eject of many of the craters in this region are warm at night, showing that rocks are still present on the steep walls inside the craters and in the ejecta material that was blasted out when the craters formed. Some craters have cold (dark) material on their floors in the night IR image, indicating that fine-grained material is accumulating within the craters. Many knobs and hills, including the 'face' have rocky (warm at night) material on their slopes and ridges.

The THEMIS infrared camera provides an excellent regional view of Mars - these images cover an area 32 kilometers (20 miles) by approximately 50 kilometers (30 miles) at a resolution of 100 meters per picture element ('pixel'). The scenes are tilted differently because the Odyssey orbit is

Microbial volatile organic compounds in moldy interiors: a long-term climate chamber study.

PubMed

Schuchardt, Sven; Strube, Andrea

2013-06-01

The present study simulated large-scale indoor mold damage in order to test the efficiency of air sampling for the detection of microbial volatile organic compounds (MVOCs). To do this, a wallpaper damaged by condensation was stored in a climate chamber (representing a hypothetical test room of 40 m(3) volume) and was inoculated with 14 typical indoor fungal strains. The chamber ventilation conditions were adjusted to common values found in moldy homes, and the mold growth was allowed to continue to higher than average values. The MVOC content of the chamber air was analyzed daily for a period of 105 days using coupled gas chromatography/mass spectrometry (GC-MS). This procedure guarantees MVOC profiling without external factors such as outdoor air, building materials, furniture, and occupants. However, only nine MVOCs could be detected during the sampling period, which indicates that the very low concentrated MVOCs are hardly accessible, even under these favorable conditions. Furthermore, most of the MVOCs that were detected cannot be considered as reliable indicators of mold growth in indoor environments. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Behaviour of volcanogenic S-bearing compounds (H2S and SO2) in air at Vulcano Island (Aeolian Archipelago, southern Italy)

NASA Astrophysics Data System (ADS)

Caponi, Chiara; Tassi, Franco; Ricci, Andrea; Capecchiacci, Francesco; Venturi, Stefania; Cabassi, Jacopo; Vaselli, Orlando

2017-04-01

The main sources of SO2 and H2S in air consist of both natural fluid emissions related to active/quiescent volcanoes and hydrothermal systems, and anthropogenic activities (e.g. gas and oil refineries, steel industries, urban traffic). These gas compounds have a strong impact on air quality, since they are strong toxic and climate forcing agents. Notwithstanding, the behaviour of these S-compounds in air once they are released from the contaminant source(s) is poorly known, due to the scarce available data from thermodynamics and direct measurements. Hydrogen sulfide is considered to be relatively reactive in the atmosphere, being easily oxidized to SO2 by photochemical reactions, even though the efficiency of the H2S to SO2 conversion is significantly lowered under dark, dry and relatively cold conditions, leading to a residence time of H2S in air up to 42 days in winter. In this work, H2S and SO2 measurements in air carried out at the Levante beach (Vulcano Island, Aeolian Archipelago), where a number of hydrothermal fluid discharges consisting of fumaroles and submarine emissions occur, are presented and discussed. These volcanic fluids, characterized by an H2S-rich chemical composition, are released in a close proximity to the touristic village of Vulcano Porto. The measurements were carried out using a Thermo Scientific™ Model 450i Analyzer coupled with a Davis® Vantage Vue weather station (air humidity and temperature, wind direction and speed) in 34 fixed spots and along 8 pathways, selected according to: (i) distance from the contaminant source, (ii) wind direction and (iii) accessibility by car (where the instrument was installed). The main aim was to provide empirical insights on the behavior of these air pollutants in relation to the physical and chemical processes controlling their spatial distribution. The measured data were elaborated using a statistical approach to construct spatial distribution maps and conceptual models able to forecast the

Genome-Based Microbial Taxonomy Coming of Age.

PubMed

Hugenholtz, Philip; Skarshewski, Adam; Parks, Donovan H

2016-06-01

Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

29 CFR 785.17 - On-call time.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 3 2010-07-01 2010-07-01 false On-call time. 785.17 Section 785.17 Labor Regulations... INTERPRETATION NOT DIRECTLY RELATED TO REGULATIONS HOURS WORKED Application of Principles Waiting Time § 785.17 On-call time. An employee who is required to remain on call on the employer's premises or so close...

29 CFR 785.17 - On-call time.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 29 Labor 3 2011-07-01 2011-07-01 false On-call time. 785.17 Section 785.17 Labor Regulations... INTERPRETATION NOT DIRECTLY RELATED TO REGULATIONS HOURS WORKED Application of Principles Waiting Time § 785.17 On-call time. An employee who is required to remain on call on the employer's premises or so close...

Microbial diversity and their roles in the vinegar fermentation process.

PubMed

Li, Sha; Li, Pan; Feng, Feng; Luo, Li-Xin

2015-06-01

Vinegar is one of the oldest acetic acid-diluted solution products in the world. It is produced from any fermentable sugary substrate by various fermentation methods. The final vinegar products possess unique functions, which are endowed with many kinds of compounds formed in the fermentation process. The quality of vinegar is determined by many factors, especially by the raw materials and microbial diversity involved in vinegar fermentation. Given that metabolic products from the fermenting strains are directly related to the quality of the final products of vinegar, the microbial diversity and features of the dominant strains involved in different fermentation stages should be analyzed to improve the strains and stabilize fermentation. Moreover, although numerous microbiological studies have been conducted to examine the process of vinegar fermentation, knowledge about microbial diversity and their roles involved in fermentation is still fragmentary and not systematic enough. Therefore, in this review, the dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized. We also summarized various physicochemical properties and crucial compounds in disparate types of vinegar. Furthermore, the merits and drawbacks of vital fermentation methods were generalized. Finally, we described in detail the relationships among microbial diversity, raw materials, fermentation methods, physicochemical properties, compounds, functionality, and final quality of vinegar. The integration of this information can provide us a detailed map about the microbial diversity and function involved in vinegar fermentation.

The diversity of anti-microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective.

PubMed

Mousa, Walaa Kamel; Raizada, Manish N

2013-01-01

Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g., Chinese herbs). However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens.

Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

PubMed

Blatter, Maxime; Sugnaux, Marc; Comninellis, Christos; Nealson, Kenneth; Fischer, Fabian

2016-07-07

A predictive model for the microbial/electrochemical base formation from wastewater was established and compared to experimental conditions within a microbial electrolysis cell. A Na2 SO4 /K2 SO4 anolyte showed that model prediction matched experimental results. Using Shewanella oneidensis MR-1, a strong base (pH≈13) was generated using applied voltages between 0.3 and 1.1 V. Due to the use of bicarbonate, the pH value in the anolyte remained unchanged, which is required to maintain microbial activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen production profiles using furans in microbial electrolysis cells.

PubMed

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.

Oxidation of aromatic contaminants coupled to microbial iron reduction

USGS Publications Warehouse

Lovley, D.R.; Baedecker, M.J.; Lonergan, D.J.; Cozzarelli, I.M.; Phillips, E.J.P.; Siegel, D.I.

1989-01-01

THE contamination of sub-surface water supplies with aromatic compounds is a significant environmental concern1,2. As these contaminated sub-surface environments are generally anaerobic, the microbial oxidation of aromatic compounds coupled to nitrate reduction, sulphate reduction and methane production has been studied intensively1-7. In addition, geochemical evidence suggests that Fe(III) can be an important electron acceptor for the oxidation of aromatic compounds in anaerobic groundwater. Until now, only abiological mechanisms for the oxidation of aromatic compounds with Fe(III) have been reported8-12. Here we show that in aquatic sediments, microbial activity is necessary for the oxidation of model aromatic compounds coupled to Fe(III) reduction. Furthermore, a pure culture of the Fe(III)-reducing bacterium GS-15 can obtain energy for growth by oxidizing benzoate, toluene, phenol or p-cresol with Fe(III) as the sole electron acceptor. These results extend the known physiological capabilities of Fe(III)-reducing organisms and provide the first example of an organism of any type which can oxidize an aromatic hydrocarbon anaerobically. ?? 1989 Nature Publishing Group.

Microbial Communities as Experimental Units

PubMed Central

DAY, MITCH D.; BECK, DANIEL; FOSTER, JAMES A.

2011-01-01

Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis. PMID:21731083

Flavins in Marine Sediments: A Potentially Ubiquitous Intermediary In Microbial Electron Transfer

NASA Astrophysics Data System (ADS)

Monteverde, D.; Sylvan, J. B.; Suffridge, C.; Berelson, W.; Sanudo-Wilhelmy, S. A.; Baronas, J. J.

2016-12-01

The flavins (riboflavin, flavin mononucleotide [FMN], flavin adenine dinucleotide [FA­­D]) are a class of organic compounds synthesized by organisms to assist in redox reactions. They represent the largest class of required coenzymes, rivaled only by iron in the number of unique enzymes they bind. In addition to internal use, cultured metal-reducing organisms such as Shewanella and Geobacter have been known to release flavins into the extracellular pool to aid in external electron transfer. So called "electron shuttles" can allow organisms to overcome unfavorable geochemical zonation by transferring electrons onto a relatively distant insoluble acceptor. Despite the extensive culture work, flavins have not been systematically measured in the environment. Here we present the first set of flavin profiles from the water column and pore waters of a marine environment. Samples were taken from San Pedro Basin, a 900 meter deep, silled basin, with high seasonal inputs of organic carbon, low bottom water oxygen concentrations, and laminated sediments - making it ideal to explore variations in sediment geochemical zonations. Dissolved flavin concentrations in the water column and pore waters collected from two cores were preconcentrated via solid phase extraction and measured via LC/MS. Flavin profiles are compared to a suite of geochemical parameters as well as sediment microbial 16s rRNA data. Preliminary results show that FMN is typically an order of magnitude higher concentration than riboflavin (800-300pM versus 100-50pM). Porewater concentrations were elevated over water column values for all analytes (ranging from 100-2000pM) and displayed an increasing trend with depth in both cores. This increasing trend correlated with a decrease in dissolved Fe (ranging from 160 µM in surface sediments to 65 µM at 40 cm) and shifts in microbial diversity from sediments shallower than 5 cm depth dominated by Delta- and Gammaproteobacteria to subsurface sediments dominated by

Microbial fuel cell treatment of fuel process wastewater

DOEpatents

Borole, Abhijeet P; Tsouris, Constantino

2013-12-03

The present invention is directed to a method for cleansing fuel processing effluent containing carbonaceous compounds and inorganic salts, the method comprising contacting the fuel processing effluent with an anode of a microbial fuel ell, the anode containing microbes thereon which oxidatively degrade one or more of the carbonaceous compounds while producing electrical energy from the oxidative degradation, and directing the produced electrical energy to drive an electrosorption mechanism that operates to reduce the concentration of one or more inorganic salts in the fuel processing effluent, wherein the anode is in electrical communication with a cathode of the microbial fuel cell. The invention is also directed to an apparatus for practicing the method.

Microbial bioinformatics 2020.

PubMed

Pallen, Mark J

2016-09-01

Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

The changing landscape of microbial biodiversity exploration and its implications for systematics.

PubMed

Hedlund, Brian P; Dodsworth, Jeremy A; Staley, James T

2015-06-01

A vast diversity of Bacteria and Archaea exists in nature that has evaded axenic culture. Advancements in single-cell genomics, metagenomics, and molecular microbial ecology approaches provide ever-improving insight into the biology of this so-called "microbial dark matter"; however, due to the International Code of Nomenclature of Prokaryotes, yet-uncultivated microorganisms are not accommodated in formal taxonomy regardless of the quantity or quality of data. Meanwhile, efforts to calibrate the existing taxonomy with phylogenetic anchors and genomic data are increasingly robust. The current climate provides an exciting opportunity to leverage rapidly expanding single-cell genomics and metagenomics datasets to improve the taxonomy of Bacteria and Archaea. However, this opportunity must be weighted carefully in light of the strengths and limitations of these approaches. We propose to expand the definition of the Candidatus taxonomy to include taxa, from the phylum level to the species level, that are described genomically, particularly when genomic work is coupled with advanced molecular ecology approaches to probe metabolic functions in situ. This system would preserve the rigor and value of traditional microbial systematics while enabling growth of a provisional taxonomic structure to facilitate communication about "dark" lineages on the tree of life. Copyright © 2015 Elsevier GmbH. All rights reserved.

High-throughput screening to identify selective inhibitors of microbial sulfate reduction (and beyond)

NASA Astrophysics Data System (ADS)

Carlson, H. K.; Coates, J. D.; Deutschbauer, A. M.

2015-12-01

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive and corrosive. Current strategies to selectively inhibit sulfidogenesis are based on non-specific biocide treatments, bio-competitive exclusion by alternative electron acceptors or sulfate-analogs which are competitive inhibitors or futile/alternative substrates of the sulfate reduction pathway. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to target SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Once inhibitor selectivity is defined, high-throughput characterization of microbial community structure across compound gradients and identification of fitness determinants using isolate bar-coded transposon mutant libraries can give insights into the genetic mechanisms whereby compounds structure microbial communities. The high-throughput (HT) approach we present can be readily applied to target SRM in diverse environments and more broadly, could be used to identify and quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant for engineering environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

Surface interaction of H2S, SO2, and SO3 on fullerene-like gallium nitride (GaN) nanostructure semiconductor

NASA Astrophysics Data System (ADS)

Salimifard, M.; Rad, A. Shokuhi; Mahanpoor, K.

2017-10-01

Density functional theory (DFT) using MPW1PW91 and B3LYP hybrid functionals was utilized for quantum-based investigations of three major sulfur compounds (H2S, SO2, and SO3) adsorption onto fullerene-like Ga12N12 nanocluster. All chemicals showed high chemisorption with the order of SO3>SO2>>H2S. Results of charge analysis showed that during adsorption, transfer of charge is from H2S to nanocluster while reverse direction of charge transfer is found for SO2 and SO3 molecules. Partial dissociation is found for adsorbates especially for SO2 and SO3 molecules. Results of thermochemistry analysis show negative values for enthalpy and Gibbs free energy of adsorption, confirming exothermic spontaneous process. Analysis of frontier molecular orbital (FMO) showed important role of orbital hybridizing towards formation of new bonds upon adsorption. As a result, we introduce Ga12N12 nanocluster as a strong adsorbent for sulfur compounds.

[Assessment of so called organic trace compounds in drinking water from the regulatory, health and aesthetic-quality points of view, with special consideration given to pharmaceuticals].

PubMed

Dieter, H H; Mückter, H

2007-03-01

More than 2500 chemically defined substances are approved as drugs in Germany. Unlike agricultural pesticides, these biologically active structures are not used in open environmental compartments and therefore their environmental toxicological data base is not nearly as complete. Nevertheless, some of them become environmental contaminants after their intended use. Therefore, from the viewpoint of environmental health protection, there are gaps in their health-related environmental risk assessment. Organic trace compounds that lack an adequate toxicological database, and their mixtures, in drinking water can be safely regulated and provisionally assessed by combining the "similar joint action" addition rule with the recommendation of the Federal Environment Agency of March 2003 "Assessing the presence of substances in drinking water without (adequate) toxicological database from the health point of view". The general precautionary value (Gesundheitlicher Orientierungswert GOW1=0.10 microg/l), which is a recommendation for weakly to not genotoxic compounds, re presents a workable compromise between preventive health protection, water management considerations and aesthetic quality claims (purity). Compliance with this value in the long term will only be possible if the chemical and biological degradation of pharmaceuticals and their metabolites in waste water and waste water treatment plants is effectively improved. Alternatively, there is the risk of drinking water degenerating into a sink for highly mobile, polar and persistent compounds. Their elimination at a stage as late as technical drinking water treatment would be neither close to the initial cause nor justifiable in terms of technical effectiveness. The risk assessment of their byproducts would give rise to further uncertainties. Possible conflicts with the therapeutic quality must be solved by developing substitute products which are environmentally sound.

The Diversity of Anti-Microbial Secondary Metabolites Produced by Fungal Endophytes: An Interdisciplinary Perspective

PubMed Central

Mousa, Walaa Kamel; Raizada, Manish N.

2013-01-01

Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g., Chinese herbs). However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens. PMID:23543048

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

PubMed Central

Wasmund, Kenneth; Mußmann, Marc

2017-01-01

Summary Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. PMID:28419734

Interaction of Human Enteric Viruses with Microbial Compounds: Implication for Virus Persistence and Disinfection Treatments.

PubMed

Waldman, Prunelle; Meseguer, Alba; Lucas, Françoise; Moulin, Laurent; Wurtzer, Sébastien

2017-12-05

Although the interaction between phages and bacteria has already been well described, it only recently emerged that human viruses also interact with bacteria in the mammalian gut. We studied whether this interaction could occur in tap water and thus confer enteric viruses protection against temperature and the classical disinfection treatments used in drinking water production. We demonstrated that the addition of lipopolysaccharide or peptidoglycan of bacterial origin to enterovirus provides thermal protection through stabilization of the viral capsid. This interaction plays a role when viruses are exposed to disinfection that targets the capsid, but less so when the virus genome is directly targeted. The interaction seems to be serotype-specific, suggesting that the capsid protein sequence could be important. The protection is linked to a direct association between viral particles and bacterial compounds as observed by microscopy. These results show that bacterial compounds present in the environment can affect virus inactivation.

High Carbon Use Efficiency is Not Explained by Production of Storage Compounds

NASA Astrophysics Data System (ADS)

Dijkstra, Paul; van Groenigen, Kees-Jan

2015-04-01

The efficiency with which microbes use substrate to make new microbial biomass (Carbon Use Efficiency or CUE; mol C / mol C) is an important variable in soil and ecosystem C cycling models. Estimates of CUE in soil microbial communities vary widely. It has been hypothesized that high values of CUE are associated with production of storage compounds following a sudden increases in substrate availability during CUE measurements. In that case, these high CUE values would not be representative for balanced microbial growth (i.e. the production of all compounds needed to make new microbial cells). To test this hypothesis, we added position-specific 13C-labeled glucose isotopomers in parallel incubations of a ponderosa pine and piñon-juniper soil. We compared the measured pattern of CO2 release for the six glucose C atoms with patterns of CO2 production expected for balanced growth with a low, medium, or high CUE, and with CO2 production patterns associated with production of storage compounds (glycogen, lipids, or polyhydroxybutyrate). The measured position-specific CO2 production did not match that for production of glycogen, lipids, or polyhydroxybutyrate, but agreed closely with that expected for balanced growth at high CUE and high pentose phosphate pathway activity. We conclude that soil microbial communities utilize glucose substrate for biomass growth with high CUE, and that addition of small amounts of 13C-labeled glucose tracers do not affect CUE or induce storage compounds production. We submit that the measurement of position-specific CO2 production offers a quick and easy way to test biochemically explicit hypotheses concerning microbial growth metabolism.

[On Atomic Nuclear Fusion Processes at Low-Temperatures. An Enhancement of the Probability of Transition through a Potential Barrier Due to the So-Called Barrier Anti-Zeno Effect].

PubMed

Namiot, V A

2016-01-01

It is known that in quantum mechanics the act of observing the experiment can affect the experimental findings in some cases. In particular, it happens under the so-called Zeno effect. In this work it is shown that in contrast to the "standard" Zeno-effect where the act of observing a process reduces the probability of its reality, an inverse situation when a particle transmits through a potential barrier (a so-called barrier anti-Zeno effect) can be observed, the observation of the particle essentially increases the probability of its transmission through the barrier. The possibility of using the barrier anti-Zeno effect is discussed to explain paradoxical results of experiments on "cold nuclear fusion" observed in various systems including biological ones. (According to the observers who performed the observations, the energy generation, which could not be explained by any chemical processes, as well as the change in the isotope and even element composition of the studied object may occur in these systems.

Newly discovered Paleocene and Eocene rocks near Fairfield, California, and correlation with rocks in Vaca Valley and the so-called Martinez Formation or Stage

USGS Publications Warehouse

Brabb, Earl E.; Ristau, Donn; Bukry, David; McDougall, Kristin; Almgren, Alvin A.; Saul, LouElla; Sanfilippo, Annika

2008-01-01

Discovery of a 3-foot thick sandstone bed with abundant Turritellid gastropods of late Paleocene age about 4 miles northeast of Fairfield and on the southwest flank of Cement Hill, Solano County provides an opportunity to reevaluate the relationships of lower Tertiary formations in this part of California. Cement Hill is named for travertine deposits in and on top of sandstone of Late Cretaceous age. In this report, the current study area where the Paleocene fossils were recently discovered is referred to as lower Cement Hill and is located in section 7 of the U.S. Geological Survey Fairfield North 7.5-minute quadrangle, Township 5 North, Range 1 West. Lower Cement Hill is about 23 miles north of the so-called Martinez 'formation' or stage area (Weaver and others, 1941) of late Paleocene age near Martinez. The Martinez 'formation' and stage have played a significant role in the development of early Tertiary stratigraphy in this part of California. The discovery of correlative rocks at Cement Hill was unsuspected and may be helpful in defining the extent of this so-called formation or stage. Coccolith identification and correlations are by David Bukry, foraminifer identifications and correlations by Alvin Almgren and Kristin McDougall, gastropod identification and correlation by LouElla Saul, and Radiolaria identifications and correlations are by Annika Sanfilippo.

Molecular characterization of organic matter mobilized from Bangladeshi aquifer sediment: tracking carbon compositional change during microbial utilization

NASA Astrophysics Data System (ADS)

Pracht, Lara E.; Tfaily, Malak M.; Ardissono, Robert J.; Neumann, Rebecca B.

2018-03-01

Bioavailable organic carbon in aquifer recharge waters and sediments can fuel microbial reactions with implications for groundwater quality. A previous incubation experiment showed that sedimentary organic carbon (SOC) mobilized off sandy sediment collected from an arsenic-contaminated and methanogenic aquifer in Bangladesh was bioavailable; it was transformed into methane. We used high-resolution mass spectrometry to molecularly characterize this mobilized SOC, reference its composition against dissolved organic carbon (DOC) in surface recharge water, track compositional changes during incubation, and advance understanding of microbial processing of organic carbon in anaerobic environments. Organic carbon mobilized off aquifer sediment was more diverse, proportionately larger, more aromatic, and more oxidized than DOC in surface recharge. Mobilized SOC was predominately composed of terrestrially derived organic matter and had characteristics signifying that it evaded microbial processing within the aquifer. Approximately 50 % of identified compounds in mobilized SOC and in DOC from surface recharge water contained sulfur. During incubation, after mobilized SOC was converted into methane, new organosulfur compounds with high S-to-C ratios and a high nominal oxidation state of carbon (NOSC) were detected. We reason that these detected compounds formed abiotically following microbial reduction of sulfate to sulfide, which could have occurred during incubation but was not directly measured or that they were microbially synthesized. Most notably, microbes transformed all carbon types during incubation, including those currently considered thermodynamically unviable for microbes to degrade in anaerobic conditions (i.e., those with a low NOSC). In anaerobic environments, energy yields from redox reactions are small and the amount of energy required to remove electrons from highly reduced carbon substrates during oxidation decreases the thermodynamic favorability of

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

PubMed Central

Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

2016-01-01

We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can

Application of Sequence-based Methods in Human MicrobialEcology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weng, Li; Rubin, Edward M.; Bristow, James

2005-08-29

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning tomore » apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.« less

C3H7NO2S effect on concrete steel-rebar corrosion in 0.5 M H2SO4 simulating industrial/microbial environment

NASA Astrophysics Data System (ADS)

Okeniyi, Joshua Olusegun; Nwadialo, Christopher Chukwuweike; Olu-Steven, Folusho Emmanuel; Ebinne, Samaru Smart; Coker, Taiwo Ebenezer; Okeniyi, Elizabeth Toyin; Ogbiye, Adebanji Samuel; Durotoye, Taiwo Omowunmi; Badmus, Emmanuel Omotunde Oluwasogo

2017-02-01

This paper investigates C3H7NO2S (Cysteine) effect on the inhibition of reinforcing steel corrosion in concrete immersed in 0.5 M H2SO4, for simulating industrial/microbial environment. Different C3H7NO2S concentrations were admixed, in duplicates, in steel-reinforced concrete samples that were partially immersed in the acidic sulphate environment. Electrochemical monitoring techniques of open circuit potential, as per ASTM C876-91 R99, and corrosion rate, by linear polarization resistance, were then employed for studying anticorrosion effect in steel-reinforced concrete samples by the organic hydrocarbon admixture. Analyses of electrochemical test-data followed ASTM G16-95 R04 prescriptions including probability distribution modeling with significant testing by Kolmogorov-Smirnov and student's t-tests statistics. Results established that all datasets of corrosion potential distributed like the Normal, the Gumbel and the Weibull distributions but that only the Weibull model described all the corrosion rate datasets in the study, as per the Kolmogorov-Smirnov test-statistics. Results of the student's t-test showed that differences of corrosion test-data between duplicated samples with the same C3H7NO2S concentrations were not statistically significant. These results indicated that 0.06878 M C3H7NO2S exhibited optimal inhibition efficiency η = 90.52±1.29% on reinforcing steel corrosion in the concrete samples immersed in 0.5 M H2SO4, simulating industrial/microbial service-environment.

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis.

PubMed

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-27

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.

Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called "species signal".

PubMed

Musser, Jacob M; Wagner, Günter P

2015-11-01

We elaborate a framework for investigating the evolutionary history of morphological characters. We argue that morphological character trees generated by phylogenetic analysis of transcriptomes provide a useful tool for identifying causal gene expression differences underlying the development and evolution of morphological characters. They also enable rigorous testing of different models of morphological character evolution and origination, including the hypothesis that characters originate via divergence of repeated ancestral characters. Finally, morphological character trees provide evidence that character transcriptomes undergo concerted evolution. We argue that concerted evolution of transcriptomes can explain the so-called "species signal" found in several recent comparative transcriptome studies. The species signal is the phenomenon that transcriptomes cluster by species rather than character type, even though the characters are older than the respective species. We suggest the species signal is a natural consequence of concerted gene expression evolution resulting from mutations that alter gene regulatory network interactions shared by the characters under comparison. Thus, character trees generated from transcriptomes allow us to investigate the variational independence, or individuation, of morphological characters at the level of genetic programs. © 2015 Wiley Periodicals, Inc.

Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds.

PubMed

Navarri, Marion; Jégou, Camille; Meslet-Cladière, Laurence; Brillet, Benjamin; Barbier, Georges; Burgaud, Gaëtan; Fleury, Yannick

2016-03-10

The evolving global threat of antimicrobial resistance requires a deep renewal of the antibiotic arsenal including the isolation and characterization of new drugs. Underexplored marine ecosystems may represent an untapped reservoir of novel bioactive molecules. Deep-sea fungi isolated from a record-depth sediment core of almost 2000 m below the seafloor were investigated for antimicrobial activities. This antimicrobial screening, using 16 microbial targets, revealed 33% of filamentous fungi synthesizing bioactive compounds with activities against pathogenic bacteria and fungi. Interestingly, occurrence of antimicrobial producing isolates was well correlated with the complexity of the habitat (in term of microbial richness), as higher antimicrobial activities were obtained at specific layers of the sediment core. It clearly highlights complex deep-sea habitats as chemical battlefields where synthesis of numerous bioactive compounds appears critical for microbial competition. The six most promising deep subseafloor fungal isolates were selected for the production and extraction of bioactive compounds. Depending on the fungal isolates, antimicrobial compounds were only biosynthesized in semi-liquid or solid-state conditions as no antimicrobial activities were ever detected using liquid fermentation. An exception was made for one fungal isolate, and the extraction procedure designed to extract amphipathic compounds was successful and highlighted the amphiphilic profile of the bioactive metabolites.

Microbial control in Asia: a bellwether for the future?

PubMed

Gelernter, Wendy D

2007-07-01

Advances and barriers faced by microbial control efforts in Asia offer instructive insights for microbial control in general. The papers in this series, which are based on plenary lectures given at the Society for Invertebrate Pathology 2006 meeting in Wuhan, China, explore the history and current status of microbial control in China, Japan, and Southeast Asia, and in doing so, bring to light the following key assumptions that deserve further examination; (1) the adoption rate of microbial control is well documented; (2) microbial control agents can compete directly with conventional insecticides; (3) microbial control agents are relatively easy and inexpensive to produce and develop; (4) patents will promote innovation and investor interest in microbial control. Alternative viewpoints are presented that can hopefully aid in future efforts to develop more safe and effective microbial control agents.

Compound-specific Isotope Analysis of Cyanobacterial Pure cultures and Microbial Mats: Effects of Photorespiration?

NASA Technical Reports Server (NTRS)

Jahnke, L. L.; Summons, R. E.

2006-01-01

Microbial mats are considered modern homologs of Precambrian stromatolites. The carbon isotopic compositions of organic matter and biomarker lipids provide clues to the depositional environments of ancient mat ecosystems. As the source of primary carbon fixation for over two billion years, an understanding of cyanobacterial lipid biosynthesis, associated isotopic discriminations, and the influence of physiological factors on growth and isotope expression is essential to help us compare modern microbial ecosystems to their ancient counterparts. Here, we report on the effects of photorespiration (PR) on the isotopic composition of cyanobacteria and biomarker lipids, and on potential PR effects associated with the composition of various microbial mats. The high light, high O2 and limiting CO2 conditions often present at the surface of microbial mats are known to support PR in cyanobacteria. The oxygenase function of ribulose bisphosphate carboxylase/oxygenase can result in photoexcretion of glycolate and subsequent degration by heterotrophic bacteria. We have found evidence which supports an isotopic depletion (increased apparent E) scaled to O2 level associated with growth of Phormidium luridum at low CO2 concentrations (less than 0.04%). Similar to previous studies, isotopic differences between biomass and lipid biomarkers, and between lipid classes were positively correlated with overall fractionation, and should provide a means of estimating the influence of PR on overall isotopic composition of microbial mats. Several examples of microbial mats growing in the hydrothermal waters of Yellowstone National Park and the hypersaline marine evaporation ponds at Guerrero Negro, Baja Sur Mexico will be compared with a view to PR as a possible explanation of the relatively heavy C-isotope composition of hypersaline mats.

Study on real-time images compounded using spatial light modulator

NASA Astrophysics Data System (ADS)

Xu, Jin; Chen, Zhebo; Ni, Xuxiang; Lu, Zukang

2007-01-01

Image compounded technology is often used on film and its facture. In common, image compounded use image processing arithmetic, get useful object, details, background or some other things from the images firstly, then compounding all these information into one image. When using this method, the film system needs a powerful processor, for the process function is very complex, we get the compounded image for a few time delay. In this paper, we introduce a new method of image real-time compounded, use this method, we can do image composite at the same time with movie shot. The whole system is made up of two camera-lens, spatial light modulator array and image sensor. In system, the spatial light modulator could be liquid crystal display (LCD), liquid crystal on silicon (LCoS), thin film transistor liquid crystal display (TFTLCD), Deformable Micro-mirror Device (DMD), and so on. Firstly, one camera-lens images the object on the spatial light modulator's panel, we call this camera-lens as first image lens. Secondly, we output an image to the panel of spatial light modulator. Then, the image of the object and image that output by spatial light modulator will be spatial compounded on the panel of spatial light modulator. Thirdly, the other camera-lens images the compounded image to the image sensor, and we call this camera-lens as second image lens. After these three steps, we will gain the compound images by image sensor. For the spatial light modulator could output the image continuously, then the image will be compounding continuously too, and the compounding procedure is completed in real-time. When using this method to compounding image, if we will put real object into invented background, we can output the invented background scene on the spatial light modulator, and the real object will be imaged by first image lens. Then, we get the compounded images by image sensor in real time. The same way, if we will put real background to an invented object, we can output the

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities

USGS Publications Warehouse

Mumford, Adam C.; Akob, Denise M.; Klinges, J. Grace; Cozzarelli, Isabelle M.

2018-01-01

The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C3H6BrNO4). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.

Imperfect asymmetry of life: earth microbial communities prefer D-lactate but can use L-lactate also.

PubMed

Moazeni, Faegheh; Zhang, Gaosen; Sun, Henry J

2010-05-01

Asymmetrical utilization of chiral compounds has been sought on Mars as evidence for biological activity. This method was recently validated in glucose. Earth organisms utilize D-glucose, not L-glucose, a perfect asymmetry. In this study, we tested the method in lactate and found utilization of both enantiomers. Soil-, sediment-, and lake-borne microbial communities prefer D-lactate but can consume L-lactate if given extra time to acclimate. This situation is termed imperfect asymmetry. Future life-detection mission investigators need to be aware of imperfect asymmetry so as not to miss relatively subtle signs of life.

Microbial and chemical properties of log ponds along the Oregon Coast.

Treesearch

Iwan Ho; Ching Yan Li

1987-01-01

The microbial and chemical properties of log ponds along the Oregon coast were investigated. The log ponds were highly eutrophic, containing high concentrations of ammonium and nitrate nitrogen, phosphate, and organic compounds. Because of large microbial populations, the biochemical oxygen demand was high and dissolved oxygen was low. Bacterial species in log ponds...

Analysis of a novel class of predictive microbial growth models and application to coculture growth.

PubMed

Poschet, F; Vereecken, K M; Geeraerd, A H; Nicolaï, B M; Van Impe, J F

2005-04-15

In this paper, a novel class of microbial growth models is analysed. In contrast with the currently used logistic type models (e.g., the model of Baranyi and Roberts [Baranyi, J., Roberts, T.A., 1994. A dynamic approach to predicting bacterial growth in food. International Journal of Food Microbiology 23, 277-294]), the novel model class, presented in Van Impe et al. (Van Impe, J.F., Poschet, F., Geeraerd, A.H., Vereecken, K.M., 2004. Towards a novel class of predictive microbial growth models. International Journal of Food Microbiology, this issue), explicitly incorporates nutrient exhaustion and/or metabolic waste product effects inducing stationary phase behaviour. As such, these novel model types can be extended in a natural way towards microbial interactions in cocultures and microbial growth in structured foods. Two illustrative case studies of the novel model types are thoroughly analysed and compared to the widely used model of Baranyi and Roberts. In a first case study, the stationary phase is assumed to be solely resulting from toxic product inhibition and is described as a function of the pH-evolution. In the second case study, substrate exhaustion is the sole cause of the stationary phase. Finally, a more complex case study of a so-called P-model is presented, dealing with a coculture inhibition of Listeria innocua mediated by lactic acid production of Lactococcus lactis.

Microbial fuel cells: From fundamentals to applications. A review.

PubMed

Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

2017-07-15

In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

Microbial fuel cells: From fundamentals to applications. A review

NASA Astrophysics Data System (ADS)

Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

2017-07-01

In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

Temporal variation in airborne microbial populations and microbially-derived allergens in a tropical urban landscape

NASA Astrophysics Data System (ADS)

Woo, Anthony C.; Brar, Manreetpal S.; Chan, Yuki; Lau, Maggie C. Y.; Leung, Frederick C. C.; Scott, James A.; Vrijmoed, Lilian L. P.; Zawar-Reza, Peyman; Pointing, Stephen B.

2013-08-01

The microbial component of outdoor aerosols was assessed along a gradient of urban development from inner-city to rural in the seasonal-tropical metropolis of Hong Kong. Sampling over a continuous one-year period was conducted, with molecular analyses to characterize bacterial and eukaryal microbial populations, immuno-assays to detect microbially-derived allergens and extensive environmental and meteorological observations. The data revealed bio-aerosol populations were not significantly impacted by the level of urban development as measured by anthropogenic pollutants and human population levels, but instead exhibited a strong seasonal trend related to general climatic variables. We applied back-trajectory analysis to establish sources of air masses and this allowed further explanation of urban bio-aerosols largely in terms of summer-marine and winter-continental origins. We also evaluated bio-aerosols for the potential to detect human health threats. Many samples supported bacterial and fungal phylotypes indicative of known pathogenic taxa, together with common indicators of human presence. The occurrence of allergenic endotoxins and beta-glucans generally tracked trends in microbial populations, with levels known to induce symptoms detected during summer months when microbial loading was higher. This strengthens calls for bio-aerosols to be considered in future risk assessments and surveillance of air quality, along with existing chemical and particulate indices.

Spectroscopic analysis of phenolic compounds for food and feed formulations

USDA-ARS?s Scientific Manuscript database

Phenolic compounds exhibit several bioactive properties including anti-oxidant, anti-microbial, and anti-fungal characteristics with potential applications as additives in functional food and feed formulations. Phenolic compounds occur in plants as secondary metabolites and may be recovered as a co-...

Combining position-specific 13C labeling with compound-specific isotope analysis: first steps towards soil fluxomics

NASA Astrophysics Data System (ADS)

Dippold, Michaela; Kuzyakov, Yakov

2015-04-01

Understanding the soil organic matter (SOM) dynamics is one of the most important challenges in soil science. Transformation of low molecular weight organic substances (LMWOS) is a key step in biogeochemical cycles because 1) all high molecular substances pass this stage during their decomposition and 2) only LMWOS will be taken up by microorganisms. Previous studies on LMWOS were focused on determining net fluxes through the LMWOS pool, but they rarely identified transformations. As LMWOS are the preferred C and energy source for microorganisms, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the biochemical pathways and its controlling factors. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools. Up to now, studies on LMWOS were nearly exclusively based on uniformly labeled organic substances i.e. all C atoms in the molecules were labeled with 13C or 14C. However, this classical approach did not allow the differentiation between use of intact initial substances in any process, or whether they were transformed to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of LMWOS and quantification of 13CO2 and 13C in bulk soil enabled following the basic metabolic pathways of soil microorganisms. However, only the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites allowed 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. So, these are the prerequisites for soil fluxomics. Our studies combining position-specific labeled glucose with amino

Development, registration and commercialization of microbial pesticides for plant protection.

PubMed

Montesinos, Emilio

2003-12-01

emerging food-borne diseases and bioterrorism do not help to create a socially receptive environment to microbial pesticides. The future of microbial pesticides is not only in developing new active ingredients based on microorganisms beneficial to plants, but in producing self-protected plants (so-called plant-incorporated pesticides) by transforming agronomically high-value crop plants with genes from biological control agents.

Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade

PubMed Central

Hodgson, Douglas M.; Smith, Ann; Dahale, Sonal; Stratford, James P.; Li, Jia V.; Grüning, André; Bushell, Michael E.; Marchesi, Julian R.; Avignone Rossa, C.

2016-01-01

Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities. PMID:27242723

Research advances on microbial genetics in China in 2015.

PubMed

Xie, Jian-ping; Han, Yu-bo; Liu, Gang; Bai, Lin-quan

2016-09-01

In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled. We also illustrated the biosynthetic pathways and regulators of multiple microbial compounds, novel enzyme reactions, and new mechanisms regulating microbial gene expression. And new findings were obtained in the microbial development, evolution and population genetics. For the industrial microbiology, more understanding on the molecular basis of the microbial factory has been gained. For the pathogenic microbiology, the genetic circuits of several pathogens were depicted, and significant progresses were achieved for understanding the pathogen-host interaction and revealing the genetic mechanisms underlying antimicrobial resistance, emerging pathogens and environmental microorganisms at the genomic level. In future, the genetic diversity of microbes can be used to obtain specific products, while gut microbiome is gathering momentum.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

PubMed

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Biofiltration for control of volatile organic compounds (VOCS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bishop, D.F.; Govind, R.

1995-10-01

Air biofiltration is a promising technology for control of air emissions of biodegradable volatile organic compounds (VOCs). In conjunction with vacuum extraction of soils or air stripping of ground water, it can be used to mineralize VOCs removed from contaminated soil or groundwater. The literature describes three major biological systems for treating contaminated air bioscrubbers, biotrickling filters and biofilters. Filter media can be classified as: bioactive fine or irregular particulates, such as soil, peat, compost or mixtures of these materials; pelletized, which are randomly packed in a bed; and structured, such as monoliths with defined or variable passage size andmore » geometry. The media can be made of sorbing and non-absorbing materials. Non-bioactive pelletized and structured media require recycled solutions of nutrients and buffer for efficient microbial activity and are thus called biotrickling filters. Extensive work has been conducted to improve biofiltration by EPA`s Risk Reduction Engineering Laboratory and the University of Cincinnati in biofilters using pelletized and structured media and improved operational approaches. Representative VOCs in these studies included compounds with a range of aqueous solubilities and octanol-water partition coefficients. The compounds include iso-pentane, toluene, methylene chloride, trichloroethylene (TCE), ethyl benzene, chlorobenzene and perchloroethylene (PCE) and alpha ({alpha}-) pinene. Comparative studies were conducted with peat/compost biofilters using isopentane and {alpha}-pinene. Control studies were also conducted to investigate adsorption/desorption of contaminants on various media using mercuric chloride solution to insure the absence of bioactivity.« less

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

PubMed Central

Maphosa, Farai; Lieten, Shakti H.; Dinkla, Inez; Stams, Alfons J.; Smidt, Hauke; Fennell, Donna E.

2012-01-01

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants. PMID:23060869

Engineering microbial factories for synthesis of value-added products

PubMed Central

Du, Jing; Shao, Zengyi; Zhao, Huimin

2011-01-01

Microorganisms have become an increasingly important platform for the production of drugs, chemicals, and biofuels from renewable resources. Advances in protein engineering, metabolic engineering, and synthetic biology enable redesigning microbial cellular networks and fine-tuning physiological capabilities, thus generating industrially viable strains for the production of natural and unnatural value-added compounds. In this review, we describe the recent progress on engineering microbial factories for synthesis of valued-added products including alkaloids, terpenoids, flavonoids, polyketides, non-ribosomal peptides, biofuels, and chemicals. Related topics on lignocellulose degradation, sugar utilization, and microbial tolerance improvement will also be discussed. PMID:21526386

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

DOE PAGES

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken; ...

2016-11-29

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less

EFFECT OF TEMPERATURE ON THE C ISOTOPIC VALUE OF MICROBIAL LIPIDS APPLIED TO DETERMINE C USAGE IN MICROBIAL COMMUNITIES

EPA Science Inventory

The combination of compound specific stable isotopic analysis with phospholipid fatty acid (PLFAS) analysis is useful in determining the source of organic carbon used by groups of a microbial community. Determination of the effect of certain environmental parameters is important ...

Bat echolocation calls facilitate social communication

PubMed Central

Knörnschild, Mirjam; Jung, Kirsten; Nagy, Martina; Metz, Markus; Kalko, Elisabeth

2012-01-01

Bat echolocation is primarily used for orientation and foraging but also holds great potential for social communication. The communicative function of echolocation calls is still largely unstudied, especially in the wild. Eavesdropping on vocal signatures encoding social information in echolocation calls has not, to our knowledge, been studied in free-living bats so far. We analysed echolocation calls of the polygynous bat Saccopteryx bilineata and found pronounced vocal signatures encoding sex and individual identity. We showed experimentally that free-living males discriminate approaching male and female conspecifics solely based on their echolocation calls. Males always produced aggressive vocalizations when hearing male echolocation calls and courtship vocalizations when hearing female echolocation calls; hence, they responded with complex social vocalizations in the appropriate social context. Our study demonstrates that social information encoded in bat echolocation calls plays a crucial and hitherto underestimated role for eavesdropping conspecifics and thus facilitates social communication in a highly mobile nocturnal mammal. PMID:23034703

Bat echolocation calls facilitate social communication.

PubMed

Knörnschild, Mirjam; Jung, Kirsten; Nagy, Martina; Metz, Markus; Kalko, Elisabeth

2012-12-07

Bat echolocation is primarily used for orientation and foraging but also holds great potential for social communication. The communicative function of echolocation calls is still largely unstudied, especially in the wild. Eavesdropping on vocal signatures encoding social information in echolocation calls has not, to our knowledge, been studied in free-living bats so far. We analysed echolocation calls of the polygynous bat Saccopteryx bilineata and found pronounced vocal signatures encoding sex and individual identity. We showed experimentally that free-living males discriminate approaching male and female conspecifics solely based on their echolocation calls. Males always produced aggressive vocalizations when hearing male echolocation calls and courtship vocalizations when hearing female echolocation calls; hence, they responded with complex social vocalizations in the appropriate social context. Our study demonstrates that social information encoded in bat echolocation calls plays a crucial and hitherto underestimated role for eavesdropping conspecifics and thus facilitates social communication in a highly mobile nocturnal mammal.

Methods for visualising active microbial benzene degraders in in situ microcosms.

PubMed

Schurig, Christian; Mueller, Carsten W; Höschen, Carmen; Prager, Andrea; Kothe, Erika; Beck, Henrike; Miltner, Anja; Kästner, Matthias

2015-01-01

Natural attenuation maybe a cost-efficient option for bioremediation of contaminated sites but requires knowledge about the activity of degrading microbes under in situ conditions. In order to link microbial activity to the spatial distribution of contaminant degraders, we combined the recently improved in situ microcosm approach, so-called 'direct-push bacterial trap' (DP-BACTRAP), with nano-scale secondary ion mass spectrometry (NanoSIMS) analysis on samples from contaminated constructed wetlands. This approach is based on initially sterile microcosms amended with (13)C-labelled benzene as a source of carbon and energy for microorganisms. The microcosms were introduced directly in the constructed wetland, where they were colonised by indigenous microorganisms from the sediment. After incubation in the field, the samples were analysed by NanoSIMS, scanning electron microscopy (SEM) and fluorescence microscopy in order to visualise (13)C-labelled microbial biomass on undisturbed samples from the microcosms. With the approach developed, we successfully visualised benzene-degrading microbes on solid materials with high surface area by means of NanoSIMS. Moreover, we could demonstrate the feasibility of NanoSIMS analysis of unembedded porous media with a highly complex topography, which was frequently reasoned to not lead to sufficient results.

Properties of pure single crystals of actinide compounds

NASA Astrophysics Data System (ADS)

Vogt, O.

1989-07-01

Actinide research started with substances of poor quality and a multitude of "unexplainable" results mostly found on powder samples of doubtful quality exerted some pressure on the crystal growers. As an example we may mention the measurements on UP. Type I antiferromagnetism was found below 123 K by neutron diffraction experiments on powdered samples. At 23 K another transition becomes apparent in susceptibility measurements. The change of the magnetic moments associated with this transition remained unexplained. It was only after the discovery of multi k structures in other actinide compounds that the need was seen to perform even inelastic neutron diffraction experiments on single crystals so that finally the true nature of the transition in UP could be revealed. NpAs is another illustrative example for the fact that sometimes it takes decades to get a clear understanding for things even so simple as macroscopic magnetic properties. The main reason for the need of single crystals is certainly the anisotropy of the magnetic moment encountered in all actinide compounds. Self-heating effects may prevent research on big crystals or might call for isotopic purity of certain samples.

Inhibitors of calling behavior of Plodia interpunctella

PubMed Central

Hirashima, Akinori; Shigeta, Yoko; Eiraku, Tomohiko; Kuwano, Eiichi

2003-01-01

Some octopamine agonists were found to suppress the calling behavior of the stored product Indian meal moth, Plodia interpunctella. Compounds were screened using a calling behavior bioassay using female P. interpunctella. Four active derivatives, with inhibitory activity at the nanomolar range, were identified in order of decreasing activity: 2-(1-phenylethylamino)-2-oxazoline > 2-(2-ethyl,6-methylanilino)oxazolidine > 2-(2-methyl benzylamino)-2-thiazoline > 2-(2,6-diethylanilino)thiazolidine. Three-dimensional pharmacophore hypotheses were built from a set of 15 compounds. Among the ten common-featured models generated by the program Catalyst/HipHop, a hypothesis including a hydrogen-bond acceptor lipid, a hydrophobic aromatic and two hydrophobic aliphatic features was considered to be essential for inhibitory activity in the calling behavior. Active compounds mapped well onto all the hydrogen-bond acceptor lipid, hydrophobic aromatic and hydrophobic aliphatic features of the hypothesis. On the other hand, less active compounds were shown not to achieve the energetically favorable conformation that is found in the active molecules in order to fit the 3D common-feature pharmacophore models. The present studies demonstrate that inhibition of calling behavior is via an octopamine receptor. Abbreviation: AII 2-(arylimino)imidazolidine AIO 2-(arylimino)oxazolidine AIT 2-(arylimino)thiazolidine CBO 2-(4-chlorobenzylamino)-2-(4-phenyl)oxazoline CDM chlordimeform Confs number of conformers DIP 2-(2,6-diethylphenylimino)piperidine Features/Confs total number of features divided by the number of conformers (summed over the entire family of conformers) HBA hydrogen-bond acceptor HBAl hydrogen-bond acceptor lipid HBD hydrogen-bond donor Hp hydrophobic HpAl hydrophobic aliphatic HpAr hydrophobic aromatic mp melting point MTO 2-(3-methyl benzylthio)-2-oxazoline NI negative ionizable NIO 2-(1-naphthylimino)oxazolidine OA octopamine ODA 2-phenyl-5,6-dihydro-4H-1,3,4-oxadiazine

Microbial liquefaction of peat for the production of synthetic fuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunasekaran, M.

1988-01-01

Objectives of this study were: to evaluate the potential of using various microorganisms to hydrolyse and liquify peat; to determine the optimal conditions for peat hydrolysis and liquefaction; to study the co-metabolizable substances; to separate the compounds present in liquified peat by alumina and silica acid chromatography and capillary gas chromatography; and to identify the compounds in liquified peat by capillary GC-Mass spectrometry. Organisms used in the study include: Coprinus comatus, Coriolus hirsutus, Ganoderma lucidum, Lentinus edodes, Lenzites trabea, Phanerochaete chrysosporium, Pleurotus ostreatus, P. sapidus, Polyporus adjustus, Neurospora sitophila, Rhizophus arrhizus, Bacillus subtilis, Acinetobacter sp. and Alcaligenes sp. The fungimore » were maintained and cultivated in potato dextrose agar at 30 C. The bacteria were maintained in nutrient agar at 30 C. We have also initiated work on coal solubilization in addition to the studies on peat liquefaction. A relatively new substratum or semi-solid base for culture media called Pluronic F-127, or Polyol (BASF, New Jersey). Objectives of this study were: (1) to study the growth patterns of Candida ML 13 on pluronic as substratum; (2) to determine the rate of microbial coal solubilization on pluronic F-127 amended in different growth media; (3) to separate the mycelial mat of Candida ML 13 from unsolubilized coal particles and solubilized coal products from pluronic F-127; (4) to determine the effects of pH on microbial coal solubilization in pluronic F-127 media; (5) the effect of concentration of pluronic F-127 in media on coal solubilization; and, (6) to study the role of extracellular factors secreted by Candida ML 13 on coal solubilization in pluronic F-127 media. Results are discussed. 4 refs.« less

Recalcitrant Carbonaceous Material: A Source of Electron Donors for Anaerobic Microbial Metabolisms in the Subsurface?

NASA Astrophysics Data System (ADS)

Nixon, S. L.; Montgomery, W.; Sephton, M. A.; Cockell, C. S.

2014-12-01

More than 90% of organic material on Earth resides in sedimentary rocks in the form of kerogens; fossilized organic matter formed through selective preservation of high molecular weight biopolymers under anoxic conditions. Despite its prevalence in the subsurface, the extent to which this material supports microbial metabolisms is unknown. Whilst aerobic microorganisms are known to derive energy from kerogens within shales, utilization in anaerobic microbial metabolisms that proliferate in the terrestrial subsurface, such as microbial iron reduction, has yet to be demonstrated. Data are presented from microbial growth experiments in which kerogens and shales were supplied as the sole electron donor source for microbial iron reduction by an enrichment culture. Four well-characterized kerogens samples (representative of Types I-IV, classified by starting material), and two shale samples, were assessed. Organic analysis was carried out to investigate major compound classes present in each starting material. Parallel experiments were conducted to test inhibition of microbial iron reduction in the presence of each material when the culture was supplied with a full redox couple. The results demonstrate that iron-reducing microorganisms in this culture were unable to use kerogens and shales as a source of electron donors for energy acquisition, despite the presence of compound classes known to support this metabolism. Furthermore, the presence of these materials was found to inhibit microbial iron reduction to varying degrees, with some samples leading to complete inhibition. These results suggest that recalcitrant carbonaceous material in the terrestrial subsurface is not available for microbial iron reduction and similar metabolisms, such as sulphate-reduction. Further research is needed to investigate the inhibition exerted by these materials, and to assess whether these findings apply to other microbial consortia. These results may have significant implications for

Not-so-Soft Skills

ERIC Educational Resources Information Center

Curran, Mary

2010-01-01

Much recent discussion about the skills needed to secure Britain's economic recovery has focused on skills for employability. However, too often, these fundamental skills are understood in narrow functional or vocational terms. So-called "soft skills", what Penelope Tobin, in her 2008 paper "Soft Skills: the hard facts", terms "traits and…

Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, Qiuming; Li, Zhou; Song, Yang

Phosphorus (P) is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting P deficiency at the gene and protein levels remains unknown. Here we report a metagenomic and metaproteomic comparison of microbial communities in P-deficient and P-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A >4-fold increase in the gene abundance of 3-phytase was the strongest response of soil communities to P deficiency. Phytase catalyzes the release of phosphate from phytate, the mostmore » recalcitrant P-containing compound in soil organic matter. Genes and proteins for the degradation of P-containing nucleic acids and phospholipids as well as the decomposition of labile carbon and nitrogen were also enhanced in the P-deficient soils. In contrast, microbial communities in the P-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, the transformation of nitrogenous compounds, and the assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints.« less

Theoretical estimation of equilibrium sulfur isotope fractionations among aqueous sulfite species: Implications for isotope models of microbial sulfate reduction

NASA Astrophysics Data System (ADS)

Eldridge, D. L.; Farquhar, J.; Guo, W.

2015-12-01

Sulfite (sensu lato), an intermediate in a variety sulfur redox processes, plays a particularly important role in microbial sulfate reduction. It exists intracellularly as multiple species between sets of enzymatic reactions that transform sulfate to sulfide, with the exact speciation depending on pH, T, and ionic strength. However, the complex speciation of sulfite is ignored in current isotope partitioning models of microbial sulfate reduction and simplified solely to the pyramidal SO32- (sulfite sensu stricto), due to a lack of appropriate constraints. We theoretically estimated the equilibrium sulfur isotope fractionations (33S/32S, 34S/32S, 36S/32S) among all documented sulfite species in aqueous solution, including sulfite (SO32-), bisulfite isomers and dimers ((HS)O3-, (HO)SO2-, S2O52-), and SO2(aq), through first principles quantum mechanical calculations. The calculations were performed at B3LYP/6-31+G(d,p) level using cluster models with 30-40 water molecules surrounding the solute. Our calculated equilibrium fractionation factors compare well to the available experimental constraints and suggest that the minor and often-ignored tetrahedral (HS)O3- isomer of bisulfite strongly influences isotope partitioning behavior in the sulfite system under most environmentally relevant conditions, particularly fractionation magnitudes and unusual temperature dependence. For example, we predict that sulfur isotope fractionation between sulfite and bulk bisulfite in solution should have an apparent inverse temperature dependence due to the influence of (HS)O3- and its increased stability at higher temperatures. Our findings highlight the need to appropriately account for speciation/isomerization of sulfur species in sulfur isotope studies. We will also present similar calculation results of other aqueous sulfur compounds (e.g., H2S/HS-, SO42-, S2O32-, S3O62-, and poorly documented SO22- species), and discuss the implication of our results for microbial sulfate

Tinted windows: The presence of the UV absorbing compounds called mycosporine-like amino acids embedded in the frustules of marine diatoms

NASA Astrophysics Data System (ADS)

Ingalls, Anitra E.; Whitehead, Kenia; Bridoux, Maxime C.

2010-01-01

Diatom frustule-bound organic compounds presumably play an important role in biomineralization and constitute an important pool of organic matter preserved in diatom frustule-rich sediments. In this study, detailed analysis of diatom frustule-bound organic matter in opal-rich Southern Ocean plankton and sediments revealed for the first time the presence of low molecular weight, UV light absorbing compounds called mycosporine-like amino acids (MAAs). Chemically cleaned diatom frustule-derived biosilica was dissolved in HF, releasing bound or entrapped organic compounds that were subsequently characterized using liquid chromatography with UV-Vis and electrospray ionization mass spectrometry (LC/PDA/ESI-MS). Palythine ([M+H] + = 245), porphyra-334 ([M+H] + = 347) and shinorine ([M+H] + = 333) were the most abundant MAAs detected in HF digests of plankton and sediment. Traces of asterina ([M+H] + = 289), palythinol ([M+H] + = 303) and palythinic acid ([M+H] + = 329) were also detected. MAAs in cleaned HF digested frustules were up to two orders of magnitude more abundant than methanol extractable MAAs. MAAs are substituted with acid hydrolysable amino acid residues. Our results suggest that MAAs, and not proteins, could be responsible for the high proportion of the amino acids glycine and threonine found in hydrolysates of HF digested diatom-rich environmental samples. Total MAAs accounted for 3-27% of the carbon and 2-18% of total nitrogen in the frustules undergoing various chemical cleaning treatments. This is the first report of MAAs in close association with a mineral phase and we hypothesize that the mineral matrix could stabilize these compounds, thereby enhancing photoprotection against the harmful effects of UV light. The presence of frustule-bound MAAs in sediment cores further suggests the possibility that they could be used in compound-specific isotope analysis of diatom-bound organic matter and as indicators of past solar irradiance.

Thermal decomposition of europium sulfates Eu2(SO4)3·8H2O and EuSO4

NASA Astrophysics Data System (ADS)

Denisenko, Yu. G.; Khritokhin, N. A.; Andreev, O. V.; Basova, S. A.; Sal'nikova, E. I.; Polkovnikov, A. A.

2017-11-01

Reactions of europium sulfates Eu2(SO4)3·8H2O and EuSO4 complete decomposition were studied by Simultaneous Thermal Analysis. It was revealed that one-step dehydratation of Eu2(SO4)3·8H2O crystallohydrate is accompanied by the formation of amorphous anhydrous europium sulfate Eu2(SO4)3. Crystallization of amorphous europium (III) sulfate occurs at 381.1 °C (in argon) and 391.3 °C (in air). The average enthalpy values for dehydratation reaction of Eu2(SO4)3·8H2O (ΔH° = 141.1 kJ/mol), decomposition reactions of Eu2(SO4)3 (ΔH = 463.1 kJ/mol), Eu2O2SO4 (ΔH = 378.4 kJ/mol) and EuSO4 (ΔH = 124.1 kJ/mol) were determined. The step process mechanisms of thermal decomposition of europium (III) sulfate in air and europium (II) sulfate in inert atmosphere were established and justified. The kinetic parameters of complete thermal decomposition of europium (III) sulfate octahydrate were calculated by Kissinger model. The standard enthalpies of compound formation were calculated using thermal effects and formation enthalpy data for binary compounds.

Common Hydraulic Fracturing Fluid Additives Alter the Structure and Function of Anaerobic Microbial Communities.

PubMed

Mumford, Adam C; Akob, Denise M; Klinges, J Grace; Cozzarelli, Isabelle M

2018-04-15

The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C 3 H 6 BrNO 4 ). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills. IMPORTANCE Organic components of UOG wastewater can alter microbial communities and biogeochemical processes, which could alter the rates of

Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review.

PubMed

Hardoim, Cristiane C P; Costa, Rodrigo

2014-09-30

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.

Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review

PubMed Central

Hardoim, Cristiane C. P.; Costa, Rodrigo

2014-01-01

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed. PMID:25272328

Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis

NASA Astrophysics Data System (ADS)

Kohl, Lukas; Cumming, Emily; Cox, Alison; Rietze, Amanda; Morrissey, Liam; Lang, Susan Q.; Richter, Andreas; Suzuki, Shino; Nealson, Kenneth H.; Morrill, Penny L.

2016-04-01

Present-day serpentinization generates groundwaters with conditions (pH > 11, Eh < -550 mV) favorable for the microbial and abiotic production of organic compounds from inorganic precursors. Elevated concentrations of methane, C2-C6 alkanes, acetate, and formate have been detected at these sites, but the microbial or abiotic origin of these compounds remains unclear. While geochemical data indicate that methane at most sites of present-day serpentinization is abiogenic, the stable carbon, hydrogen, and clumped isotope data as well as the hydrocarbon gas composition from The Cedars, CA, USA, are consistent with a microbial origin for methane. However, there is no direct evidence of methanogenesis at this site of serpentinization. We report on laboratory experiments in which the microbial communities in fluids and sediments from The Cedars were incubated with 13C labeled substrates. Increasing methane concentrations and the incorporation of 13C into methane in live experiments, but not in killed controls, demonstrated that methanogens converted methanol, formate, acetate (methyl group), and bicarbonate to methane. The apparent fractionation between methane and potential substrates (α13CCH4-CO2(g) = 1.059 to 1.105, α13CCH4-acetate = 1.042 to 1.119) indicated that methanogenesis was dominated by the carbonate reduction pathway. Increasing concentrations of volatile organic acid anions indicated microbial acetogenesis. α13CCO2(g)-acetate values (0.999 to 1.000), however, were inconsistent with autotrophic acetogenesis, thus suggesting that acetate was produced through fermentation. This is the first study to show direct evidence of microbial methanogenesis and acetogenesis by the native microbial community at a site of present-day serpentinization.

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

PubMed Central

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA. PMID:28134828

Crown Ether Complexes of Alkali-Metal Chlorides from SO2.

PubMed

Reuter, Kirsten; Rudel, Stefan S; Buchner, Magnus R; Kraus, Florian; von Hänisch, Carsten

2017-07-18

The structures of alkali-metal chloride SO 2 solvates (Li-Cs) in conjunction with 12-crown-4 or 1,2-disila-12-crown-4 show strong discrepancies, despite the structural similarity of the ligands. Both types of crown ethers form 1:1 complexes with LiCl to give [Li(1,2-disila-12-crown-4)(SO 2 Cl)] (1) and [Li(12-crown-4)Cl]⋅4 SO 2 (2). However, 1,2-disila-12-crown-4 proved unable to coordinate cations too large for the cavity diameter, for example, by the formation of sandwich-type complexes. As a result, 12-crown-4 reacts exclusively with the heavier alkali-metal chlorides NaCl, KCl and RbCl. Compounds [Na(12-crown-4) 2 ]Cl⋅4 SO 2 (3) and [M(12-crown-4) 2 (SO 2 )]Cl⋅4 SO 2 (4: M=K; 5: M=Rb) all showed S-coordination to the chloride ions through four SO 2 molecules. Compounds 4 and 5 additionally exhibit the first crystallographically confirmed non-bridging O,O'-coordination mode of SO 2 . Unexpectedly, the disila-crown ether supports the dissolution of RbCl and CsCl in the solvent and gives the homoleptic SO 2 -solvated alkali-metal chlorides [MCl⋅3 SO 2 ] (6: M=Rb; 7: M=Cs), which incorporate bridging μ-O,O'-coordinating moieties and the unprecedented side-on O,O'-coordination mode. All compounds were characterised by single-crystal X-ray diffraction. The crown ether complexes were additionally studied by using NMR spectroscopy, and the presence of SO 2 at ambient temperature was revealed by IR spectroscopy of the neat compounds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of Microbial Transglutaminase on Physicochemical, Microbial and Sensorial Properties of Kefir Produced by Using Mixture Cow's and Soymilk.

PubMed

Temiz, Hasan; Dağyıldız, Kübra

2017-01-01

The objective of this research was to investigate the effects microbial transglutaminase (m-TGs) on the physicochemical, microbial and sensory properties of kefir produced by using mix cow and soymilk. Kefir batches were prepared using 0, 0.5, 1 and 1.5 Units m-TGs for per g of milk protein. Adding m-TGs to milk caused an increase in the pH and viscosity and caused a decrease in titratable acidity and syneresis in the kefir samples. Total bacteria, lactobacilli and streptococci counts decreased, while yeast counts increased in all the samples during storage. Alcohols and acids compounds have increased in all the samples except in the control samples, while carbonyl compounds have decreased in all the samples during storage (1-30 d). The differences in the percentage of alcohols, carbonyl compounds and acids in total volatiles on the 1st and the 30th d of storage were observed at 8.47-23.52%, 6.94-25.46% and 59.64-63.69%, respectively. The consumer evaluation of the kefir samples showed that greater levels of acceptability were found for samples which had been added 1.5 U m-TGs for per g of milk protein.

EPS in Environmental Microbial Biofilms as Examined by Advanced Imaging Techniques

NASA Astrophysics Data System (ADS)

Neu, T. R.; Lawrence, J. R.

2006-12-01

lectin-binding- analysis has been suggested as a suitable approach to image glycoconjugates within the polymer matrix of biofilm communities. More recently synchrotron radiation is increasingly recognized as a powerful tool for studying biological samples. Hard X-ray excitation can be used to map elemental composition whereas IR imaging allows examination of biological macromolecules. A further technique called soft X-ray scanning transmission microscopy (STXM) has the advantage of both techniques and may be employed to detect elements as well as biomolecules. Using the appropriate spectra, near edge X-ray absorption fine structure (NEXAFS) microscopy allows quantitative chemical mapping at 50 nm resolution. In this presentation the applicability of LSM and STXM will be demonstrated using several examples of different environmental biofilm systems. The techniques in combination provide a new view of complex microbial communities and their interaction with the environment. These advanced imaging techniques offer the possibility to study the spatial structure of cellular and polymeric compounds in biofilms as well as biofilm microhabitats, biofilm functionality and biofilm processes.

Changes in the ginsenoside content during the fermentation process using microbial strains.

PubMed

Lee, So Jin; Kim, Yunjeong; Kim, Min-Gul

2015-10-01

Red ginseng (RG) is processed from Panax ginseng via several methods including heat treatment, mild acid hydrolysis, and microbial conversion to transform the major ginsenosides into minor ginsenosides, which have greater pharmaceutical activities. During the fermentation process using microbial strains in a machine for making red ginseng, a change of composition occurs after heating. Therefore, we confirmed that fermentation had occurred using only microbial strains and evaluated the changes in the ginsenosides and their chemical composition. To confirm the fermentation by microbial strains, the fermented red ginseng was made with microbial strains (w-FRG) or without microbial strains (n-FRG), and the fermentation process was performed to tertiary fermentation. The changes in the ginsenoside composition of the self-manufactured FRG using the machine were evaluated using HPLC, and the 20 ginsenosides were analyzed. Additionally, we investigated changes of the reducing sugar and polyphenol contents during fermentation process. In the fermentation process, ginsenosides Re, Rg1, and Rb1 decreased but ginsenosides Rh1, F2, Rg3, and Compound Y (C.Y) increased in primary FRG more than in the raw ginseng and RG. The content of phenolic compounds was high in FRG and the highest in the tertiary w-FRG. Moreover, the reducing sugar content was approximately three times higher in the tertiary w-FRG than in the other n-FRG. As the results indicate, we confirmed the changes in the ginsenoside content and the role of microbial strains in the fermentation process.

Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

NASA Astrophysics Data System (ADS)

Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

2015-04-01

Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary

Microbial enzymes: industrial progress in 21st century.

PubMed

Singh, Rajendra; Kumar, Manoj; Mittal, Anshumali; Mehta, Praveen Kumar

2016-12-01

Biocatalytic potential of microorganisms have been employed for centuries to produce bread, wine, vinegar and other common products without understanding the biochemical basis of their ingredients. Microbial enzymes have gained interest for their widespread uses in industries and medicine owing to their stability, catalytic activity, and ease of production and optimization than plant and animal enzymes. The use of enzymes in various industries (e.g., food, agriculture, chemicals, and pharmaceuticals) is increasing rapidly due to reduced processing time, low energy input, cost effectiveness, nontoxic and eco-friendly characteristics. Microbial enzymes are capable of degrading toxic chemical compounds of industrial and domestic wastes (phenolic compounds, nitriles, amines etc.) either via degradation or conversion. Here in this review, we highlight and discuss current technical and scientific involvement of microorganisms in enzyme production and their present status in worldwide enzyme market.

Product quality and microbial dynamics during vermicomposting and maturation of compost from pig manure.

PubMed

Villar, Iria; Alves, David; Mato, Salustiano

2017-11-01

This research evaluates, through microbial dynamics, the use of earthworms Eisenia andrei for maturation of pre-composted pig manure in comparison with maturation under static conditions and with vermicomposting of fresh pig manure. Therefore, two substrates were used (fresh and pre-composted pig manure) and four treatments were developed: fresh manure vermicomposting, control of fresh manure without earthworms, pre-composting followed by vermicomposting and static maturation of pre-composted manure. In order to determine the microbial dynamics, the enzymatic activities and profiles of phospholipid fatty acids (PLFAs) were evaluated over a 112-days period. Physicochemical and biological parameters of the obtained products were also analyzed. The presence of earthworms significantly reduced (p<0.05) microbial biomass and all the microbial groups (Gram+bacteria, Gram-bacteria, and fungi) in both substrates. The enzymatic activities (cellulase, β-glucosidase and acid phosphatase) behaved in a significantly distinctive manner (p<0.05) depending on the treatment. Microbial communities had significant correlations (p<0.05) with hydrolytic activities during static maturation of pre-composted manure. This indicates a direct effect of microbiota evolution on the degradative processes; however, complex earthworm-microbiota interactions were established in the presence of E. andrei. After earthworms' removal from vermicompost of fresh substrate at 70day, an increase in Gram + (4.4 times), Gram - (3.8 times) and fungi (2.8 times) were observed and, although the vermicompost achieved quality values, it is necessary to optimize the vermicompost aging phase period to improve the stability. Static maturation presented stability on microbial dynamics that indicated a slow degradation of organic compounds so that, maturation of pre-composted manure through vermicomposting is better option. Copyright © 2017 Elsevier Ltd. All rights reserved.

Understanding Mechanism of Photocatalytic Microbial Decontamination of Environmental Wastewater

PubMed Central

Regmi, Chhabilal; Joshi, Bhupendra; Ray, Schindra K.; Gyawali, Gobinda; Pandey, Ramesh P.

2018-01-01

Several photocatalytic nanoparticles are synthesized and studied for potential application for the degradation of organic and biological wastes. Although these materials degrade organic compounds by advance oxidation process, the exact mechanisms of microbial decontamination remains partially known. Understanding the real mechanisms of these materials for microbial cell death and growth inhibition helps to fabricate more efficient semiconductor photocatalyst for large-scale decontamination of environmental wastewater or industries and hospitals/biomedical labs generating highly pathogenic bacteria and toxic molecules containing liquid waste by designing a reactor. Recent studies on microbial decontamination by photocatalytic nanoparticles and their possible mechanisms of action is highlighted with examples in this mini review. PMID:29541632

Microbial-Catalyzed Biotransformation of Multifunctional Triterpenoids Derived from Phytonutrients

PubMed Central

Shah, Syed Adnan Ali; Tan, Huey Ling; Sultan, Sadia; Mohd Faridz, Muhammad Afifi Bin; Mohd Shah, Mohamad Azlan Bin; Nurfazilah, Sharifah; Hussain, Munawar

2014-01-01

Microbial-catalyzed biotransformations have considerable potential for the generation of an enormous variety of structurally diversified organic compounds, especially natural products with complex structures like triterpenoids. They offer efficient and economical ways to produce semi-synthetic analogues and novel lead molecules. Microorganisms such as bacteria and fungi could catalyze chemo-, regio- and stereospecific hydroxylations of diverse triterpenoid substrates that are extremely difficult to produce by chemical routes. During recent years, considerable research has been performed on the microbial transformation of bioactive triterpenoids, in order to obtain biologically active molecules with diverse structures features. This article reviews the microbial modifications of tetranortriterpenoids, tetracyclic triterpenoids and pentacyclic triterpenoids. PMID:25003642

[Chromatographic mass spectrometric determination of low-molecular-weight aromatic compounds of microbial origin in the serum from patients with sepsis].

PubMed

Beloborodova, N V; Arkhipova, A S; Beloborodov, D M; Boĭko, N B; Mel'ko, A I; Olenin, A Iu

2006-02-01

The investigation quantitatively determined the content of low-molecular-weight aromatic compounds of microbial origin in the sera of 34 individuals by chromatographic mass spectrometry. An "Agilent Technogies 6890N" gas chromatograph with a 5973 mass selective detector was applied; chromatographic separation of components was effected on an Hp-5MS quartz capillary column. Aromatic small molecules originating from microbes (SMOM) were determined in the sera of 7 patients with sepsis. The diagnosis of sepsis was documented by the presence of the systemic inflammation syndrome and by that of bacteriemia and/or artificial ventilation-associated pneumonia along with the level of procalcitonin of higher than 10 ng/ml. The levels of aromatic SMOM were compared in 10 healthy donors, 8 preoperative cardiosurgical patients, and 9 patients with different abnormalities without sepsis treated in an intensive care unit (ICU). Serum phenylacetic and 3-phenylpropionic acids were found to be prevalent in the healthy donors and postoperative cardiosurgical patients. In ICU patients with different complications without sepsis, more than half the compounds under study were undetectable, the others were found in very low concentrations, which may be accounted for by antibiotic therapy. At the same time, almost the whole spectrum of the test compounds (other than 3-phenylpropionic acid) with the highest concentrations of 3-phenyllactic, p-hydroxyphenylacetic, 3-(p-hydroxyphenyl)lactic and 2-hydroxybutanic acids, was detectable in septic patients receiving a more intensive therapy. The differences were statistically significant (by the Mann-Whitney U-test; p < 0.05). By taking into account the potentially high biological activity of the test compounds, studies are to be continued in this area.

A call for more transparency of registered clinical trials on endometriosis

PubMed Central

Guo, Sun-Wei; Hummelshoj, Lone; Olive, David L.; Bulun, Serdar E.; D'Hooghe, Thomas M.; Evers, Johannes L.H.

2009-01-01

In response to the pressing need for more efficacious and safer therapeutics for endometriosis, there have been numerous reports in the last decade of positive results from animal and in vitro studies of various compounds as potential therapeutics for endometriosis. A handful of these have undergone phase II/III clinical trials. Since the announcement of the International Committee of Medical Journal Editors that mandated registration as a prerequisite for publication, 57 endometriosis-related clinical trials have been registered at ClinicalTrials.gov, an Internet-based public depository for information on drug studies. Among them, 25 are listed as completed, and 2 as suspended. There are 15 completed phase II/III trials, which evaluated the efficacy of various promising compounds. Yet only three of the 15 trials (20%) have published their results. The remaining 12 (80%) studies so far have not published their findings. We argue that this apparent lack of transparency will actually not benefit the trial sponsors or the public, and will ultimately prove detrimental to research efforts attempting to develop more efficacious and safer therapeutics for endometriosis. Thus we call for more transparency of clinical trials on endometriosis. PMID:19264712

Microbial transformation of the Deepwater Horizon oil spill—past, present, and future perspectives

PubMed Central

Kimes, Nikole E.; Callaghan, Amy V.; Suflita, Joseph M.; Morris, Pamela J.

2014-01-01

The Deepwater Horizon blowout, which occurred on April 20, 2010, resulted in an unprecedented oil spill. Despite a complex effort to cap the well, oil and gas spewed from the site until July 15, 2010. Although a large proportion of the hydrocarbons was depleted via natural processes and human intervention, a substantial portion of the oil remained unaccounted for and impacted multiple ecosystems throughout the Gulf of Mexico. The depth, duration and magnitude of this spill were unique, raising many questions and concerns regarding the fate of the hydrocarbons released. One major question was whether or not microbial communities would be capable of metabolizing the hydrocarbons, and if so, by what mechanisms and to what extent? In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years, providing an overview of the different responses associated with the water column, surface waters, deep-sea sediments, and coastal sands/sediments. Collectively, these studies provide evidence that the microbial response to the Deepwater Horizon oil spill was rapid and robust, displaying common attenuation mechanisms optimized for low molecular weight aliphatic and aromatic hydrocarbons. In contrast, the lack of evidence for the attenuation of more recalcitrant hydrocarbon components suggests that future work should focus on both the environmental impact and metabolic fate of recalcitrant compounds, such as oxygenated oil components. PMID:25477866

Microbial Synthesis of the Forskolin Precursor Manoyl Oxide in an Enantiomerically Pure Form.

PubMed

Nielsen, Morten T; Ranberg, Johan Andersen; Christensen, Ulla; Christensen, Hanne Bjerre; Harrison, Scott J; Olsen, Carl Erik; Hamberger, Björn; Møller, Birger Lindberg; Nørholm, Morten H H

2014-12-01

Forskolin is a promising medicinal compound belonging to a plethora of specialized plant metabolites that constitute a rich source of bioactive high-value compounds. A major obstacle for exploitation of plant metabolites is that they often are produced in small amounts and in plants difficult to cultivate. This may result in insufficient and unreliable supply leading to fluctuating and high sales prices. Hence, substantial efforts and resources have been invested in developing sustainable and reliable supply routes based on microbial cell factories. Here, we report microbial synthesis of (13R)-manoyl oxide, a proposed intermediate in the biosynthesis of forskolin and other medically important labdane-type terpenoids. Process optimization enabled synthesis of enantiomerically pure (13R)-manoyl oxide as the sole metabolite, providing a pure compound in just two steps with a yield of 10 mg/liter. The work presented here demonstrates the value of a standardized bioengineering pipeline and the large potential of microbial cell factories as sources for sustainable synthesis of complex biochemicals. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Pulmonary tumor types induced in Wistar rats of the so-called "19-dust study".

PubMed

Mohr, Ulrich; Ernst, Heinrich; Roller, Markus; Pott, Friedrich

2006-08-01

The incidences of primary lung tumor types histologically diagnosed in 28 groups of Wistar rats of the so-called "19-dust study" are described, the total study having been already presented by Pott and Roller (Carcinogenicity study with nineteen granular dusts in rats. Eur J Oncol, 2005; 10: 249-81). Each exposed group was repeatedly instilled intratracheally with a suspension of one type and dose of 13 non-mining dusts differing in at least one of the following properties: chemical composition, density, specific surface area, and mean particle size. Eleven of the 13 dusts were classified as respirable granular bio-durable particles without known significant specific toxicity (abbreviation of the nine-word definition: GBP). In 579 (58%) lungs of 1002 rats which survived more than 26 weeks after the first instillation of GBP, at least one primary lung tumor type was observed, and in 306 (31%) at least two types. Three benign tumor types were diagnosed in the 579 tumor-bearing rats: bronchiolo-alveolar adenoma in 46%, cystic keratinizing epithelioma in 53%, and non-keratinizing epithelioma in 2.6% of the rats. Two of three malignant tumor types (bronchiolo-alveolar carcinoma and squamous cell carcinoma) occurred in 46% and 31% of the tumor-bearing rats, respectively, and adenosquamous carcinoma was diagnosed in 0.9%. Numerous lungs with a malignant tumor also showed one or more benign tumor types. In addition, single or multiple metastases from primary tumors of other sites (mainly carcinoma of the uterus) were diagnosed in 14% of the 1002 lungs. The proportionate incidences of the four predominantly diagnosed tumor types were compared with three summarized experimental groups which were exposed either to carbon black (two size classes), to titanium dioxide (two size classes), or to the total of the other nine GBP. A significant difference was not detected. The combination of dust volume with particle size correlated best with the carcinogenic effect, in contrast to

Possibilities for extremophilic microorganisms in microbial electrochemical systems

PubMed Central

Dopson, Mark; Ni, Gaofeng; Sleutels, Tom HJA

2015-01-01

Microbial electrochemical systems exploit the metabolism of microorganisms to generate electrical energy or a useful product. In the past couple of decades, the application of microbial electrochemical systems has increased from the use of wastewaters to produce electricity to a versatile technology that can use numerous sources for the extraction of electrons on the one hand, while on the other hand these electrons can be used to serve an ever increasing number of functions. Extremophilic microorganisms grow in environments that are hostile to most forms of life and their utilization in microbial electrochemical systems has opened new possibilities to oxidize substrates in the anode and produce novel products in the cathode. For example, extremophiles can be used to oxidize sulfur compounds in acidic pH to remediate wastewaters, generate electrical energy from marine sediment microbial fuel cells at low temperatures, desalinate wastewaters and act as biosensors of low amounts of organic carbon. In this review, we will discuss the recent advances that have been made in using microbial catalysts under extreme conditions and show possible new routes that extremophilic microorganisms open for microbial electrochemical systems. PMID:26474966

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

PubMed

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.

Microbial carbon turnover in the plant-rhizosphere-soil continuum

NASA Astrophysics Data System (ADS)

Malik, Ashish; Dannert, Helena; Griffiths, Robert; Thomson, Bruce; Gleixner, Gerd

2014-05-01

Soil microbial biomass contributes significantly to maintenance of soil organic matter (SOM). It is well known that biochemical fractions of soil microorganisms have varying turnover and therefore contribute differentially to soil C storage. Here we compare the turnover rates of different microbial biochemical fractions using a pulse chase 13CO2 plant labelling experiment. The isotope signal was temporally traced into rhizosphere soil microorganisms using the following biomarkers: DNA, RNA, fatty acids and chloroform fumigation extraction derived microbial biomass size classes. C flow into soil microbial functional groups was assessed through phospholipid and neutral lipid fatty acid (PLFA/NLFA) analyses. Highest 13C enrichment was seen in the low molecular weight (LMW) size class of microbial biomass (Δδ13C =151) and in nucleic acids (DNA: 38o RNA: 66) immediately after the pulse followed by a sharp drop. The amount of 13C in the high molecular weight (HMW) microbial biomass (17-81) and total fatty acids (32-54) was lower initially and stayed relatively steady over the 4 weeks experimental period. We found significant differences in turnover rates of different microbial biochemical and size fractions. We infer that LMW cytosolic soluble compounds are rapidly metabolized and linked to respiratory C fluxes, whereas mid-sized products of microbial degradation and HMW polymeric compounds have lower renewal rate in that order. The turnover of cell wall fatty acids was also very slow. DNA and RNA showed faster turnover rate; and as expected RNA renewal was the fastest due to its rapid production by active microorganisms independent of cell replication. 13C incorporation into different functional groups confirmed that mutualistic arbuscular mycorrhizal fungi rely on root C and are important in the initial plant C flux. We substantiated through measurements of isotope incorporation into bacterial RNA that rhizosphere bacteria are also important in the initial C conduit

Microbial contributions to the Precambrian Earth

NASA Technical Reports Server (NTRS)

Margulis, L.; Bermudes, D.; Obar, R.

1986-01-01

Life has existed on Earth for approximately 3.5 billion years. For most of this time, prokaryotic communities provided the major biological forces changing the Earth. Many changes in atmospheric gas composition occurred during the Archean and Proterozoic eons as a result of microbial activity. Extant microbial communities were used to help understand the dynamics which contributed to these atmospheric changes. The microbial mat communities were characterized according to the organismic constituents. Symbiosis in microbial communities is recognized as a major force in cell evolution. Among the evolutinary enigmas investigated is the problem of the origin of the undulipodia. Undulipodial microtubules are still deployed for major cellular processes such as mitosis and meiosis. Several prokaryotes were tested for the presence of the S1-type protein, so far only spirochetes were found to possess it. The S1-type protein is being sought in cyanobacteria reported to contain microtubules.

Analysis of phenolic compounds for poultry feed by supercritical fluid chromatography

USDA-ARS?s Scientific Manuscript database

Phenolic compounds have generated interest as components in functional feed formulations due to their anti-oxidant, anti-microbial, and anti-fungal properties. These compounds may have greater significance in the future as the routine use of antibiotics is reduced and the prevalence of resistant bac...

Microbial reduction of vanadium (V) in groundwater: Interactions with coexisting common electron acceptors and analysis of microbial community.

PubMed

Liu, Hui; Zhang, Baogang; Yuan, Heyang; Cheng, Yutong; Wang, Song; He, Zhen

2017-12-01

Vanadium (V) pollution in groundwater has posed serious risks to the environment and public health. Anaerobic microbial reduction can achieve efficient and cost-effective remediation of V(V) pollution, but its interactions with coexisting common electron acceptors such as NO 3 - , Fe 3+ , SO 4 2- and CO 2 in groundwater remain unknown. In this study, the interactions between V(V) reduction and reduction of common electron acceptors were examined with revealing relevant microbial community and identifying dominant species. The results showed that the presence of NO 3 - slowed down the removal of V(V) in the early stage of the reaction but eventually led to a similar reduction efficiency (90.0% ± 0.4% in 72-h operation) to that in the reactor without NO 3 - . The addition of Fe 3+ , SO 4 2- , or CO 2 decreased the efficiency of V(V) reduction. Furthermore, the microbial reduction of these coexisting electron acceptors was also adversely affected by the presence of V(V). The addition of V(V) as well as the extra dose of Fe 3+ , SO 4 2- and CO 2 decreased microbial diversity and evenness, whereas the reactor supplied with NO 3 - showed the increased diversity. High-throughput 16S rRNA gene pyrosequencing analysis indicated the accumulation of Geobacter, Longilinea, Syntrophobacter, Spirochaeta and Anaerolinea, which might be responsible for the reduction of multiple electron acceptors. The findings of this study have demonstrated the feasibility of anaerobic bioremediation of V(V) and the possible influence of coexisting electron acceptors commonly found in groundwater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils.

PubMed

Schwarz, Alexandra; Adetutu, Eric M; Juhasz, Albert L; Aburto-Medina, Arturo; Ball, Andrew S; Shahsavari, Esmaeil

2018-05-01

Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active 13 C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event ( 14 C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community's ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil.

Microbial bio-fuels: a solution to carbon emissions and energy crisis.

PubMed

Kumar, Arun; Kaushal, Sumit; Saraf, Shubhini A; Singh, Jay Shankar

2018-06-01

Increasing energy demand, limited fossil fuel resources and climate change have prompted development of alternative sustainable and economical fuel resources such as crop-based bio-ethanol and bio-diesel. However, there is concern over use of arable land that is used for food agriculture for creation of biofuel. Thus, there is a renewed interest in the use of microbes particularly microalgae for bio-fuel production. Microbes such as micro-algae and cyanobacteria that are used for biofuel production also produce other bioactive compounds under stressed conditions. Microbial agents used for biofuel production also produce bioactive compounds with antimicrobial, antiviral, anticoagulant, antioxidant, antifungal, anti-inflammatory and anticancer activity. Because of importance of such high-value compounds in aquaculture and bioremediation, and the potential to reduce carbon emissions and energy security, the biofuels produced by microbial biotechnology might substitute the crop-based bio-ethanol and bio-diesel production.

Hypersaline Microbial Mat Lipid Biomarkers

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Embaye, Tsegereda; Turk, Kendra A.; Summons, Roger E.

2002-01-01

Lipid biomarkers and compound specific isotopic abundances are powerful tools for studies of contemporary microbial ecosystems. Knowledge of the relationship of biomarkers to microbial physiology and community structure creates important links for understanding the nature of early organisms and paleoenvironments. Our recent work has focused on the hypersaline microbial mats in evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, sulfur oxidizing and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface. The delta C-13 of cyanobacterial biomarkers such as the monomethylalkanes and hopanoids are consistent with the delta C-13 measured for bulk mat (-10%o), while a GNS biomarker, wax esters (WXE), suggests a more depleted delta C-13 for GNS biomass (-16%o). This isotopic relationship is different than that observed in mats at Octopus Spring, Yellowstone National Park (YSNP) where GNS appear to grow photoheterotrophic ally. WXE abundance, while relatively low, is most pronounced in an anaerobic zone just below the cyanobacterial layer. The WXE isotope composition at GN suggests that these bacteria utilize photoautotrophy incorporating dissolved inorganic carbon (DIC) via the 3-hydroxypropionate pathway using H2S or H2.

Mechanisms Controlling Carbon Turnover from Diverse Microbial Groups in Temperate and Tropical Forest Soils

NASA Astrophysics Data System (ADS)

Throckmorton, H.; Dane, L.; Bird, J. A.; Firestone, M. K.; Horwath, W. R.

2010-12-01

bound to the mineral matrix (MF) exhibited similar turnover dynamics for the two sites. Py-GC-MS-IRMS examined the fate of labeled temperate fungal residues at the molecular level in CA (30 days) and in PR (17 days) in whole soils and soil fractions. Results showed notably high enrichment of two polysaccharide biomarkers at both sites (2-furancarboxaldehyde, 5-methyl; and levoglucosanone); as well as an enol compound. These compounds did not occur in high abundance in the original fungal residues, suggesting selective preservation or secondary formation of these compounds in both CA and PR soils. Two additional lipid biomarkers exhibited notably high enrichment in CA but not PR soils, suggesting some distinct pathways of humification may be occurring at each site. Physical fractionation combined with molecular analysis suggests that protection by aggregate-occlusion (OF) and chemical complexation with soil mineral surfaces (MF) represent distinct protection mechanisms that operate on different microbial compounds.

The application of bioactive compounds from the food industry to control mold growth in indoor waterborne coatings.

PubMed

Bellotti, N; Salvatore, L; Deyá, C; Del Panno, M T; del Amo, B; Romagnoli, R

2013-04-01

Microbial growth in indoor environments creates health problems, especially in people with asthma; approximately 80% of these patients are allergic to mold. Antimicrobial coatings are formulated to generate surfaces that are easy to clean and may also incorporate active agents, commonly called biocides, which inhibit microbial colonization, subsequent growth and bio-deterioration of the substrates. Some research lines seek to replace traditional organometallic and organochlorines biocides with environmentally acceptable ones. The aim of this research was, primarily, to explore the possible application of different compounds used in food industry like preservatives to be used as antimicrobial additives for antimicrobial coatings. Four biocides were tested against two different ambient molds isolated from an interior painted wall (Chaetomium globosum and Alternaria alternate). The selected biocides were zinc salicylate, zinc benzoate, calcium benzoate and potassium sorbate. The resulting paints were subjected to biological and physical tests (viscosity, hiding power, humidity absorption and biocides leaching rate). Bioassays revealed that zinc benzoate and zinc salicylate resulted active against both fungi. Copyright © 2012 Elsevier B.V. All rights reserved.

Microbial Metagenomics: Beyond the Genome

NASA Astrophysics Data System (ADS)

Gilbert, Jack A.; Dupont, Christopher L.

2011-01-01

Metagenomics literally means “beyond the genome.” Marine microbial metagenomic databases presently comprise ˜400 billion base pairs of DNA, only ˜3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.

A great leap forward in microbial ecology.

PubMed

Okabe, Satoshi; Oshiki, Mamoru; Kamagata, Yoichi; Yamaguchi, Nobuyasu; Toyofuku, Masanori; Yawata, Yutaka; Tashiro, Yosuke; Nomura, Nobuhiko; Ohta, Hiroyuki; Ohkuma, Moriya; Hiraishi, Akira; Minamisawa, Kiwamu

2010-01-01

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

[Indoor air pollution by polychlorinated biphenyl compounds in permanently elastic sealants].

PubMed

Burkhardt, U; Bork, M; Balfanz, E; Leidel, J

1990-10-01

A common cause for indoor pollution by polycholorinated biphenyls (PCB) are defective capacitors of luminous discharge lamps. This paper describes elastic sealing compounds as another source of PCB pollution in buildings. In several rooms of a large school building indoor concentrations of 1000 ng PCB/m3 and more were registered. The total PCB concentration in sealing compounds ranged between 124,000 and 327,000 ppm. Blood specimens drawn from the school's personnel did not show elevated PCB concentrations, but additional incorporation of PCB via the respiratory tract cannot be excluded. We do not presume that any impairment of the health has been caused by this pollutant, but we think that reduction of the PCB indoor concentrations would be advisable for prophylactic purposes. Attention should be given to so-called open PCB systems such as elastic sealing compounds. Although they have been prohibited 1978, there might be a widespread use in older buildings.

Shear and shearless Lagrangian structures in compound channels

NASA Astrophysics Data System (ADS)

Enrile, F.; Besio, G.; Stocchino, A.

2018-03-01

Transport processes in a physical model of a natural stream with a composite cross-section (compound channel) are investigated by means of a Lagrangian analysis based on nonlinear dynamical system theory. Two-dimensional free surface Eulerian experimental velocity fields of a uniform flow in a compound channel form the basis for the identification of the so-called Lagrangian Coherent Structures. Lagrangian structures are recognized as the key features that govern particle trajectories. We seek for two particular class of Lagrangian structures: Shear and shearless structures. The former are generated whenever the shear dominates the flow whereas the latter behave as jet-cores. These two type of structures are detected as ridges and trenches of the Finite-Time Lyapunov Exponents fields, respectively. Besides, shearlines computed applying the geodesic theory of transport barriers mark Shear Lagrangian Coherent Structures. So far, the detection of these structures in real experimental flows has not been deeply investigated. Indeed, the present results obtained in a wide range of the controlling parameters clearly show a different behaviour depending on the shallowness of the flow. Shear and Shearless Lagrangian Structures detected from laboratory experiments clearly appear as the flow develops in shallow conditions. The presence of these Lagrangian Structures tends to fade in deep flow conditions.

Increased electrical output when a bacterial ABTS oxidizer is used in a microbial fuel cell

USDA-ARS?s Scientific Manuscript database

Microbial fuel cells (MFCs) are a technology that provides electrical energy from the microbial oxidation of organic compounds. Most MFCs use oxygen as the oxidant in the cathode chamber. The present study examined the formation in culture of an unidentified bacterial oxidant and investigated the ...

Microbial transformation of nitroaromatic compounds in sewage effluent.

PubMed

Hallas, L E; Alexander, M

1983-04-01

The transformation of mono- and dinitroaromatic compounds was measured in sewage effluent maintained under aerobic or anaerobic conditions. Most of the nitrobenzene, 3- and 4-nitrobenzoic acids, and 3- and 4-nitrotoluenes and much of the 1,2- and 1,3-dinitrobenzenes disappeared both in the presence and absence of oxygen. Under anaerobiosis, 2,6-dinitrotoluene and 3,5-dinitrobenzoic acid disappeared slowly, but no loss was evident in 28 days in aerated sewage. Aromatic amines did not accumulate during the aerobic decomposition of the mononitro compounds. They did appear in nonsterile, but not in sterile, sewage incubated aerobically with the dinitro compounds and anaerobically with all the chemicals. Analysis by gas chromatography and combined gas chromatography-mass spectrometry showed that aniline was formed from nitrobenzene, toluidine was formed from 3- and 4-nitrotoluenes, and aminobenzoic acid was formed from 3- and 4-nitrobenzoic acids under anaerobiosis, and that nitroaniline was formed from 1,2- and 1,3-dinitrobenzenes, aminonitrotoluene resulted from 2,6-dinitrotoluene, and aminonitrobenzoic acid was a product of 3,5-dinitrobenzoic acid under both conditions. The isomeric forms of the metabolites were not established. Aniline, 4-toluidine, and 4-aminobenzoic acid added to sewage disappeared from aerated nonsterile, but not from sterile, sewage or sewage in the absence of oxygen. 2-Nitroaniline, 2-amino-3-nitrotoluene, and 2-amino-5-nitrobenzoic acid added to sewage persisted for at least 60 days in aerobic or anaerobic conditions. Gas chromatographic and gas chromatographic-mass spectrometric analyses demonstrated that acetanilide and 2-methylquinoline were formed from aniline, 4-methylformanilide and 4-methylacetanilide were formed from 4-toluidine, 2-methylbenzimidazole was a product of 2-nitroaniline, and unidentified benzimidazoles were formed from 2-amino-3-nitrotoluene in the absence of oxygen, and that 2-nitroacetanilide and 2-methyl-6

Microbial Transformation of Nitroaromatic Compounds in Sewage Effluent

PubMed Central

Hallas, Laurence E.; Alexander, Martin

1983-01-01

The transformation of mono- and dinitroaromatic compounds was measured in sewage effluent maintained under aerobic or anaerobic conditions. Most of the nitrobenzene, 3- and 4-nitrobenzoic acids, and 3- and 4-nitrotoluenes and much of the 1,2- and 1,3-dinitrobenzenes disappeared both in the presence and absence of oxygen. Under anaerobiosis, 2,6-dinitrotoluene and 3,5-dinitrobenzoic acid disappeared slowly, but no loss was evident in 28 days in aerated sewage. Aromatic amines did not accumulate during the aerobic decomposition of the mononitro compounds. They did appear in nonsterile, but not in sterile, sewage incubated aerobically with the dinitro compounds and anaerobically with all the chemicals. Analysis by gas chromatography and combined gas chromatography-mass spectrometry showed that aniline was formed from nitrobenzene, toluidine was formed from 3- and 4-nitrotoluenes, and aminobenzoic acid was formed from 3- and 4-nitrobenzoic acids under anaerobiosis, and that nitroaniline was formed from 1,2- and 1,3-dinitrobenzenes, aminonitrotoluene resulted from 2,6-dinitrotoluene, and aminonitrobenzoic acid was a product of 3,5-dinitrobenzoic acid under both conditions. The isomeric forms of the metabolites were not established. Aniline, 4-toluidine, and 4-aminobenzoic acid added to sewage disappeared from aerated nonsterile, but not from sterile, sewage or sewage in the absence of oxygen. 2-Nitroaniline, 2-amino-3-nitrotoluene, and 2-amino-5-nitrobenzoic acid added to sewage persisted for at least 60 days in aerobic or anaerobic conditions. Gas chromatographic and gas chromatographic-mass spectrometric analyses demonstrated that acetanilide and 2-methylquinoline were formed from aniline, 4-methylformanilide and 4-methylacetanilide were formed from 4-toluidine, 2-methylbenzimidazole was a product of 2-nitroaniline, and unidentified benzimidazoles were formed from 2-amino-3-nitrotoluene in the absence of oxygen, and that 2-nitroacetanilide and 2-methyl-6

Microbial degradation of chloroethenes: a review.

PubMed

Dolinová, Iva; Štrojsová, Martina; Černík, Miroslav; Němeček, Jan; Macháčková, Jiřina; Ševců, Alena

2017-05-01

Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.

PubMed

Hadjithomas, Michalis; Chen, I-Min A; Chu, Ken; Huang, Jinghua; Ratner, Anna; Palaniappan, Krishna; Andersen, Evan; Markowitz, Victor; Kyrpides, Nikos C; Ivanova, Natalia N

2017-01-04

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Spotsizer: High-throughput quantitative analysis of microbial growth.

PubMed

Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

2016-10-01

Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

Microbial processing of carbon in hydrothermal systems (Invited)

NASA Astrophysics Data System (ADS)

LaRowe, D.; Amend, J. P.

2013-12-01

Microorganisms are known to be active in hydrothermal systems. They catalyze reactions that consume and produce carbon compounds as a result of their efforts to gain energy, grow and replace biomass. However, the rates of these processes, as well as the size of the active component of microbial populations, are poorly constrained in hydrothermal environments. In order to better characterize biogeochemical processes in these settings, a quantitative relationship between rates of microbial catalysis, energy supply and demand and population size is presented. Within this formulation, rates of biomass change are determined as a function of the proportion of catabolic power that is converted into biomass - either new microorganisms or the replacement of existing cell components - and the amount of energy that is required to synthesize biomass. The constraints that hydrothermal conditions place on power supply and demand are explicitly taken into account. The chemical composition, including the concentrations of organic compounds, of diffuse and focused flow hydrothermal fluids, hydrothermally influenced sediment pore water and fluids from the oceanic lithosphere are used in conjunction with cell count data and the model described above to constrain the rates of microbial processes that influence the carbon cycle in the Juan de Fuca hydrothermal system.

Insights into the phylogeny and coding potential of microbial dark matter

NASA Astrophysics Data System (ADS)

Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; Ivanova, Natalia N.; Anderson, Iain J.; Cheng, Jan-Fang; Darling, Aaron; Malfatti, Stephanie; Swan, Brandon K.; Gies, Esther A.; Dodsworth, Jeremy A.; Hedlund, Brian P.; Tsiamis, George; Sievert, Stefan M.; Liu, Wen-Tso; Eisen, Jonathan A.; Hallam, Steven J.; Kyrpides, Nikos C.; Stepanauskas, Ramunas; Rubin, Edward M.; Hugenholtz, Philip; Woyke, Tanja

2013-07-01

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called `microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.

Insights into the phylogeny and coding potential of microbial dark matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells fromnine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called microbial dark matter. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla.more » We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20percent of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.« less

Don't Call It School

ERIC Educational Resources Information Center

Robb, Daniel

2006-01-01

"Homeschooling," "deschooling," and "unschooling" are commonly used terms in the alternative-education world, but each lacks specificity. In this article, the author describes what he discovered during several visits to North Star. Known officially as North Star: Self-Directed Learning for Teens, it is not as structured as a so-called "free"…

Performance assessment of a submerged membrane bioreactor using a novel microbial consortium.

PubMed

Chon, Kangmin; Lee, Kyungpyo; Kim, In-Soo; Jang, Am

2016-06-01

The performance of a submerged membrane bioreactor (MBR) with and without a novel microbial consortium (NMBR vs. CMBR) was compared to provide deeper insights into the effects of changes in water quality and dissolved organic matter (DOM) characteristics by a novel microbial consortium on the fouling characteristics of MBR processes. Despite similar operating conditions and identical DOM properties in the feed waters, NMBR exhibited a lower propensity to release polysaccharide-like compounds with low molecular weight by bacterial activities compared to CMBR. These compounds have a great fouling potential for MBR processes. Therefore, an increase in the transmembrane pressure (TMP) of NMBR (normalized TMP (TMP/TMP0): 1.14) was much slower and less significant than that observed in CMBR (TMP/TMP0: 2.61). These observations imply that the novel microbial consortium can efficiently mitigate membrane fouling by hydrophilic DOM in MBR processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial enhanced oil recovery research. Annex 5, Summary annual report, 1991--1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, M.M.; Georgiou, G.

1992-12-31

The surface active lipopeptide produced by Bacillus licheniformis JF-2 was isolated to near apparent homogeneity. NMR experiments revealed that this compound consists of a heptapeptide with an amino acid sequence similar to surfactin and a heterogeneous fatty acid consisting of the normal-, anteiso-, and iso- branched isomers. The surface activity of the B. licheniformis JF-2 surfactant was shown to depend on the presence of fermentation products and is strongly affected by the pH. Under conditions of optimal salinity and pH the interfacial tension against decane was 6 {times} 10{sup 3} mN/m which is one of the lowest values ever obtainedmore » with a microbial surfactant. Microbial compounds which exhibit particularly high surface activity are classified as biosurfactants. Microbial biosurfactants include a wide variety of surface and interfacially active compounds, such as glycolipids, lipopeptides polysaccharideprotein complexes, phospholipids, fatty acids and neutral lipids. Biosurfactants are easily biodegradable and thus are particularly suited for environmental applications such as bioremediation and the dispersion of oil spills. Bacillus licheniformis strain JF-2 has been shown to be able to grow and produce a very effective biosurfactant under both aerobic and anaerobic conditions and in the presence of high salt concentrations. The production of biosurfactants in anaerobic, high salt environments is potentially important for a variety of in situ applications such as microbial enhanced oil recovery. As a first step towards evaluating the commercial utility of the B. licheniformis JF-2 surfactant, we isolated t-he active. compound from the culture supernatant, characterized its chemical structure and investigated its phase behavior. We found that the surface activity of the surfactant is strongly dependent on the pH of the aqueous. phase. This may be important for the biological function of the surfactant and is of interest for several applications in

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

PubMed Central

Oni, Oluwatobi E.; Schmidt, Frauke; Miyatake, Tetsuro; Kasten, Sabine; Witt, Matthias; Hinrichs, Kai-Uwe; Friedrich, Michael W.

2015-01-01

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30–530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments. PMID:26635758

Alteration of soil microbial communities and water quality in restored wetlands

USGS Publications Warehouse

Bossio, D.A.; Fleck, J.A.; Scow, K.M.; Fujii, R.

2006-01-01

Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage. ?? 2005 Elsevier Ltd. All

Work Tasks as Determinants of Grain Dust and Microbial Exposure in the Norwegian Grain and Compound Feed Industry.

PubMed

Straumfors, Anne; Heldal, Kari Kulvik; Wouters, Inge M; Eduard, Wijnand

2015-07-01

The grain and compound feed industry entails inevitable risks of exposure to grain dust and its microbial content. The objective of this study was therefore to investigate task-dependent exposure differences in order to create knowledge basis for awareness and exposure reducing measures in the Norwegian grain and compound feed industry. A total of 166 samples of airborne dust were collected by full-shift personal sampling during work in 20 grain elevators and compound feed mills during one autumn season and two winter seasons. The personal exposure to grain dust, endotoxins, β-1→3-glucans, bacteria, and fungal spores was quantified and used as individual outcomes in mixed models with worker nested in company as random effect and different departments and tasks as fixed effects. The exposure levels were highest in grain elevator departments. Exposure to endotoxins was particularly high. Tasks that represented the highest and lowest exposures varied depending on the bioaerosol component. The most important determinants for elevated dust exposure were cleaning and process controlling. Cleaning increased the dust exposure level by a factor of 2.44 of the reference, from 0.65 to 1.58mg m(-3), whereas process controlling increased the dust exposure level by a factor of 2.97, from 0.65 to 1.93mg m(-3). Process controlling was associated with significantly less grain dust exposure in compound feed mills and the combined grain elevators and compound feed mills, than in grain elevators. The exposure was reduced by a factor of 0.18 and 0.22, from 1.93 to 0.34mg m(-3) and to 0.42mg m(-3), respectively, compared with the grain elevators. Inspection/maintenance, cleaning, and grain rotation and emptying were determinants of higher exposure to both endotoxin and β-1→3-glucans. Seed winnowing was in addition a strong determinant for endotoxin, whereas mixing of animal feed implied higher β-1→3-glucan exposure. Cleaning was the only task that contributed significantly to

Microbial toxicity and biodegradability of perfluorooctane sulfonate (PFOS) and shorter chain perfluoroalkyl and polyfluoroalkyl substances (PFASs).

PubMed

Ochoa-Herrera, Valeria; Field, Jim A; Luna-Velasco, Antonia; Sierra-Alvarez, Reyes

2016-09-14

Perfluorooctane sulfonate (PFOS) and related perfluoroalkyl and polyfluoroalkyl substances (PFASs) are emerging contaminants that have been widely applied in consumer and industrial applications for decades. However, PFOS has raised public concern due to its high bioaccumulative character, environmental persistence, and toxicity. Shorter PFASs such as perfluorobutane sulfonate (PFBS) and polyfluoroalkyl compounds have been proposed as alternatives to PFOS but it is unclear whether these fluorinated substances pose a risk for public health and the environment. The objective of this research was to investigate the microbial toxicity and the susceptibility to microbial degradation of PFOS and several related fluorinated compounds, i.e., short-chain perfluoroalkyl and polyfluoroalkyl sulfonic and carboxylic acids. None of the compounds tested were toxic to the methanogenic activity of anaerobic wastewater sludge even at very high concentrations (up to 500 mg L -1 ). All PFASs evaluated were highly resistant to microbial degradation. PFOS was not reductively dehalogenated by the anaerobic microbial consortium even after very long periods of incubation (3.4 years). Similarly, the tested short chain perfluoroalkyl substances (i.e., PFBS and trifluoroacetic acid) and a polyfluoroalkyl PFOS analogue, 6 : 2 fluorotelomer sulfonic acid (FTSA) were also resistant to anaerobic biodegradation. Likewise, no conclusive evidence of microbial degradation was observed under aerobic conditions for any of the short-chain perfluoroalkyl and polyfluoroalkyl carboxylic acids tested after 32 weeks of incubation. Collectively, these results indicate that PFOS and its alternatives such as short chain perfluoroalkyl sulfonates and carboxylates and their polyfluorinated homologues are highly resistant to microbial degradation.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

PubMed

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.

3-(1,3,4-Thiadiazole-2-yl)quinoline derivatives: synthesis, characterization and anti-microbial activity.

PubMed

Bhat, Abdul R; Tazeem; Azam, Amir; Choi, Inho; Athar, Fareeda

2011-07-01

A new series of thiadiazoles and intermediate thiosemicarbazones were synthesized from the chloroquinone molecule, with an aim to explore their effect on in vitro growth of microorganisms causing microbial infection. The chemical structures of the compound were elucidated by elemental analysis, FTIR, 1H and 13C NMR and ESI-MS spectral data. In vitro anti-microbial activity was performed against Staphylococcusaureus, Streptococcuspyogenes, Salmonellatyphimurium, and Escherichiacoli. The MIC was detected using the double dilution method. The results were compared by calculating percent inhibit area/μg of the compounds and the standard "amoxicillin". The selected compounds were tested for cytotoxic results using MTT assay H9c2 cardiac myoblasts cell line and the results showed that all the compounds offered remarkable >80% viability to a concentration of 200 μg/mL. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Uranium Biomineralization By Natural Microbial Phosphatase Activities in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taillefert, Martial

This project investigated the geochemical and microbial processes associated with the biomineralization of radionuclides in subsurface soils. During this study, it was determined that microbial communities from the Oak Ridge Field Research subsurface are able to express phosphatase activities that hydrolyze exogenous organophosphate compounds and result in the non-reductive bioimmobilization of U(VI) phosphate minerals in both aerobic and anaerobic conditions. The changes of the microbial community structure associated with the biomineralization of U(VI) was determined to identify the main organisms involved in the biomineralization process, and the complete genome of two isolates was sequenced. In addition, it was determined thatmore » both phytate, the main source of natural organophosphate compounds in natural environments, and polyphosphate accumulated in cells could also be hydrolyzed by native microbial population to liberate enough orthophosphate and precipitate uranium phosphate minerals. Finally, the minerals produced during this process are stable in low pH conditions or environments where the production of dissolved inorganic carbon is moderate. These findings suggest that the biomineralization of U(VI) phosphate minerals is an attractive bioremediation strategy to uranium bioreduction in low pH uranium-contaminated environments. These efforts support the goals of the SBR long-term performance measure by providing key information on "biological processes influencing the form and mobility of DOE contaminants in the subsurface".« less

Antibiotic activity and microbial community of the temperate sponge, Haliclona sp.

PubMed

Hoppers, A; Stoudenmire, J; Wu, S; Lopanik, N B

2015-02-01

Sessile marine invertebrates engage in a diverse array of beneficial interactions with bacterial symbionts. One feature of some of these relationships is the presence of bioactive natural products that can defend the holobiont from predation, competition or disease. In this study, we investigated the antimicrobial activity and microbial community of a common temperate sponge from coastal North Carolina. The sponge was identified as a member of the genus Haliclona, a prolific source of bioactive natural products, based on its 18S rRNA gene sequence. The crude chemical extract and methanol partition had broad activity against the assayed Gram-negative and Gram-positive pathogenic bacteria. Further fractionation resulted in two groups of compounds with differing antimicrobial activity, primarily against Gram-positive test organisms. There was, however, notable activity against the Gram-negative marine pathogen, Vibrio parahaemolyticus. Microbial community analysis of the sponge and surrounding sea water via denaturing gradient gel electrophoresis (DGGE) indicates that it harbours a distinct group of bacterial associates. The common temperate sponge, Haliclona sp., is a source of multiple antimicrobial compounds and has some consistent microbial community members that may play a role in secondary metabolite production. These data suggest that common temperate sponges can be a source of bioactive chemical and microbial diversity. Further studies may reveal the importance of the microbial associates to the sponge and natural product biosynthesis. © 2014 The Society for Applied Microbiology.

Effect of sulfur supplements on cellulolytic rumen micro-organisms and microbial protein synthesis in cattle fed a high fibre diet.

PubMed

McSweeney, C S; Denman, S E

2007-11-01

To examine the effect of sulfur-containing compounds on the growth of anaerobic rumen fungi and the fibrolytic rumen bacteria Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes in pure culture and within the cattle rumen. The effect of two reduced sulfur compounds, 3-mercaptopropionic acid (MPA) or 3-mercapto-1-propanesulfonic acid as the sole S source on growth of pure fibroyltic fungal and bacterial cultures showed that these compounds were capable of sustaining growth. An in vivo trial was then conducted to determine the effect of sulfur supplements (MPA and sodium sulfate) on microbial population dynamics in cattle fed the roughage Dichanthium aristatum. Real-time PCR showed significant increases in fibrolytic bacterial and fungal populations when cattle were supplemented with these compounds. Sulfate supplementation leads to an increase in dry matter intake without a change in whole tract dry matter digestibility. Supplementation of low S-containing diets with either sodium sulfate or MPA stimulates microbial growth with an increase in rumen microbial protein supply to the animal. Through the use of real-time PCR monitoring, a better understanding of the effect of S supplementation on discrete microbial populations within the rumen is provided.

Microbial transformation of citral by Penicillium sp..

PubMed

Esmaeili, Akbar; Tavassoli, Afsaneh

2010-01-01

Thymol is present in the essential oils from herbs and spices, such as thyme. It is produced by these plant species as a chemical defense against phytopathogenic microorganisms. Therefore, this compound has attracted great attention in food industry, i.e., it has been used as a natural preservative in foods such as cheese to prevent fungal growth. Previous studies concerning the biotransformation of nerol by Penicillium sp. and microbial transformation of citral by sporulated surface cultures method (SSCM) of Penicillium digitatum have been reported. The objective of this research was to study the pathway involved during biotransformation of citral by Penicillium sp. using two methods. The culture preparation was done using different microbial methods and incubation periods to obtain Penicillium for citral biotransformation. The biotransformation products were identified by gas chromatography (GC) and gas chromatography/mass spectroscopy (GC/MS). A comparison of the two methods showed that SSCM was more effective, its major products were thymol (21.5 %), geranial (18.6 %) and nerol (13.7 %). LM produced only one compound — thymol — with a low efficiency.

Effects of Microbial Transglutaminase on Physicochemical, Microbial and Sensorial Properties of Kefir Produced by Using Mixture Cow’s and Soymilk

PubMed Central

2017-01-01

The objective of this research was to investigate the effects microbial transglutaminase (m-TGs) on the physicochemical, microbial and sensory properties of kefir produced by using mix cow and soymilk. Kefir batches were prepared using 0, 0.5, 1 and 1.5 Units m-TGs for per g of milk protein. Adding m-TGs to milk caused an increase in the pH and viscosity and caused a decrease in titratable acidity and syneresis in the kefir samples. Total bacteria, lactobacilli and streptococci counts decreased, while yeast counts increased in all the samples during storage. Alcohols and acids compounds have increased in all the samples except in the control samples, while carbonyl compounds have decreased in all the samples during storage (1-30 d). The differences in the percentage of alcohols, carbonyl compounds and acids in total volatiles on the 1st and the 30th d of storage were observed at 8.47-23.52%, 6.94-25.46% and 59.64-63.69%, respectively. The consumer evaluation of the kefir samples showed that greater levels of acceptability were found for samples which had been added 1.5 U m-TGs for per g of milk protein. PMID:28943774

Microbial and long-range terrestrial contributions of organic matter to Antarctica

NASA Astrophysics Data System (ADS)

Antony, R.; Grannas, A. M.; Priest, A. S.; Sleighter, R. L.; Meloth, T.; Hatcher, P.

2012-12-01

Composition and cycling of dissolved organic matter in glacial systems is important because of its great significance to global carbon dynamics, snow photochemistry, and air-snow exchange processes. But, due to the trace nature of specific organic components in Polar ice sheets, detecting and studying these species in molecular level detail has been an analytical challenge. Electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) enabled the elucidation of molecular level details of natural organic matter in snow samples collected along a coast to inland transect from the Princesses Elizabeth Land, East Antarctica. Thousands of distinct molecular species comprising of different compound classes were identified providing clues to the nature and sources of organic carbon in Antarctic snow. The major biochemical classes of compounds detected were lignins, tannins, carbohydrates, proteins, amino sugars, lipids, unsaturated hydrocarbons and condensed aromatics. Specifically, lignin molecules comprising up to 50% and compounds derived from algal and microbial biomass comprising up to 45% of the total assigned formulas dominated the organic carbon pool. The identification of a variety of lignin compounds demonstrates substantial input of vascular plant-derived materials to the identified molecular species, presumably from long range atmospheric transport and deposition. The detection of proteins, lipids and amino sugars suggests that a large proportion of the identified supraglacial organic matter likely originates from in situ microbial activity. This corroborates well with the presence of significant numbers of bacteria, picoplankton and microalgae in these samples. These results suggest that organic matter in the supraglacial environments have both a microbial and terrestrial provenance.

Bovine rumen metagenomics – moving beyond microbial diversity

USDA-ARS?s Scientific Manuscript database

The rumen is a large bioreactor that enables dairy cattle to derive nutrition from otherwise inedible plant polymers and compounds. Despite the direct contribution of the rumen’s microbial community toward the nutrition of the dairy cow, only a general knowledge has been gained of the metabolic proc...

Compounding pharmacy conundrum: "we cannot live without them but we cannot live with them" according to the present paradigm.

PubMed

Guharoy, Roy; Noviasky, John; Haydar, Ziad; Fakih, Mohamad G; Hartman, Christian

2013-04-01

Compounding pharmacies serve a critical role in modern health care to meet special patient care needs. Although the US Food and Drug Administration (FDA) has clearly delineated jurisdiction over drug companies and products manufactured under Good Manufacturing Practice (GMP) regulations to ensure quality, potency, and purity, compounding pharmacies are regulated by the State Boards and are not registered by the FDA. In recent years, some compounding pharmacies acted like a manufacturer, preparing large amounts of injectable drugs with interstate activities. Multiple outbreaks have been linked to compounding pharmacies, including a recent outbreak of fungal meningitis related to contaminated methylprednisolone, exposing > 14,000 patients in multiple states. This tragedy underscores the urgency of addressing safety related to compounding pharmacies. There is a call for action at the federal and state levels to set minimum production standards, impose new labeling conditions on compounded drugs, and require large-scale compounders be regulated by the FDA. "Industrial" compounding must come under FDA oversight, require those pharmacies to meet GMP standards, and ensure quality and safe products for patient use. Moreover, compliance with the Institute for Safe Medication Practices 2011 recommendations that any type of sterile compounding must be in compliance with the United States Pharmacopoeia chapter 797 guidelines will reduce the risk of patient harm from microbial contamination. Finally, other critical factors that require close attention include addressing injectable products compounded in hospitals and other outpatient health-care centers. The FDA and State Boards of Pharmacy must be adequately funded to exercise the oversight effectively.

Agricultural by-products with bioactive effects: A multivariate approach to evaluate microbial and physicochemical changes in a fresh pork sausage enriched with phenolic compounds from olive vegetation water.

PubMed

Fasolato, Luca; Carraro, Lisa; Facco, Pierantonio; Cardazzo, Barbara; Balzan, Stefania; Taticchi, Agnese; Andreani, Nadia Andrea; Montemurro, Filomena; Martino, Maria Elena; Di Lecce, Giuseppe; Toschi, Tullia Gallina; Novelli, Enrico

2016-07-02

The use of phenolic compounds derived from agricultural by-products could be considered as an eco-friendly strategy for food preservation. In this study a purified phenol extract from olive vegetation water (PEOVW) was explored as a potential bioactive ingredient for meat products using Italian fresh sausage as food model. The research was developed in two steps: first, an in vitro delineation of the extract antimicrobial activities was performed, then, the PEOVW was tested in the food model to investigate the possible application in food manufacturing. The in vitro tests showed that PEOVW clearly inhibits the growth of food-borne pathogens such as Listeria monocytogenes and Staphylococcus aureus. The major part of Gram-positive strains was inhibited at the low concentrations (0.375-3mg/mL). In the production of raw sausages, two concentrates of PEOVW (L1: 0.075% and L2: 0.15%) were used taking into account both organoleptic traits and the bactericidal effects. A multivariate statistical approach allowed the definition of the microbial and physicochemical changes of sausages during the shelf life (14days). In general, the inclusion of the L2 concentration reduced the growth of several microbial targets, especially Staphylococcus spp. and LABs (2log10CFU/g reduction), while the increasing the growth of yeasts was observed. The reduction of microbial growth could be involved in the reduced lipolysis of raw sausages supplemented with PEOVW as highlighted by the lower amount of diacylglycerols. Moisture and aw had a significant effect on the variability of microbiological features, while food matrix (the sausages' environment) can mask the effects of PEOVW on other targets (e.g. Pseudomonas). Moreover, the molecular identification of the main representative taxa collected during the experimentation allowed the evaluation of the effects of phenols on the selection of bacteria. Genetic data suggested a possible strain selection based on storage time and the addition of

Microbial biodiversity assessment of the European Space Agency's ExoMars 2016 mission.

PubMed

Koskinen, Kaisa; Rettberg, Petra; Pukall, Rüdiger; Auerbach, Anna; Wink, Lisa; Barczyk, Simon; Perras, Alexandra; Mahnert, Alexander; Margheritis, Diana; Kminek, Gerhard; Moissl-Eichinger, Christine

2017-10-25

The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli lander was subject to strict requirements for microbial cleanliness according to the obligatory planetary protection policy. To reach the required cleanliness, the ExoMars 2016 flight hardware was assembled in a newly built, biocontrolled cleanroom complex at Thales Alenia Space in Turin, Italy. In this study, we performed microbiological surveys of the cleanroom facilities and the spacecraft hardware before and during the assembly, integration and testing (AIT) activities. Besides the European Space Agency (ESA) standard bioburden assay, that served as a proxy for the microbiological contamination in general, we performed various alternative cultivation assays and utilised molecular techniques, including quantitative PCR and next generation sequencing, to assess the absolute and relative abundance and broadest diversity of microorganisms and their signatures in the cleanroom and on the spacecraft hardware. Our results show that the bioburden, detected microbial contamination and microbial diversity decreased continuously after the cleanroom was decontaminated with more effective cleaning agents and during the ongoing AIT. The studied cleanrooms and change room were occupied by very distinct microbial communities: Overall, the change room harboured a higher number and diversity of microorganisms, including Propionibacterium, which was found to be significantly increased in the change room. In particular, the so called alternative cultivation assays proved important in detecting a broader cultivable diversity than covered by the standard bioburden assay and thus completed the picture on the cleanroom microbiota. During the whole project, the bioburden stayed at acceptable level and did not raise any concern for the ExoMars 2016 mission. The cleanroom complex at

Simultaneous efficient removal of oxyfluorfen with electricity generation in a microbial fuel cell and its microbial community analysis.

PubMed

Zhang, Qinghua; Zhang, Lei; Wang, Han; Jiang, Qinrui; Zhu, Xiaoyu

2018-02-01

The performance of a microbial fuel cell (MFC) to degrade oxyfluorfen was investigated. Approximately 77% of 50 mg/L oxyfluorfen was degraded within 24 h by anodic biofilm. The temperature, pH, and initial oxyfluorfen concentration had a significant effect on oxyfluorfen degrading, and a maximum degradation rate of 94.95% could theoretically be achieved at 31.96 °C, a pH of 7.65, and an initial oxyfluorfen concentration of 120.05 mg/L. Oxyfluorfen was further catabolized through various microbial metabolism pathways. Moreover, the anodic biofilm exhibited multiple catabolic capacities to 4-nitrophenol, chloramphenicol, pyraclostrobin, and sulfamethoxazole. Microbial community analysis indicated that functional bacteria Arcobacter, Acinetobacter, Azospirillum, Azonexus, and Comamonas were the predominant genera in the anodic biofilm. In terms of the efficient removal of various organic compounds and energy recovery, the MFC seemed to be a promising approach for the treatment of environmental contaminants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of Environmental Toxicants on Metabolic Activity of Natural Microbial Communities

PubMed Central

Barnhart, Carole L. H.; Vestal, J. Robie

1983-01-01

Two methods of measuring microbial activity were used to study the effects of toxicants on natural microbial communities. The methods were compared for suitability for toxicity testing, sensitivity, and adaptability to field applications. This study included measurements of the incorporation of 14C-labeled acetate into microbial lipids and microbial glucosidase activity. Activities were measured per unit biomass, determined as lipid phosphate. The effects of various organic and inorganic toxicants on various natural microbial communities were studied. Both methods were useful in detecting toxicity, and their comparative sensitivities varied with the system studied. In one system, the methods showed approximately the same sensitivities in testing the effects of metals, but the acetate incorporation method was more sensitive in detecting the toxicity of organic compounds. The incorporation method was used to study the effects of a point source of pollution on the microbiota of a receiving stream. Toxic doses were found to be two orders of magnitude higher in sediments than in water taken from the same site, indicating chelation or adsorption of the toxicant by the sediment. The microbiota taken from below a point source outfall was 2 to 100 times more resistant to the toxicants tested than was that taken from above the outfall. Downstream filtrates in most cases had an inhibitory effect on the natural microbiota taken from above the pollution source. The microbial methods were compared with commonly used bioassay methods, using higher organisms, and were found to be similar in ability to detect comparative toxicities of compounds, but were less sensitive than methods which use standard media because of the influences of environmental factors. PMID:16346432

Green tea yogurt: major phenolic compounds and microbial growth.

PubMed

Amirdivani, Shabboo; Baba, Ahmad Salihin Hj

2015-07-01

The purpose of this study was to evaluate fermentation of milk in the presence of green tea (Camellia sinensis) with respect to changes in antioxidant activity, phenolic compounds and the growth of lactic acid bacteria. Pasteurized full fat cow's milk and starter culture were incubated at 41 °C in the presence of two different types of green tea extracts. The yogurts formed were refrigerated (4 °C) for further analysis. The total phenolic content was highest (p < 0.05) in air-dried green tea-yogurt (MGT) followed by steam-treated green tea (JGT) and plain yogurts. Four major compounds in MGTY and JGTY were detected. The highest concentration of major phenolic compounds in both samples was related to quercetin-rhamnosylgalactoside and quercetin-3-O-galactosyl-rhamnosyl-glucoside for MGTY and JGTY respectively during first 7 day of storage. Diphenyl picrylhydrazyl and ferric reducing antioxidant power methods showed highest antioxidant capacity in MGTY, JGTY and PY. Streptococcus thermophillus and Lactobacillus spp. were highest in MGTY followed by JGTY and PY. This paper evaluates the implementation of green tea yogurt as a new product with functional properties and valuable component to promote the growth of beneficial yogurt bacteria and prevention of oxidative stress by enhancing the antioxidant activity of yogurt.

Optimizing sample pretreatment for compound-specific stable carbon isotopic analysis of amino sugars in marine sediment

NASA Astrophysics Data System (ADS)

Zhu, R.; Lin, Y.-S.; Lipp, J. S.; Meador, T. B.; Hinrichs, K.-U.

2014-09-01

Amino sugars are quantitatively significant constituents of soil and marine sediment, but their sources and turnover in environmental samples remain poorly understood. The stable carbon isotopic composition of amino sugars can provide information on the lifestyles of their source organisms and can be monitored during incubations with labeled substrates to estimate the turnover rates of microbial populations. However, until now, such investigation has been carried out only with soil samples, partly because of the much lower abundance of amino sugars in marine environments. We therefore optimized a procedure for compound-specific isotopic analysis of amino sugars in marine sediment, employing gas chromatography-isotope ratio mass spectrometry. The whole procedure consisted of hydrolysis, neutralization, enrichment, and derivatization of amino sugars. Except for the derivatization step, the protocol introduced negligible isotopic fractionation, and the minimum requirement of amino sugar for isotopic analysis was 20 ng, i.e., equivalent to ~8 ng of amino sugar carbon. Compound-specific stable carbon isotopic analysis of amino sugars obtained from marine sediment extracts indicated that glucosamine and galactosamine were mainly derived from organic detritus, whereas muramic acid showed isotopic imprints from indigenous bacterial activities. The δ13C analysis of amino sugars provides a valuable addition to the biomarker-based characterization of microbial metabolism in the deep marine biosphere, which so far has been lipid oriented and biased towards the detection of archaeal signals.

Understanding and Modulating Mammalian-Microbial Communication for Improved Human Health

PubMed Central

Mani, Sridhar; Boelsterli, Urs A.; Redinbo, Matthew R.

2013-01-01

The fact that the bacteria in the human gastrointestinal (GI) tract play a symbiotic role was noted as early as 1885, well before we began to manage microbial infections using antibiotics. However, even with the first antimicrobial compounds used in humans, the sulfa drugs, microbes were recognized to be critically involved in the biotransformation of these therapeutics. Thus, the roles played by the microbiota in physiology and in the management of human health have long been appreciated. Detailed examinations of GI symbiotic bacteria that started in the early 2000s and the first phases of the Human Microbiome Project that were completed in 2012 have ushered in an exciting period of granularity with respect to the ecology, genetics, and chemistry of the mammalian-microbial axes of communication. Here we review aspects of the biochemical pathways at play between commensal GI bacteria and several mammalian systems, including both local-epithelia and nonlocal responses including inflammation, immunology, metabolism, and neurobiology. Finally, we discuss how the microbial biotransformation of therapeutic compounds, such as anticancer or nonsteroidal anti-inflammatory drugs, can be modulated to reduce toxicity and potentially improve therapeutic efficacy. PMID:24160697

Antimicrobial compounds of porcine mucosa

NASA Astrophysics Data System (ADS)

Kotenkova, E. A.; Lukinova, E. A.; Fedulova, L. V.

2017-09-01

The aim of the study was to investigate porcine oral cavity mucosa (OCM), nasal cavity mucosa (NCM), rectal mucosa (RM) and tongue mucosa (TM) as sources of antimicrobial compounds. Ultrafiltrates with MW >30 kDa, MW 5-30 kDa and MW <5 kDa were obtained. All ultrafiltrates had antimicrobial activity against Escherichia coli and Proteus vulgaris. NCM ultrafiltrates revealed the highest antibacterial activity in respect to negative control: for the fraction with MW >30 kDa, the zone of microbial growth inhibition was 7.5 mm, for the MW<5 kDa fraction, it was 7 mm, and for MW 5-30 kDa fraction, it was 4.5 mm. No significant differences were found in high molecular weight proteomic profile, while qualitative and quantitative differences were observed in the medium and low molecular weight areas, especially in OCM and NCM. HPLC showed 221 tissue-specific peptides in OCM, 156 in NCM, 225 in RM, but only 5 in TM. The results observed confirmed porcine mucous tissues as a good source of antimicrobial compounds, which could be an actual alternative for reduction of microbial spoilage of foods.

Ceramic oxide reactions with V2O5 and SO3

NASA Technical Reports Server (NTRS)

Jones, R. L.; Williams, C. E.

1985-01-01

Ceramic oxides are not inert in combustion environments, but can react with, inter alia, SO3, and Na2SO4 to yield low melting mixed sulfate eutectics, and with vanadium compounds to produce vanadates. Assuming ceramic degradation to become severe only when molten phases are generated in the surface salt (as found for metallic hot corrosion), the reactivity of ceramic oxides can be quantified by determining the SO3 partial pressure necessary for molten mixed sulfate formation with Na2SO3. Vanadium pentoxide is an acidic oxide that reacts with Na2O, SO3, and the different ceramic oxides in a series of Lux-Flood type of acid-base displacement reactions. To elucidate the various possible vanadium compound-ceramic oxide interactions, a study was made of the reactions of a matrix involving, on the one axis, ceramix oxides of increasing acidity, and on the other axis, vanadium compounds of increasing acidity. Resistance to vanadium compound reaction increased as the oxide acidity increased. Oxides more acidic than ZrO2 displaced V2O5. Examination of Y2O3- and CeO2-stabilized ZrO2 sintered ceramics which were degraded in 700 C NaVO3 has shown good agreement with the reactions predicted above, except that the CeO2-ZrO2 ceramic appears to be inexplicably degraded by NaVO3.

Utilization of microbial iron assimilation processes for the development of new antibiotics and inspiration for the design of new anticancer agents.

PubMed

Miller, Marvin J; Zhu, Helen; Xu, Yanping; Wu, Chunrui; Walz, Andrew J; Vergne, Anne; Roosenberg, John M; Moraski, Garrett; Minnick, Albert A; McKee-Dolence, Julia; Hu, Jingdan; Fennell, Kelley; Kurt Dolence, E; Dong, Li; Franzblau, Scott; Malouin, Francois; Möllmann, Ute

2009-02-01

Pathogenic microbes rapidly develop resistance to antibiotics. To keep ahead in the "microbial war", extensive interdisciplinary research is needed. A primary cause of drug resistance is the overuse of antibiotics that can result in alteration of microbial permeability, alteration of drug target binding sites, induction of enzymes that destroy antibiotics (ie., beta-lactamase) and even induction of efflux mechanisms. A combination of chemical syntheses, microbiological and biochemical studies demonstrate that the known critical dependence of iron assimilation by microbes for growth and virulence can be exploited for the development of new approaches to antibiotic therapy. Iron recognition and active transport relies on the biosyntheses and use of microbe-selective iron-chelating compounds called siderophores. Our studies, and those of others, demonstrate that siderophores and analogs can be used for iron transport-mediated drug delivery ("Trojan Horse" antibiotics) and induction of iron limitation/starvation (Development of new agents to block iron assimilation). Recent extensions of the use of siderophores for the development of novel potent and selective anticancer agents are also described.

Utilization of microbial iron assimilation processes for the development of new antibiotics and inspiration for the design of new anticancer agents

PubMed Central

Zhu, Helen; Xu, Yanping; Wu, Chunrui; Walz, Andrew J.; Vergne, Anne; Roosenberg, John M.; Moraski, Garrett; Minnick, Albert A.; McKee-Dolence, Julia; Hu, Jingdan; Fennell, Kelley; Dolence, E. Kurt; Dong, Li; Franzblau, Scott; Malouin, Francois; Möllmann, Ute

2014-01-01

Pathogenic microbes rapidly develop resistance to antibiotics. To keep ahead in the “microbial war”, extensive interdisciplinary research is needed. A primary cause of drug resistance is the overuse of antibiotics that can result in alteration of microbial permeability, alteration of drug target binding sites, induction of enzymes that destroy antibiotics (ie., beta-lactamase) and even induction of efflux mechanisms. A combination of chemical syntheses, microbiological and biochemical studies demonstrate that the known critical dependence of iron assimilation by microbes for growth and virulence can be exploited for the development of new approaches to antibiotic therapy. Iron recognition and active transport relies on the biosyntheses and use of microbe-selective iron-chelating compounds called siderophores. Our studies, and those of others, demonstrate that siderophores and analogs can be used for iron transport-mediated drug delivery (“Trojan Horse” antibiotics) and induction of iron limitation/starvation (Development of new agents to block iron assimilation). Recent extensions of the use of siderophores for the development of novel potent and selective anticancer agents are also described. PMID:19130268

Microbial production of organic acids in aquitard sediments and its role in aquifer geochemistry

USGS Publications Warehouse

McMahon, P.B.; Chapelle, F.H.

1991-01-01

MICROBIAL activity in aquifers plays an important part in the chemical evolution of ground water1-5. The most important terminal electron-accepting microbial processes in deeply buried anaerobic aquifers are iron reduction, sulphate reduction and methanogenesis5-8, each of which requires simple organic compounds or hydrogen (H2) as electron donors. Until now, the source of these compounds was unknown because the concentrations of dissolved organic carbon and sedimentary organic carbon in aquifers are extremely low9-11. Here we show that rates of microbial fermentation exceed rates of respiration in organic-rich aquitards (low-permeability sediments stratigraphically adjacent to higher-permeability aquifer sediments), resulting in a net accumulation of simple organic acids in pore waters. In aquifers, however, respiration outpaces fermentation, resulting in a net consumption of organic acids. The concentration gradient that develops in response to these two processes drives a net diffusive flux of organic acids from aquitards to aquifers. Diffusion calculations demonstrate that rates of organic acid transport are sufficient to account for observed rates of microbial respiration in aquifers. This overall process effectively links the large pool of sedimentary organic carbon in aquitards to microbial respiration in aquifers, and is a principal mechanism driving groundwater chemistry changes in aquifers.

Application of bioinformatics tools and databases in microbial dehalogenation research (a review).

PubMed

Satpathy, R; Konkimalla, V B; Ratha, J

2015-01-01

Microbial dehalogenation is a biochemical process in which the halogenated substances are catalyzed enzymatically in to their non-halogenated form. The microorganisms have a wide range of organohalogen degradation ability both explicit and non-specific in nature. Most of these halogenated organic compounds being pollutants need to be remediated; therefore, the current approaches are to explore the potential of microbes at a molecular level for effective biodegradation of these substances. Several microorganisms with dehalogenation activity have been identified and characterized. In this aspect, the bioinformatics plays a key role to gain deeper knowledge in this field of dehalogenation. To facilitate the data mining, many tools have been developed to annotate these data from databases. Therefore, with the discovery of a microorganism one can predict a gene/protein, sequence analysis, can perform structural modelling, metabolic pathway analysis, biodegradation study and so on. This review highlights various methods of bioinformatics approach that describes the application of various databases and specific tools in the microbial dehalogenation fields with special focus on dehalogenase enzymes. Attempts have also been made to decipher some recent applications of in silico modeling methods that comprise of gene finding, protein modelling, Quantitative Structure Biodegradibility Relationship (QSBR) study and reconstruction of metabolic pathways employed in dehalogenation research area.

Microbial survival in deep space environment.

NASA Technical Reports Server (NTRS)

Silverman, G. J.

1971-01-01

Review of the knowledge available on the extent to which microorganisms (mainly microbial spores, vegetative cells, and fungi) are capable of surviving the environment of deep space, based on recent simulation experiments of deep space. A description of the experimental procedures used is followed by a discussion of deep space ecology, the behavior of microorganisms in ultrahigh vacuum, and factors influencing microbial survival. It is concluded that, so far, simulation experiments have proved far less lethal to microorganisms than to other forms of life. There are, however, wide gaps in the knowledge available, and no accurate predictions can as yet be made on the degree of lethality that might be incurred by a microbial population on a given mission. Therefore, sterilization of spacecraft surfaces is deemed necessary if induced panspermia (i.e., interplanetary life propagation) is to be avoided.

Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.

PubMed

Ni, Gaofeng; Christel, Stephan; Roman, Pawel; Wong, Zhen Lim; Bijmans, Martijn F M; Dopson, Mark

2016-09-01

Sulfide mineral processing often produces large quantities of wastewaters containing acid-generating inorganic sulfur compounds. If released untreated, these wastewaters can cause catastrophic environmental damage. In this study, microbial fuel cells were inoculated with acidophilic microorganisms to investigate whether inorganic sulfur compound oxidation can generate an electrical current. Cyclic voltammetry suggested that acidophilic microorganisms mediated electron transfer to the anode, and that electricity generation was catalyzed by microorganisms. A cation exchange membrane microbial fuel cell, fed with artificial wastewater containing tetrathionate as electron donor, reached a maximum whole cell voltage of 72 ± 9 mV. Stepwise replacement of the artificial anolyte with real mining process wastewater had no adverse effect on bioelectrochemical performance and generated a maximum voltage of 105 ± 42 mV. 16S rRNA gene sequencing of the microbial consortia resulted in sequences that aligned within the genera Thermoplasma, Ferroplasma, Leptospirillum, Sulfobacillus and Acidithiobacillus. This study opens up possibilities to bioremediate mining wastewater using microbial fuel cell technology. Copyright © 2016 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Soil biochemical properties of grassland ecosystems under anthropogenic emission of nitrogen compounds

NASA Astrophysics Data System (ADS)

Kudrevatykh, Irina; Ivashchenko, Kristina; Ananyeva, Nadezhda

2016-04-01

Inflow of pollutants in terrestrial ecosystems nowadays increases dramatically, that might be led to disturbance of natural biogeochemical cycles and landscapes structure. Production of nitrogen fertilizers is one of the air pollution sources, namely by nitrogen compounds (NH4+, NO3-, NO2-). Air pollution by nitrogen compounds of terrestrial ecosystems might be affected on soil biochemical properties, which results increasing mineral nitrogen content in soil, changing soil P/N and Al/Ca ratios, and, finally, the deterioration of soil microbial community functioning. The research is focused on the assessment of anthropogenic emission of nitrogen compounds on soil properties of grassland ecosystems in European Russia. Soil samples (Voronic Chernozem Pachic, upper 10 cm mineral layer, totally 10) were taken from grassland ecosystem: near (5-10 m) nitrogen fertilizer factory (NFF), and far from it (20-30 km, served as a control) in Tula region. In soil samples the NH4+ and NO3- (Kudeyarov's photocolorimetric method), P, Ca, Al (X-ray fluorescence method) contents were measured. Soil microbial biomass carbon (Cmic) was analyzed by substrate-induced respiration method. Soil microbial respiration (MR) was assessed by CO2 rate production. Soil microbial metabolic quotient (qCO2) was calculated as MR/Cmic ratio. Near NFF the soil ammonium and nitrate nitrogen contents were a strongly varied, variation coefficient (CV) was 42 and 86This study was supported by Russian Foundation of Basic Research Grant No. 14-04-00098, 15-44-03220, 15-04-00915.

Systems Biology of Microbial Exopolysaccharides Production.

PubMed

Ates, Ozlem

2015-01-01

Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

Systems Biology of Microbial Exopolysaccharides Production

PubMed Central

Ates, Ozlem

2015-01-01

Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran. PMID:26734603

Chemistry of green encapsulating molding compounds at interfaces with other materials in electronic devices

NASA Astrophysics Data System (ADS)

Scandurra, A.; Zafarana, R.; Tenya, Y.; Pignataro, S.

2004-07-01

The interface chemistry between encapsulating epoxy phenolic molding compound (EMC) containing phosphorous based organic flame retardant (the so called "green materials") and copper oxide-hydroxide and aluminum oxide-hydroxide surfaces have been studied in comparison with "conventional" EMC containing bromine and antimony as flame retardant. These green materials are designed to reduce the presence of toxic elements in the electronic packages and, consequently, in the environment. For the study were used a Scanning Acoustic Microscopy for delamination measurements, a dynamometer for the pull strength measurements and an ESCA spectrometer for chemical analysis of the interface. The general behavior of the green compound in terms of delamination, adhesion, and corrosion is found better or at least comparable than that of the conventional EMC.

Graph Theoretical Analysis, In Silico Modeling, Synthesis, Anti-Microbial and Anti-TB Evaluation of Novel Quinoxaline Derivatives.

PubMed

Saravanan, Govindaraj; Selvam, Theivendren Panneer; Alagarsamy, Veerachamy; Kunjiappan, Selvaraj; Joshi, Shrinivas D; Indhumathy, Murugan; Kumar, Pandurangan Dinesh

2018-05-01

We designed to synthesize a number of 2-(2-(substituted benzylidene) hydrazinyl)-N-(4-((3-(phenyl imino)-3,4-dihydro quinoxalin-2(1 H)-ylidene)amino) phenyl) acetamide S1-S13: with the hope to obtain more active and less toxic anti-microbial and anti-TB agents. A series of novel quinoxaline Schiff bases S1-S13: were synthesized from o-phenylenediamine and oxalic acid by a multistep synthesis. In present work, we are introducing graph theoretical analysis to identify drug target. In the connection of graph theoretical analysis, we utilised KEGG database and Cytoscape software. All the title compounds were evaluated for their in-vitro anti-microbial activity by using agar well diffusion method at three different concentration levels (50, 100 and 150 µg/ml). The MIC of the compounds was also determined by agar streak dilution method. The identified study report through graph theoretical analysis were highlights that the key virulence factor for pathogenic mycobacteria is a eukaryotic-like serine/threonine protein kinase, termed PknG. All compounds were found to display significant activity against entire tested bacteria and fungi. In addition the synthesized scaffolds were screened for their in vitro antituberculosis (anti-TB) activity against Mycobacterium tuberculosis (Mtb) strain H 37 Ra using standard drug Rifampicin. A number of analogs found markedly potent anti-microbial and anti-TB activity. The relationship between the functional group variation and the biological activity of the evaluated compounds were well discussed. The observed study report was showing that the compound S6: (4-nitro substitution) exhibited most potent effective anti-microbial and anti-TB activity out of various tested compounds. © Georg Thieme Verlag KG Stuttgart · New York.

Compound-specific stable isotope analysis of nitrogen-containing intact polar lipids.

PubMed

Svensson, Elisabeth; Schouten, Stefan; Stam, Axel; Middelburg, Jack J; Sinninghe Damsté, Jaap S

2015-12-15

Compound-specific isotope analysis (CSIA) of nitrogen in amino acids has proven a valuable tool in many fields (e.g. ecology). Several intact polar lipids (IPLs) also contain nitrogen, and their nitrogen isotope ratios have the potential to elucidate food-web interactions or metabolic pathways. Here we have developed novel methodology for the determination of δ(15)N values of nitrogen-containing headgroups of IPLs using gas chromatography coupled with isotope-ratio mass spectrometry. Intact polar lipids with nitrogen-containing headgroups were hydrolyzed and the resulting compounds were derivatized by (1) acetylation with pivaloyl chloride for compounds with amine and hydroxyl groups or (2) esterification using acidified 2-propanol followed by acetylation with pivaloyl chloride for compounds with both carboxyl and amine groups. The δ(15)N values of the derivatives were subsequently determined using gas chromatography/combustion/isotope-ratio mass spectrometry. Intact polar lipids with ethanolamine and amino acid headgroups, such as phosphatidylethanolamine and phosphatidylserine, were successfully released from the IPLs and derivatized. Using commercially available pure compounds it was established that δ(15)N values of ethanolamine and glycine were not statistically different from the offline-determined values. Application of the technique to microbial cultures and a microbial mat showed that the method works well for the release and derivatization of the headgroup of phosphatidylethanolamine, a common IPL in bacteria. A method to enable CSIA of nitrogen of selected IPLs has been developed. The method is suitable for measuring natural stable nitrogen isotope ratios in microbial lipids, in particular phosphatidylethanolamine, and will be especially useful for tracing the fate of nitrogen in deliberate tracer experiments. Copyright © 2015 John Wiley & Sons, Ltd.

Diffuse emissions of Volatile Organic Compounds (VOCs) from soil in volcanic and hydrothermal systems: evidences for the influence of microbial activity on the carbon budget

NASA Astrophysics Data System (ADS)

Venturi, Stefania; Tassi, Franco; Fazi, Stefano; Vaselli, Orlando; Crognale, Simona; Rossetti, Simona; Cabassi, Jacopo; Capecchiacci, Francesco

2017-04-01

Soils in volcanic and hydrothermal areas are affected by anomalously high concentrations of gases released from the deep reservoirs, which consists of both inorganic (mainly CO2 and H2S) and organic (volatile organic compounds; VOCs) species. VOCs in volcanic and hydrothermal fluids are mainly composed of saturated and unsaturated hydrocarbons (alkanes, aromatics, alkenes, and cyclics), with variable concentrations of O- and S-bearing compounds and halocarbons, depending on the physicochemical conditions at depth. VOCs in interstitial soil gases and fumarolic emissions from four volcanic and hydrothermal systems in the Mediterranean area (Solfatara Crater, Poggio dell'Olivo and Cava dei Selci, in Italy, and Nisyros Island, in Greece) evidenced clear compositional differences, suggesting that their behavior is strongly affected by secondary processes occurring at shallow depths and likely controlled by microbial activity. Long-chain saturated hydrocarbons were significantly depleted in interstitial soil gases with respect to those from fumarolic discharges, whereas enrichments in O-bearing compounds (e.g. aldehydes, ketones), DMSO2 and cyclics were commonly observed. Benzene was recalcitrant to degradation processes, whereas methylated aromatics were relatively instable. The chemical and isotopic (δ13C in CO2 and CH4) composition of soil gases collected along vertical profiles down to 50 cm depth at both Solfatara Crater and Poggio dell'Olivo (Italy) showed evidences of relevant oxidation processes in the soil, confirming that microbial activity likely plays a major role in modifying the composition of deep-derived VOCs. Despite their harsh conditions, being typically characterized by high temperatures, low pH, and high toxic gases and metal contents, the variety of habitats characterizing volcanic and hydrothermal environments offers ideal biomes to extremophilic microbes, whose metabolic activity can consume and/or produce VOCs. In the Solfatara Crater, microbial

Microbial surfactants: fundamentals and applicability in the formulation of nano-sized drug delivery vectors.

PubMed

Rodrigues, Ligia R

2015-07-01

Microbial surfactants, so-called biosurfactants, comprise a wide variety of structurally distinct amphipathic molecules produced by several microorganisms. Besides exhibiting surface activity at the interfaces, these molecules present powerful characteristics including high biodegradability, low toxicity and special biological activities (e.g. antimicrobial, antiviral, anticancer, among others), that make them an alternative to their chemical counterparts. Several medical-related applications have been suggested for these molecules, including some reports on their potential use in the formulation of nano-sized drug delivery vectors. However, despite their promises, due to the generalized lack of knowledge on microbial surfactants phase behavior and stability under diverse physicochemical conditions, these applications remain largely unexplored, thus representing an exciting field of research. These nano-sized vectors are a powerful approach towards the current medical challenges regarding the development of efficient and targeted treatments for several diseases. In this review, a special emphasis will be given to nanoparticles and microemulsions. Nanoparticles are very auspicious as their size, shape and stability can be manipulated by changing the environmental conditions. On the other hand, the easiness of formulation, as well as the broad possibilities of administration justifies the recent popularity of the microemulsions. Notwithstanding, both vector types still require further developments to overcome some critical limitations related with toxicity and costs, among others. Such developments may include the search for other system components, as the microbial surfactants, that can display improved features. Copyright © 2015 Elsevier Inc. All rights reserved.

Engineering microbial hosts for production of bacterial natural products.

PubMed

Zhang, Mingzi M; Wang, Yajie; Ang, Ee Lui; Zhao, Huimin

2016-08-27

Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.

[Microbial secondary metabolites as potential reserve of pharmaceuticals].

PubMed

Orlova, T I; Bulgakova, V G; Polin, A N

2014-01-01

The major characteristics of new bioactive microbial secondary metabolites are summarized in the review. A wide range of new molecular targets are implicated in discovery of new nonantibiotic compounds with some other pharmacological activities (noninfectious diseases). Microorganisms represent fascinating resources due to their production of novel products with broad spectra of bioactivities.

Application and microbial preparation of D-valine.

PubMed

Chen, Ming; Shi, Chao; Zhao, Jing; Gao, Ziqing; Zhang, Chunzhi

2016-10-01

D-Valine is an important organic chiral source and has extensive industrial application, which is used as intermediate for the synthesis of agricultural pesticides, semi-synthetic veterinary antibiotics and pharmaceutical drugs. Its derivatives have shown great activity in clinical use, such as penicillamine for the treatment of immune-deficiency diseases, and actinomycin D for antitumor therapy. Fluvalinate, a pyrethroid pesticide made from D-valine, is a broad-spectrum insecticide with low mammalian toxicity. Valnemulin, a semi-synthetic pleuromutilin derivative synthesized from D-valine, is an antibiotic for animals. Moreover, D-valine is also used in cell culture for selectively inhibiting fibroblasts proliferation. Due to its widespread application, D-valine is gaining more and more attention and some approaches for D-valine preparation have been investigated. In comparison with other approaches, microbial preparation of D-valine is more competitive and promising because of its high stereo selectivity, mild reaction conditions and environmental friendly process. So far, microbial preparation of D-valine can be mainly classified into three categories: microbial asymmetric degradation of DL-valine, microbial stereoselective hydrolysis of N-acyl-DL-valine by D-aminoacylase, and microbial specific hydrolysis of DL-5-isopropylhydantoin by D-hydantoinase coupled with D-carbamoylase. In this paper, the industrial application of D-valine and its microbial preparation are reviewed.

Impacts of Microbial Growth on the Air Quality of the International Space Station

NASA Technical Reports Server (NTRS)

Macatangay, Ariel V.; Bruce, Rebekah J.

2009-01-01

An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples.

Impacts of Microbial Growth on the Air Quality of the International Space Station

NASA Technical Reports Server (NTRS)

Macatangay, Ariel V.; Bruce, Rebekah J.

2010-01-01

An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples

Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

PubMed

Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

2015-01-01

Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

Simultaneous UPLC-MS/MS analysis of native catechins and procyanidins and their microbial metabolites in intestinal contents and tissues of male Wistar Furth inbred rats.

PubMed

Goodrich, Katheryn M; Neilson, Andrew P

2014-05-01

Procyanidins have been extensively investigated for their potential health protective activities. However, the potential bioactivities of procyanidins are limited by their poor bioavailability. The majority of the ingested dose remains unabsorbed and reaches the colon where extensive microbial metabolism occurs. Most existing analytical methods measure either native compounds (catechins and procyanidins), or their microbial metabolites. The objectives of this study were to develop a high-throughput extraction and UPLC-MS/MS method for simultaneous measurement of both native procyanidins and their metabolites, facilitating high-throughput analysis of native and metabolite profiles in various regions of the colon. The present UPLC-MS/MS method facilitates simultaneous resolution and detection of authentic standards of 14 native catechin monomers and procyanidins, as well as 24 microbial metabolites. Detection and resolution of an additional 3 procyanidin dimers and 10 metabolites for which standards were not available was achieved. Elution and adequate resolution of both native compounds and metabolites were achieved within 10min. The intraday repeatability for native compounds was between 1.1 and 16.5%, and the interday repeatability for native compounds was between 2.2 and 25%. Intraday and interday repeatability for metabolites was between 0.6 and 24.1% and 1 and 23.9%, respectively. Observed lower limits of quantification for native compounds were ∼9-350fmol on-column, and for the microbial metabolites were ∼0.8-12,000fmol on-column. Observed lower limits of detection for native compounds were ∼4.5-190fmol on-column, and for metabolites were 0.304-6020fmol on-column. For native monomers and procyanidins, extraction recoveries ranged from 38 to 102%. Extraction recoveries for the 9 microbial metabolites tested ranged from 41 to 95%. Data from tissue analysis of rats gavaged with grape seed extract indicate fairly high accumulation of native compounds

Utilization of subsurface microbial electrochemical systems to elucidate the mechanisms of competition between methanogenesis and microbial iron(III)/humic acid reduction in Arctic peat soils

NASA Astrophysics Data System (ADS)

Friedman, E. S.; Miller, K.; Lipson, D.; Angenent, L. T.

2012-12-01

High-latitude peat soils are a major carbon reservoir, and there is growing concern that previously dormant carbon from this reservoir could be released to the atmosphere as a result of continued climate change. Microbial processes, such as methanogenesis and carbon dioxide production via iron(III) or humic acid reduction, are at the heart of the carbon cycle in Arctic peat soils [1]. A deeper understanding of the factors governing microbial dominance in these soils is crucial for predicting the effects of continued climate change. In previous years, we have demonstrated the viability of a potentiostatically-controlled subsurface microbial electrochemical system-based biosensor that measures microbial respiration via exocellular electron transfer [2]. This system utilizes a graphite working electrode poised at 0.1 V NHE to mimic ferric iron and humic acid compounds. Microbes that would normally utilize these compounds as electron acceptors donate electrons to the electrode instead. The resulting current is a measure of microbial respiration with the electrode and is recorded with respect to time. Here, we examine the mechanistic relationship between methanogenesis and iron(III)- or humic acid-reduction by using these same microbial-three electrode systems to provide an inexhaustible source of alternate electron acceptor to microbes in these soils. Chamber-based carbon dioxide and methane fluxes were measured from soil collars with and without microbial three-electrode systems over a period of four weeks. In addition, in some collars we simulated increased fermentation by applying acetate treatments to understand possible effects of continued climate change on microbial processes in these carbon-rich soils. The results from this work aim to increase our fundamental understanding of competition between electron acceptors, and will provide valuable data for climate modeling scenarios. 1. Lipson, D.A., et al., Reduction of iron (III) and humic substances plays a major

Downstream reactions and engineering in the microbially reconstituted pathway for Taxol.

PubMed

Jiang, Ming; Stephanopoulos, Gregory; Pfeifer, Blaine A

2012-05-01

Taxol (a trademarked product of Bristol-Myers Squibb) is a complex isoprenoid natural product which has displayed potent anticancer activity. Originally isolated from the Pacific yew tree (Taxus brevifolia), Taxol has been mass-produced through processes reliant on plant-derived biosynthesis. Recently, there have been alternative efforts to reconstitute the biosynthetic process through technically convenient microbial hosts, which offer unmatched growth kinetics and engineering potential. Such an approach is made challenging by the need to successfully introduce the significantly foreign enzymatic steps responsible for eventual biosynthesis. Doing so, however, offers the potential to engineer more efficient and economical production processes and the opportunity to design and produce tailored analog compounds with enhanced properties. This mini review will specifically focus on heterologous biosynthesis as it applies to Taxol with an emphasis on the challenges associated with introducing and reconstituting the downstream reaction steps needed for final bioactivity.

The re-emerging role of microbial natural products in antibiotic discovery.

PubMed

Genilloud, Olga

2014-07-01

New classes of antibacterial compounds are urgently needed to respond to the high frequency of occurrence of resistances to all major classes of known antibiotics. Microbial natural products have been for decades one of the most successful sources of drugs to treat infectious diseases but today, the emerging unmet clinical need poses completely new challenges to the discovery of novel candidates with the desired properties to be developed as antibiotics. While natural products discovery programs have been gradually abandoned by the big pharma, smaller biotechnology companies and research organizations are taking over the lead in the discovery of novel antibacterials. Recent years have seen new approaches and technologies being developed and integrated in a multidisciplinary effort to further exploit microbial resources and their biosynthetic potential as an untapped source of novel molecules. New strategies to isolate novel species thought to be uncultivable, and synthetic biology approaches ranging from genome mining of microbial strains for cryptic biosynthetic pathways to their heterologous expression have been emerging in combination with high throughput sequencing platforms, integrated bioinformatic analysis, and on-site analytical detection and dereplication tools for novel compounds. These different innovative approaches are defining a completely new framework that is setting the bases for the future discovery of novel chemical scaffolds that should foster a renewed interest in the identification of novel classes of natural product antibiotics from the microbial world.

Biomimicry of volatile-based microbial control for managing emerging fungal pathogens.

PubMed

Gabriel, K T; Joseph Sexton, D; Cornelison, C T

2018-05-01

Volatile organic compounds (VOCs) are known to be produced by a wide range of micro-organisms and for a number of purposes. Volatile-based microbial inhibition in environments such as soil is well-founded, with numerous antimicrobial VOCs having been identified. Inhibitory VOCs are of interest as microbial control agents, as low concentrations of gaseous VOCs can elicit significant antimicrobial effects. Volatile organic compounds are organic chemicals typically characterized as having low molecular weight, low solubility in water, and high vapour pressure. Consequently, VOCs readily evaporate to the gaseous phase at standard temperature and pressure. This contact-independent antagonism presents unique advantages over traditional, contact-dependent microbial control methods, including increased surface exposure and reduced environmental persistence. This approach has been the focus of our recent research, with positive results suggesting it may be particularly promising for the management of emerging fungal pathogens, such as the causative agents of white-nose syndrome of bats and snake fungal disease, which are difficult or impossible to treat using traditional approaches. Here, we review the history of volatile-based microbial control, discuss recent progress in formulations that mimic naturally antagonistic VOCs, outline the development of a novel treatment device, and highlight areas where further work is needed to successfully deploy VOCs against existing and emerging fungal pathogens. © 2017 The Society for Applied Microbiology.

Investigation of product quality between extemporaneously compounded progesterone vaginal suppositories and an approved progesterone vaginal gel.

PubMed

Mahaguna, Vorapann; McDermott, J Mario; Zhang, Feng; Ochoa, Felipe

2004-01-01

The purpose of this investigation was to compare quality parameters, including product appearance, content uniformity, pH, weight uniformity, microbial limit testing and preservative effectiveness testing on extemporaneously compounded progesterone vaginal suppositories obtained from 10 randomly chosen compounding pharmacies (90 suppositories each) across the United States, to the Food and Drug Administration (FDA) approved prescription progesterone gel product (Prochieve/Crinone) which is manufactured in a cGMP regulated facility. The content uniformity and pH were determined using qualified methods. The microbial limits testing and preservative effectiveness testing were conducted according to compendial methods. Only one pharmacy provided suppositories that were all within the potency limits required for the prescription progesterone gel product. The other pharmacies provided at least some suppositories where progesterone content was either subpotent or superpotent for progesterone. The pH of most of the compounded suppository products was in the range of 4.22 to 7.68 with a median of 6.30 (normal vaginal pH is <5), whereas the gel product was 2.80. For compounded product from one of the pharmacies, microbial limits testing indicated CDC group IVC-2 and Comamonas acidovorans were detected. This data indicates that pharmacy compounded delivery systems for progesterone should be used with caution.

Aerobic Microbial Respiration in Oceanic Oxygen Minimum Zones

NASA Astrophysics Data System (ADS)

Kalvelage, Tim; Lavik, Gaute; Jensen, Marlene M.; Revsbech, Niels Peter; Schunck, Harald; Loescher, Carolin; Desai, Dhwani K.; LaRoche, Julie; Schmitz-Streit, Ruth; Kuypers, Marcel M. M.

2014-05-01

In the oxygen minimum zones (OMZs) of the tropical oceans, sluggish ventilation combined with strong microbial respiration of sinking organic matter results in the depletion of oxygen (O2). When O2 concentrations drop below ~5 µmol/L, organic matter is generally assumed to be respired with nitrate, ultimately leading to the loss of fixed inorganic nitrogen via anammox and denitrification. However, direct measurements of microbial O2 consumption at low O2 levels are - apart from a single experiment conducted in the OMZ off Peru - so far lacking. At the same time, consistently observed active aerobic ammonium and nitrite oxidation at non-detectable O2 concentrations (<1 µmol/L) in all major OMZs, suggests aerobic microorganisms, likely including heterotrophs, to be well adapted to near-anoxic conditions. Consequently, microaerobic (≤5 µmol/L) remineralization of organic matter, and thus release of ammonium, in low- O2 environments might be significantly underestimated at present. Here we present extensive measurements of microbial O2 consumption in OMZ waters, combined with highly sensitive O2 (STOX) measurements and meta-omic functional gene analyses. Short-term incubation experiments with labelled O2 (18-18O2) carried out in the Namibian and Peruvian OMZ, revealed persistent aerobic microbial activity at depths with non-detectable concentrations of O2 (≤50 nmol/L). In accordance, examination of metagenomes and metatranscriptomes from Chilean and Peruvian OMZ waters identified genes encoding for terminal respiratory oxidases with high O2 affinities as well as their expression by diverse microbial communities. Oxygen consumption was particularly enhanced near the upper OMZ boundaries and could mostly (~80%) be assigned to heterotrophic microbial activity. Compared to previously identified anaerobic microbial processes, microaerobic organic matter respiration was the dominant remineralization pathway and source of ammonium (~90%) in the upper Namibian and

INFLUENCE OF SURFACTANTS ON MICROBIAL DEGRADATION OF ORGANIC COMPOUNDS

EPA Science Inventory

Surfactants have the ability to increase aqueous concentrations of poorly soluble compounds and interfacial areas between immiscible fluids, thus potentially improving the accessibility of these substrates to microorganisms. However, both enhancements and inhibitions of biodegrad...

DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bill W. Bogan; Brigid M. Lamb; John J. Kilbane II

2004-10-30

The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing indicated that the growth, and the metal corrosion caused by pure cultures of sulfate reducing bacteria were inhibited by hexane extracts of some pepper plants. This quarter tests were performed to determine ifmore » chemical compounds other than pepper extracts could inhibit the growth of corrosion-associated microbes and to determine if pepper extracts and other compounds can inhibit corrosion when mature biofilms are present. Several chemical compounds were shown to be capable of inhibiting the growth of corrosion-associated microorganisms, and all of these compounds limited the amount of corrosion caused by mature biofilms to a similar extent. It is difficult to control corrosion caused by mature biofilms, but any compound that disrupts the metabolism of any of the major microbial groups present in corrosion-associated biofilms shows promise in limiting the amount/rate of corrosion.« less

Natural compounds and combination therapy in colorectal cancer treatment.

PubMed

Rejhová, A; Opattová, A; Čumová, A; Slíva, D; Vodička, P

2018-01-20

Colorectal cancer (CRC) therapy using conventional chemotherapeutics represents a considerable burden for the patient's organism because of high toxicity while the response is relatively low. Our review summarizes the findings about natural compounds as chemoprotective agents for decreasing risk of CRC. It also identifies natural compounds which possess anti-tumor effects of various characteristics, mainly in vitro on colorectal cell lines or in vivo studies on experimental models, but also in a few clinical trials. Many of natural compounds suppress proliferation by inducing cell cycle arrest or induce apoptosis of CRC cells resulting in the inhibition of tumor growth. A novel employment of natural substances is a so-called combination therapy - administration of two or more substances - conventional chemotherapeutics and a natural compound or more natural compounds at a time. Some natural compounds may sensitize to conventional cytotoxic therapy, reinforce the drug effective concentration, intensify the combined effect of both administered therapeutics or exert cytotoxic effects specifically on tumor cells. Moreover, combined therapy by targeting multiple signaling pathways, uses various mechanisms to reduce the development of resistance to antitumor drugs. The desired effect could be to diminish burden on the patient's organism by replacing part of the dose of a conventional chemotherapeutic with a natural substance with a defined effect. Many natural compounds are well tolerated by the patients and do not cause toxic effects even at high doses. Interaction of conventional chemotherapeutics with natural compounds introduces a new aspect in the research and therapy of cancer. It could be a promising approach to potentially achieve improvements, while minimizing of adverse effects associated with conventional chemotherapy. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

USE OF THE COMPOSITION AND STABLE CARBON ISOTOPE RATIO OF MICROBIAL FATTY ACIDS TO STUDY CARBON CYCLING

EPA Science Inventory

We use measurements of the concentration and stable carbon isotopic ratio (Gamma 13C) of individual microbial phospholipid fatty acids (PLFAS) in soils and sediments as indicators of live microbial biomass levels and microbial carbon source. For studies of soil organic matter (SO...

[On the neuro-psychiatric symptomatology of the so-called "hepatic coma" (author's transl)].

PubMed

Binder, H

1981-01-01

The definition of hepatic coma has been used for the most severe course of hepatic insufficiency, independent from the pathogenesis. This means, that from the psychiatric point of view the hole survey of the exogen reaction type was subdivided. The neurologic symptomatology was rather neglected. In this study an attempt is made to show--using the reports of 77 patients with severe hepatic insufficiency of different etiology--that with very exact and repeated examinations a typical course of neuro-psychiatric symptoms can be observed. A distinct hierarchy of symptoms is existing, which is similar to the well known princip of dissolution (Jackson). As a main factor one has to differentiate between an acute and a subacute course. The acute course is characterized by a rapid decrease of vigilance and increase of neurologic symptoms, which end in most of the cases with an acute midbrain- and bulbarbrain-syndrome, while the subacute course shows primary a disturbance of thymo- and noopsychic function in different relations. In addition to the organic "Achsensyndrom" amnestic or amentiell symptoms can be found, which might be covered by a decrease of the vigilance--if the primary noxis continoues--end up with unconsciousness. The parallel developing neurologic symptomatology shows a distraction of the general motoric, including so-called basic movements. later stereotypies and automatismes, and the delicate distal movements change into rough general-rotation-and pointing movements of the hole body. There is also a temporary bending of all extremities and at this time also a rigidospasticity. In the following course preponderate transient bending or stretching, finally there exists a lack condition, which does not respond to external provocations. The symptomatology is not always symmetric. Transient or longstanding hemiparetic symptoms and also crossed brainstem symptoms can be seen frequently. Sometimes there are general or focal epileptic seizures. If a brain edema

Microbial fuel cell with improved anode

DOEpatents

Borole, Abhijeet P.

2010-04-13

The present invention relates to a method for preparing a microbial fuel cell, wherein the method includes: (i) inoculating an anodic liquid medium in contact with an anode of the microbial fuel cell with one or more types of microorganisms capable of functioning by an exoelectrogenic mechanism; (ii) establishing a biofilm of the microorganisms on and/or within the anode along with a substantial absence of planktonic forms of the microorganisms by substantial removal of the planktonic microorganisms during forced flow and recirculation conditions of the anodic liquid medium; and (iii) subjecting the microorganisms of the biofilm to a growth stage by incorporating one or more carbon-containing nutritive compounds in the anodic liquid medium during biofilm formation or after biofilm formation on the anode has been established.

Microbial transformation of resibufogenin by Curvularia lunata AS 3.4381.

PubMed

Xin, Xiu-Lan; Sun, Jiang-Hao; Wang, Xiao-Bo; Xi, Rong-Gang; Wang, Gang; Lan, Rong; Su, Dong-Hai; Li, Hua; Huo, Xiao-Kui; Wang, Chao

2014-01-01

In this paper, the microbial transformation of resibufogenin by Curvularia lunata AS 3.4381 was investigated, and four transformed products were isolated and characterized as 3-epi-resibufogenin (2), 12α-hydroxy-3-epi-resibufogenin (3), 12-oxo-16β-hydroxy-3-epi-resibufogenin (4), and 12β,15-epoxy-3-epi-bufalin-14,15-ene (5). Among them, 4 and 5 are new compounds, and isomerization, hydroxylation, and oxidation reactions in microbial transformation process were observed. Additionally, the cytotoxicities of transformed products (2-5) were also investigated.

Continuous desulfurization and bacterial community structure of an integrated bioreactor developed to treat SO2 from a gas stream.

PubMed

Lin, Jian; Li, Lin; Ding, Wenjie; Zhang, Jingying; Liu, Junxin

2015-11-01

Sulfide dioxide (SO2) is often released during the combustion processes of fossil fuels. An integrated bioreactor with two sections, namely, a suspended zone (SZ) and immobilized zone (IZ), was applied to treat SO2 for 6months. Sampling ports were set in both sections to investigate the performance and microbial characteristics of the integrated bioreactor. SO2 was effectively removed by the synergistic effect of the SZ and IZ, and more than 85% removal efficiency was achieved at steady state. The average elimination capacity of SO2 in the bioreactor was 2.80g/(m(3)·hr) for the SZ and 1.50g/(m(3)·hr) for the IZ. Most SO2 was eliminated in the SZ. The liquid level of the SZ and the water content ratio of the packing material in the IZ affected SO2 removal efficiency. The SZ served a key function not only in SO2 elimination, but also in moisture maintenance for the IZ. The desired water content in IZ could be feasibly maintained without any additional pre-humidification facilities. Clone libraries of 16S rDNA directly amplified from the DNA of each sample were constructed and sequenced to analyze the community composition and diversity in the individual zones. The desulfurization bacteria dominated both zones. Paenibacillus sp. was present in both zones, whereas Ralstonia sp. existed only in the SZ. The transfer of SO2 to the SZ involved dissolution in the nutrient solution and biodegradation by the sulfur-oxidizing bacteria. This work presents a potential biological treatment method for waste gases containing hydrophilic compounds. Copyright © 2015. Published by Elsevier B.V.

20 CFR 702.312 - Informal conferences; called by and held before whom.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 20 Employees' Benefits 3 2011-04-01 2011-04-01 false Informal conferences; called by and held...; called by and held before whom. Informal conferences shall be called by the district director or his... unavailable. When so assigned, the designee shall perform the duties set forth below assigned to the district...

Removal of Microbial Contamination from Surface by Plasma

NASA Astrophysics Data System (ADS)

Feng, Xinxin; Liu, Hongxia; Shen, Zhenxing; Wang, Taobo

2018-01-01

Microbial contamination is closely associated with human and environmental health, they can be tested on food surfaces, medical devices, packing material and so on. In this paper the removal of the microbial contamination from surface using plasma treatment is investigated. The Escherichia coli (E. coli) has been chosen as a bio-indicator enabling to evaluate the effect of plasma assisted microbial inactivation. Oxygen gas was as the working gas. The plasma RF power, plasma exposition time, gas flow and the concentration of organic pollutant were varied in order to see the effect of the plasma treatment on the Gram-negative germ removal. After the treatment, the microbial abatement was evaluated by the standard plate count method. This proved a positive effect of the plasma treatment on Gram-negative germ removal. The kinetics and mathematical model of removal were studied after plasma treatment, and then the removing course of E. coli was analyzed. This work is meaningful for deepening our understanding of the fundamental scientific principles regarding microbial contamination from surface by plasma.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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

2016-11-28

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.

Microbial degradation of petroleum hydrocarbons.

PubMed

Varjani, Sunita J

2017-01-01

Petroleum hydrocarbon pollutants are recalcitrant compounds and are classified as priority pollutants. Cleaning up of these pollutants from environment is a real world problem. Bioremediation has become a major method employed in restoration of petroleum hydrocarbon polluted environments that makes use of natural microbial biodegradation activity. Petroleum hydrocarbons utilizing microorganisms are ubiquitously distributed in environment. They naturally biodegrade pollutants and thereby remove them from the environment. Removal of petroleum hydrocarbon pollutants from environment by applying oleophilic microorganisms (individual isolate/consortium of microorganisms) is ecofriendly and economic. Microbial biodegradation of petroleum hydrocarbon pollutants employs the enzyme catalytic activities of microorganisms to enhance the rate of pollutants degradation. This article provides an overview about bioremediation for petroleum hydrocarbon pollutants. It also includes explanation about hydrocarbon metabolism in microorganisms with a special focus on new insights obtained during past couple of years. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biodegradation of ciprofloxacin in water and soil and its effects on the microbial communities.

PubMed

Girardi, Cristobal; Greve, Josephine; Lamshöft, Marc; Fetzer, Ingo; Miltner, Anja; Schäffer, Andreas; Kästner, Matthias

2011-12-30

While antibiotics are frequently found in the environment, their biodegradability and ecotoxicological effects are not well understood. Ciprofloxacin inhibits active and growing microorganisms and therefore can represent an important risk for the environment, especially for soil microbial ecology and microbial ecosystem services. We investigated the biodegradation of (14)C-ciprofloxacin in water and soil following OECD tests (301B, 307) to compare its fate in both systems. Ciprofloxacin is recalcitrant to biodegradation and transformation in the aqueous system. However, some mineralisation was observed in soil. The lower bioavailability of ciprofloxacin seems to reduce the compound's toxicity against microorganisms and allows its biodegradation. Moreover, ciprofloxacin strongly inhibits the microbial activities in both systems. Higher inhibition was observed in water than in soil and although its antimicrobial potency is reduced by sorption and aging in soil, ciprofloxacin remains biologically active over time. Therefore sorption does not completely eliminate the effects of this compound. Copyright © 2011 Elsevier B.V. All rights reserved.

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

PubMed Central

Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A.; Van Bodegom, Peter M.; Lennon, Jay T.; Bertilsson, Stefan; Grossart, Hans-Peter; Philippot, Laurent; Bodelier, Paul L. E.

2014-01-01

In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology. PMID:24904563

Engineering of Microbial Cell Factories for the Production of Plant Polyphenols with Health-Beneficial Properties.

PubMed

Dudnik, Alexey; Gaspar, Paula; Neves, Ana Rute; Forster, Jochen

2018-05-15

Polyphenols form a group of important natural bioactive compounds with numerous ascribed health-beneficial attributes (e.g. antioxidant, anti-inflammatory, anti-microbial and tumor-suppressing properties). Some polyphenols can also be used as natural dyes or plastic precursors. Notwithstanding their relevance, production of most of these compounds still relies on extraction from plant material, which for most of it is a costly and an inefficient procedure. The use of microbial cell factories for this purpose is an emerging alternative that could allow a more efficient and sustainable production. The most recent advances in molecular biology and genetic engineering, combined with the ever-growing understanding of microbial physiology have led to multiple success stories. Production of multiple polyphenolic compounds or their direct precursors has been achieved not only in the common production hosts, such as Escherichia coli and Saccharomyces cerevisiae but also in Corynebacterium glutamicum and Lactococcus lactis. However, boosting production of native compounds or introduction of heterologous biosynthetic pathways also brings certain challenges, such as the need to express, balance and maintain efficient precursor supply. This review will discuss the most recent advances in the field of metabolic engineering of microorganisms for polyphenol biosynthesis and its future perspectives, as well as outlines their potential health benefits and current production methods. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Role of the microbial population on the flavor of the soft-bodied cheese Torta del Casar.

PubMed

Ordiales, Elena; Martín, Alberto; Benito, María José; Hernández, Alejandro; Ruiz-Moyano, Santiago; Córdoba, María de Guía

2013-09-01

The purpose of this work was to investigate the influence of the spontaneous microbial population on the flavor of Torta del Casar cheese. A total of 16 batches of cheeses with different microbial qualities were used. Their physicochemical and microbial characteristics were evaluated during ripening and then related with the volatile compounds, taste, and flavor properties of the finished cheeses. Acids were the most abundant volatile compounds, followed by alcohols and carbonyls. The amount of acetic acid and several alcohols were linked to cheeses with higher counts of lactic acid bacteria (LAB), whereas Enterobacteriaceae counts were associated with semivolatile fatty acids. The gram-positive catalase-positive cocci counts were correlated with esters and methyl ketones. Although the role of the LAB in the flavor development of Torta del Casar is the most relevant, other microbial groups are necessary to impart the flavor of the cheese and to minimize the possible off-flavor derived from excessive concentrations of LAB metabolites, such as acetic acid. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Microbial Community Structure of an Alluvial Aquifer Treated to Encourage Microbial Induced Calcite Precipitation

NASA Astrophysics Data System (ADS)

Ohan, J.; Saneiyan, S.; Lee, J.; Ntarlagiannis, D.; Burns, S.; Colwell, F. S.

2017-12-01

microbial community structure, and the functional attributes associated with community change, so that physical strengthening of soils by microbial action can be accomplished.

Selected phenolic compounds in cultivated plants: ecologic functions, health implications, and modulation by pesticides.

PubMed Central

Daniel, O; Meier, M S; Schlatter, J; Frischknecht, P

1999-01-01

Phenolic compounds are widely distributed in the plant kingdom. Plant tissues may contain up to several grams per kilogram. External stimuli such as microbial infections, ultraviolet radiation, and chemical stressors induce their synthesis. The phenolic compounds resveratrol, flavonoids, and furanocoumarins have many ecologic functions and affect human health. Ecologic functions include defense against microbial pathogens and herbivorous animals. Phenolic compounds may have both beneficial and toxic effects on human health. Effects on low-density lipoproteins and aggregation of platelets are beneficial because they reduce the risk of coronary heart disease. Mutagenic, cancerogenic, and phototoxic effects are risk factors of human health. The synthesis of phenolic compounds in plants can be modulated by the application of herbicides and, to a lesser extent, insecticides and fungicides. The effects on ecosystem functioning and human health are complex and cannot be predicted with great certainty. The consequences of the combined natural and pesticide-induced modulating effects for ecologic functions and human health should be further evaluated. PMID:10229712

Microbial utilization of nitrogen in cold core eddies: size does matter

NASA Astrophysics Data System (ADS)

McInnes, A.; Messer, L. F.; Laiolo, L.; Laverock, B.; Laczka, O.; Brown, M. V.; Seymour, J.; Doblin, M.

2016-02-01

determine the N compound utilization and microbial community composition and as the feature grows in size and age a community succession will lead to differential more diverse N compound utilization.

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

PubMed

Walsh, Aaron M; Crispie, Fiona; Kilcawley, Kieran; O'Sullivan, Orla; O'Sullivan, Maurice G; Claesson, Marcus J; Cotter, Paul D

2016-01-01

Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides . Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand

Research supporting potential modification of the NASA specification for dry heat microbial reduction of spacecraft hardware

NASA Astrophysics Data System (ADS)

Spry, James A.; Beaudet, Robert; Schubert, Wayne

Dry heat microbial reduction (DHMR) is the primary method currently used to reduce the microbial load of spacecraft and component parts to comply with planetary protection re-quirements. However, manufacturing processes often involve heating flight hardware to high temperatures for purposes other than planetary protection DHMR. At present, the specifica-tion in NASA document NPR8020.12, describing the process lethality on B. atrophaeus (ATCC 9372) bacterial spores, does not allow for additional planetary protection bioburden reduction credit for processing outside a narrow temperature, time and humidity window. Our results from a comprehensive multi-year laboratory research effort have generated en-hanced data sets on four aspects of the current specification: time and temperature effects in combination, the effect that humidity has on spore lethality, and the lethality for spores with exceptionally high thermal resistance (so called "hardies"). This paper describes potential modifications to the specification, based on the data set gener-ated in the referenced studies. The proposed modifications are intended to broaden the scope of the current specification while still maintaining confidence in a conservative interpretation of the lethality of the DHMR process on microorganisms.

Synthesis of coumarin-theophylline hybrids as a new class of anti-tubercular and anti-microbial agents.

PubMed

Mangasuli, Sumitra N; Hosamani, Kallappa M; Devarajegowda, Hirihalli C; Kurjogi, Mahantesh M; Joshi, Shrinivas D

2018-02-25

A series of novel coumarin-theophylline hybrids were synthesized and examined for their anti-tubercular activity in vitro against Mycobacterium tuberculosis H 37 Rv, anti-microbial activity in vitro against gram-positive bacteria (Staphylococcus aureus) and gram-negative bacterias (Escherichia coli, Salmonella typhi) as well as fungi (Candida albicans). The compound (3a) has shown excellent anti-tubercular activity with MIC of 0.12 μg/mL. Electron donating compounds (3a, 3f) have displayed significant anti-microbial activity. The compounds have also been precisely elucidated using single crystal X-ray diffraction techniques. Molecular docking study has been performed against 4DQU enzyme of Mycobacterium tuberculosis showed good binding interactions and is in agreement with the in vitro results. Copyright © 2018. Published by Elsevier Masson SAS.

Seasonal variability of microbial biomass phosphorus in urban soils.

PubMed

Halecki, W; Gąsiorek, M

2015-01-01

Urban soils have been formed through human activities. Seasonal evaluation with time-control procedure are essential for plant, and activity of microorganisms. Therefore, these processes are crucial in the urban area due to geochemical changes in the past years. The purpose of this study was to investigate the changes of content of microbial biomass phosphorus (P) in the top layer of soils throughout the season. In this research, the concentration of microbial biomass P ranged from 0.01 to 6.29 mg·kg(-1). We used single-factor repeated-measure analysis of variance to test the effect of season on microbial biomass P content of selected urban soils. We found no statistically significant differences between the concentration of microbial biomass P in the investigated urban and sub-urban soils during the growing season. This analysis explicitly recognised that environmental urban conditions are steady. Specifically, we have studied how vegetation seasonality and ability of microbial biomass P are useful for detecting quality deviations, which affect the equilibrium of urban soil. In conclusion, seasonal variability of the stringency of assurance across the different compounds of soil reveals, as expected, the stable condition of the urban soils. Seasonal responses in microbial biomass P under urban soil use should establish a framework as a reference to the activity of the microorganisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

PubMed Central

Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V.; Garcia-Trejo, Juan F.; Guevara-Gonzalez, Ramon G.

2015-01-01

Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems. PMID:26509157

[The relationship between abiotic factors and microbial activities of microbial eco-system in contaminated soil with petroleum hydrocarbons].

PubMed

Jia, Jian-li; Li, Guang-he; Zhong, Yi

2004-05-01

By means of the biostimulation and bioaugmentation in the micro-ecological environment of contaminated soil with petrochemical hydrocarbons, the biodegradation rates and mode of the contaminants were significantly improved. Based on the investigations carried out in some oilfields and petrochemical industrial area of Northern China, the relationship between the abiotic factors such as nutrient, pH, contaminants, water content, alkalinity, etc., and microbial activities was interpreted and identified in this paper. The results from the investigations and indoor and in-situ experiments conducted recent years indicated that the soils in the areas, to the extent, have been polluted by the different kinds of organic compounds composed of monoaromatic benzene, PAHs, chlorinated solvent, and alkanes, and the concentrations of the compounds mostly were elevated as compared to the background, with the highest 34,000 mg/kg dry soil. The column chromatography analysis results showed that the alkyl and aromatic compounds were accounted for more than 50% of the total hydrocarbon contents, which was readily degraded by degrading bacteria and improved the degrading microbe activities. The effective nitrogen and phosphorus encountered in the soil was less than 30 mg/kg dry soil and 10 mg/kg dry soil, only about 5% of total contents of them respectively. Based on the stoichiometric calculation and reasonable ratio of carbon to nutrient content regarding the biodegradation of organic compounds, the nutrient levels mainly composed of nitrogen and phosphorus in polluted soil as importantly limiting factors to degrading bacterial growth and activity were insufficient to the biodegradation of petrochemicals, and it is needed to add the nutrient for the bioremediation of contaminated soil. It is undoubted that the optimization of abiotic factors play significant role in increasing the microbial activity and improving the biodegradation rates.

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

DOE PAGES

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

2016-11-28

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 producemore » chemically diverse, stable SOM. As a result, 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.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 producemore » chemically diverse, stable SOM. As a result, 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.« less

Inhibiting Microbial Toxins Using Plant-Derived Compounds and Plant Extracts

PubMed Central

Upadhyay, Abhinav; Mooyottu, Shankumar; Yin, Hsinbai; Surendran Nair, Meera; Bhattaram, Varunkumar; Venkitanarayanan, Kumar

2015-01-01

Many pathogenic bacteria and fungi produce potentially lethal toxins that cause cytotoxicity or impaired cellular function either at the site of colonization or other locations in the body through receptor-mediated interactions. Various factors, including biotic and abiotic environments, competing microbes, and chemical cues affect toxin expression in these pathogens. Recent work suggests that several natural compounds can modulate toxin production in pathogenic microbes. However, studies explaining the mechanistic basis for their effect are scanty. This review discusses the potential of various plant-derived compounds for reducing toxin production in foodborne and other microbes. In addition, studies highlighting their anti-toxigenic mechanism(s) are discussed. PMID:28930207

Microbial mats as a biological treatment approach for saline wastewaters: the case of produced water from hydraulic fracturing.

PubMed

Akyon, Benay; Stachler, Elyse; Wei, Na; Bibby, Kyle

2015-05-19

Treatment of produced water, i.e. wastewater from hydraulic fracturing, for reuse or final disposal is challenged by both high salinity and the presence of organic compounds. Organic compounds in produced water may foul physical-chemical treatment processes or support microbial corrosion, fouling, and sulfide release. Biological approaches have potential applications in produced water treatment, including reducing fouling of physical-chemical treatment processes and decreasing biological activity during produced water holding; however, conventional activated sludge treatments are intolerant of high salinity. In this study, a biofilm treatment approach using constructed microbial mats was evaluated for biodegradation performance, microbial community structure, and metabolic potential in both simulated and real produced water. Results demonstrated that engineered microbial mats are active at total dissolved solids (TDS) concentrations up to at least 100,000 mg/L, and experiments in real produced water showed a biodegradation capacity of 1.45 mg COD/gramwet-day at a TDS concentration of 91,351 mg/L. Additionally, microbial community and metagenomic analyses revealed an adaptive microbial community that shifted based upon the sample being treated and has the metabolic potential to degrade a wide array of contaminants, suggesting the potential of this approach to treat produced waters with varying composition.

Microbial degradation of chloroethenes in groundwater systems

USGS Publications Warehouse

Bradley, Paul M.

2000-01-01

 The chloroethenes, tetrachloroethene (PCE) and trichloroethene (TCE) are among the most common contaminants detected in groundwater systems. As recently as 1980, the consensus was that chloroethene compounds were not significantly biodegradable in groundwater. Consequently, efforts to remediate chloroethene-contaminated groundwater were limited to largely unsuccessful pump-and-treat attempts. Subsequent investigation revealed that under reducing conditions, aquifer microorganisms can reductively dechlorinate PCE and TCE to the less chlorinated daughter products dichloroethene (DCE) and vinyl chloride (VC). Although recent laboratory studies conducted with halorespiring microorganisms suggest that complete reduction to ethene is possible, in the majority of groundwater systems reductive dechlorination apparently stops at DCE or VC. However, recent investigations conducted with aquifer and stream-bed sediments have demonstrated that microbial oxidation of these reduced daughter products can be significant under anaerobic redox conditions. The combination of reductive dechlorination of PCE and TCE under anaerobic conditions followed by anaerobic microbial oxidation of DCE and VC provides a possible microbial pathway for complete degradation of chloroethene contaminants in groundwater systems.

Microbial degradation of chloroethenes in groundwater systems

USGS Publications Warehouse

Bradley, P.M.

2000-01-01

The chloroethenes, tetrachloroethene (PCE) and trichloroethene (TCE) are among the most common contaminants detected in groundwater systems. As recently as 1980, the consensus was that chloroethene compounds were not significantly biodegradable in groundwater. Consequently, efforts to remediate chloroethene-contaminated groundwater were limited to largely unsuccessful pump-and-treat attempts. Subsequent investigation revealed that under reducing conditions, aquifer microorganisms can reductively dechlorinate PCE and TCE to the less chlorinated daughter products dichloroethene (DCE) and vinyl chloride (VC). Although recent laboratory studies conducted with halorespiring microorganisms suggest that complete reduction to ethene is possible, in the majority of groundwater systems reductive dechlorination apparently stops at DCE or VC. However, recent investigations conducted with aquifer and stream-bed sediments have demonstrated that microbial oxidation of these reduced daughter products can be significant under anaerobic redox conditions. The combination of reductive dechlorination of PCE and TCE under anaerobic conditions followed by anaerobic microbial oxidation of DCE and VC provides a possible microbial pathway for complete degradation of chloroethene contaminants in groundwater systems.

Microbial community composition affects soil fungistasis.

PubMed

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.

Microbial Community Composition Affects Soil Fungistasis†

PubMed Central

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

2003-01-01

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. PMID:12571002

Microbial volatile organic compound emissions from Stachybotrys chartarum growing on gypsum wallboard and ceiling tile.

PubMed

Betancourt, Doris A; Krebs, Ken; Moore, Scott A; Martin, Shayna M

2013-12-05

Stachybotrys chartarum is a filamentous mold frequently identified among the mycobiota of water-damaged building materials. Growth of S. chartarum on suitable substrates and under favorable environmental conditions leads to the production of secondary metabolites such as mycotoxins and microbial volatile organic compounds (MVOCs). The aim of this study was to characterize MVOC emission profiles of seven toxigenic strains of S. chartarum, isolated from water-damaged buildings, in order to identify unique MVOCs generated during growth on gypsum wallboard and ceiling tile coupons. Inoculated coupons were incubated and monitored for emissions and growth using a closed glass environmental growth chamber maintained at a constant room temperature. Gas samples were collected from the headspace for three to four weeks using Tenax TA tubes. Most of the MVOCs identified were alcohols, ketones, ethers and esters. The data showed that anisole (methoxybenzene) was emitted from all of the S. chartarum strains tested on both types of substrates. Maximum anisole concentration was detected after seven days of incubation. MVOCs are suitable markers for fungal identification because they easily diffuse through weak barriers like wallpaper, and could be used for early detection of mold growth in hidden cavities. This study identifies the production of anisole by seven toxigenic strains of Stachybotrys chartarum within a period of one week of growth on gypsum wallboard and ceiling tiles. These data could provide useful information for the future construction of a robust MVOC library for the early detection of this mold.

Effects of Ga substitution on the structural and magnetic properties of half metallic Fe2MnSi Heusler compound

NASA Astrophysics Data System (ADS)

Pedro, S. S.; Caraballo Vivas, R. J.; Andrade, V. M.; Cruz, C.; Paixão, L. S.; Contreras, C.; Costa-Soares, T.; Caldeira, L.; Coelho, A. A.; Carvalho, A. Magnus G.; Rocco, D. L.; Reis, M. S.

2015-01-01

The so-called half-metallic magnets have been proposed as good candidates for spintronic applications due to the feature of exhibiting a hundred percent spin polarization at the Fermi level. Such materials follow the Slater-Pauling rule, which relates the magnetic moment with the valence electrons in the system. In this paper, we study the bulk polycrystalline half-metallic Fe2MnSi Heusler compound replacing Si by Ga to determine how the Ga addition changes the magnetic, the structural, and the half-metal properties of this compound. The material does not follow the Slater-Pauling rule, probably due to a minor structural disorder degree in the system, but a linear dependence on the magnetic transition temperature with the valence electron number points to the half-metallic behavior of this compound.

Microbial response to triepthylphosphate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazen, T.C.; Santo Domingo, J.W.; Berry, C.J.

1997-05-01

The effect of triethylphosphate (TEP) on the activity of a landfill aquifer microbial community was evaluated using standard techniques and in situ hybridizations with phylogenetic probes. Benzene was used as an external carbon source to monitor degradation of an aromatic compound in TEP amended microcosms. Microscopical and viable counts were higher in TEP containing microcosms when compared to unamended controls. A significant increase in metabolic activity was also observed for TEP amended samples as determined by the number of cells hybridizing to an eubacterial probe. In addition, the number of beta and gamma Proteobacteria increased from undetectable levels prior tomore » the study to 15-29% of the total bacteria in microcosms containing TEP and benzene. In these microcosms, nearly 40% of the benzene was degraded during the incubation period compared to less than 5% in unamended microcosms. While TEP has previously been used as an alternate phosphate source in the bioremediation of chlorinated aliphatics, this study shows that it can also stimulate the microbial degradation of aromatics in phosphate limited aquifers.« less

Oxygen transfer rate identifies priming compounds in parsley cells.

PubMed

Schilling, Jana Viola; Schillheim, Britta; Mahr, Stefan; Reufer, Yannik; Sanjoyo, Sandi; Conrath, Uwe; Büchs, Jochen

2015-11-25

In modern agriculture, the call for an alternative crop protection strategy increases because of the desired reduction of fungicide and pesticide use and the continuously evolving resistance of pathogens and pests to agrochemicals. The direct activation of the plant immune system does not provide a promising plant protection measure because of high fitness costs. However, upon treatment with certain natural or synthetic compounds, plant cells can promote to a fitness cost-saving, primed state of enhanced defense. In the primed state, plants respond to biotic and abiotic stress with faster and stronger activation of defense, and this is often associated with immunity and abiotic stress tolerance. Until now, the identification of chemical compounds with priming-inducing activity (so-called plant activators) relied on tedious and invasive approaches, or required the late detection of secreted furanocoumarin phytoalexins in parsley cell cultures. Thus, simple, fast, straightforward, and noninvasive techniques for identifying priming-inducing compounds for plant protection are very welcome. This report demonstrates that a respiration activity-monitoring system (RAMOS) can identify compounds with defense priming-inducing activity in parsley cell suspension in culture. RAMOS relies on the quasi-continuous, noninvasive online determination of the oxygen transfer rate (OTR). Treatment of parsley culture cells with the known plant activator salicylic acid (SA), a natural plant defense signal, resulted in an OTR increase. Addition of the defense elicitor Pep13, a cell wall peptide of Phythophthora sojae, induced two distinctive OTR peaks that were higher in SA-primed cells than in unprimed cells upon Pep13 challenge. Both, the OTR increase after priming with SA and the Pep13 challenge were dose-dependent. Furthermore, there was a close correlation of a compound's activity to enhance the oxygen consumption in parsley cells and its capacity to prime Pep13-induced furanocoumarin

fac-[Re(CO)3(dmso-O)3](CF3SO3): a new versatile and efficient Re(I) precursor for the preparation of mono and polynuclear compounds containing fac-[Re(CO)3]+ fragments.

PubMed

Casanova, Massimo; Zangrando, Ennio; Munini, Fabio; Iengo, Elisabetta; Alessio, Enzo

2006-11-14

We show here that the new complex fac-[Re(CO)3(dmso-O)3](CF3SO3) (1), efficiently prepared in one step from [ReBr(CO)5] and featuring a broad range of solubility, is, in general, a better precursor for the one-step synthesis of mono- and polynuclear inorganic compounds containing fac-[Re(CO)3]+ fragments compared to the commonly used (NEt4)2fac-[ReBr3(CO)3] and fac-[Re(CO)3(CH3CN)3](Y) (Y = PF6, BF4, ClO4) species. Compound 1 is the first example of a Re(I)-dmso complex structurally characterized and confirms the rule that dmso is always O-bonded when trans to CO. The reactivity of 1 was tested in the one-step preparation of several new and known complexes. The O-bonded sulfoxides of 1 are replaced under mild conditions by tri- (L3) and bidentate ligands (L2) to produce fac-[Re(CO)3(L3)]+ and fac-[Re(CO)3(L2)(dmso-O)]+ compounds, respectively. An excess of monodentate ligands (L) and more forcing conditions are needed to prepare fac-[Re(CO)3(L)3]+ compounds. The new compounds include fac-[Re(CO)3(bipy)(dmso-O)](CF3SO3) (4), that turned out to be an excellent precursor for binding the luminescent fac-[Re(CO)3(bipy)]+ fragment to polytopic ligands for the construction of more elaborate assemblies. One example reported here is the two-step preparation of fac-[{Re(CO)3(bipy)}(mu-4,4'-bipy){Ru(TPP)(CO)}](CF3SO3) (8) (TPP = tetraphenylporphyrin). The X-ray structures of the new compounds 1, 4, of the bis-porphyrin complex fac-[Re(CO)3Cl(4'MPyP)2] (13) (4'MPyP = 5-(4'pyridyl)-10,15,20-triphenylporphyrin), and of the rhenium-cyclophane [{(CO)3Re(mu-OH)2Re(CO)3}2(micro-4,4'-bipy)2] (15), among others, are described. Compound 1 might find useful applications in supramolecular chemistry (metal-mediated assembly of large architectures), in the in situ preparation of stable Re compounds to be used in nuclear medicine, and for the labeling of biomolecules.

Microbial astronauts: assembling microbial communities for advanced life support systems

NASA Technical Reports Server (NTRS)

Roberts, M. S.; Garland, J. L.; Mills, A. L.

2004-01-01

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem

Microbial astronauts: assembling microbial communities for advanced life support systems.

PubMed

Roberts, M S; Garland, J L; Mills, A L

2004-02-01

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem

Bioremediation of trace organic compounds found in precious metals refineries' wastewaters: a review of potential options.

PubMed

Barbosa, V L; Tandlich, R; Burgess, J E

2007-07-01

Platinum group metal (PGM) refining processes produce large quantities of wastewater, which is contaminated with the compounds that make up the solvents/extractants mixtures used in the process. These compounds often include solvesso, beta-hydroxyxime, amines, amides and methyl isobutyl ketone. A process to clean up PGM refinery wastewaters so that they could be re-used in the refining process would greatly contribute to continual water storage problems and to cost reduction for the industry. Based on the concept that organic compounds that are produced biologically can be destroyed biologically, the use of biological processes for the treatment of organic compounds in other types of waste stream has been favoured in recent years, owing to their low cost and environmental acceptability. This review examines the available biotechnologies and their effectiveness for treating compounds likely to be contained in precious metal extraction process wastewaters. The processes examined include: biofilters, fluidized bed reactors, trickle-bed bioreactors, bioscrubbers, two-phase partitioning bioreactors, membrane bioreactors and activated sludge. Although all processes examined showed adequate to excellent removal of organic compounds from various gaseous and fewer liquid waste streams, there was a variation in their effectiveness. Variations in performance of laboratory-scale biological processes are probably due to the inherent change in the microbial population composition due to selection pressure, environmental conditions and the time allowed for adaptation to the organic compounds. However, if these factors are disregarded, it can be established that activated sludge and membrane bioreactors are the most promising processes for use in the treatment of PGM refinery wastewaters.

A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil

PubMed Central

Weigold, Pascal; El-Hadidi, Mohamed; Ruecker, Alexander; Huson, Daniel H.; Scholten, Thomas; Jochmann, Maik; Kappler, Andreas; Behrens, Sebastian

2016-01-01

In soils halogens (fluorine, chlorine, bromine, iodine) are cycled through the transformation of inorganic halides into organohalogen compounds and vice versa. There is evidence that these reactions are microbially driven but the key enzymes and groups of microorganisms involved are largely unknown. Our aim was to uncover the diversity, abundance and distribution of genes encoding for halogenating and dehalogenating enzymes in a German forest soil by shotgun metagenomic sequencing. Metagenomic libraries of three soil horizons revealed the presence of genera known to be involved in halogenation and dehalogenation processes such as Bradyrhizobium or Pseudomonas. We detected a so far unknown diversity of genes encoding for (de)halogenating enzymes in the soil metagenome including specific and unspecific halogenases as well as metabolic and cometabolic dehalogenases. Genes for non-heme, no-metal chloroperoxidases and haloalkane dehalogenases were the most abundant halogenase and dehalogenase genes, respectively. The high diversity and abundance of (de)halogenating enzymes suggests a strong microbial contribution to natural halogen cycling. This was also confirmed in microcosm experiments in which we quantified the biotic formation of chloroform and bromoform. Knowledge on microorganisms and genes that catalyze (de)halogenation reactions is critical because they are highly relevant to industrial biotechnologies and bioremediation applications. PMID:27353292

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.

PubMed

Binga, Erik K; Lasken, Roger S; Neufeld, Josh D

2008-03-01

Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

Microbial production of volatile sulphur compounds in the large intestine of pigs fed two different diets.

PubMed

Poulsen, H V; Jensen, B B; Finster, K; Spence, C; Whitehead, T R; Cotta, M A; Canibe, N

2012-07-01

  To investigate the production of volatile sulphur compounds (VSC) in the segments of the large intestine of pigs and to assess the impact of diet on this production.   Pigs were fed two diets based on either wheat and barley (STD) or wheat and dried distillers grains with solubles (DDGS). Net production of VSC and potential sulphate reduction rate (SRR) (sulphate saturated) along the large intestine were determined by means of in vitro incubations. The net production rate of hydrogen sulphide and potential SRR increased from caecum towards distal colon and were significantly higher in the STD group. Conversely, the net methanethiol production rate was significantly higher in the DDGS group, while no difference was observed for dimethyl sulphide. The number of sulphate-reducing bacteria and total bacteria were determined by quantitative PCR and showed a significant increase along the large intestine, whereas no diet-related differences were observed.   VSC net production varies widely throughout the large intestine of pigs and the microbial processes involved in this production can be affected by diet.   This first report on intestinal production of all VSC shows both spatial and dietary effects, which are relevant to both bowel disease- and odour mitigation research. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Basics of Compounding: Compounding Irrigation Solutions for Sterile and Nonsterile Preparations.

PubMed

Allen, Loyd V

2017-01-01

Compounding pharmacists are sometimes called upon to prepare irrigation solutions, especially in the hospital or clinical setting. Irrigations are indicated for washing or bathing surgical incisions, wounds, and body tissues, including body cavities. Some irrigation solutions coming in contact with exposed tissue, must meet stringent requirements of sterility and bacterial endotoxins. Compounded irrigation solutions may involve wound(s), the bladder, and also may be for ophthalmic, otic, and nasal application. Some vaginal douches/instillations and rectal solutions may also be used as irrigations. As with any medication administered to the body or used on body tissues, there are requirements, and these may vary depending on the type of irrigation solution involved. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

Considering the Lives of Microbes in Microbial Communities.

PubMed

Shank, Elizabeth A

2018-01-01

Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Even so, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering "the lives of microbes": we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.

Origin of the color of Cv. rhapsody in blue rose and some other so-called "blue" roses.

PubMed

Gonnet, Jean-François

2003-08-13

Flowers of the rose cultivar Rhapsody in Blue display unusual colors, changing as they age, from a vivid red-purple to a lighter and duller purple, which are based on tonalities corresponding to hue angles between 340 and 320 degrees in the CIELAB scale. Unexpectedly, the chemical basis of these colors is among the simplest, featuring cyanin (cyanidin 3,5-di-O-glucoside), the most frequent anthocyanin in flowers, as the sole pigment and quercetin kaempferol glycosides as copigments at a relatively low copigment/pigment ratio (about 3/1), which usually produces magenta or red shades in roses. This color shift to bluer shades is coupled with the progressive accumulation of cyanin into vacuolar anthocyanic inclusions (AVIs), the occurrence of which increases as the petals grow older. In addition to the normal lambda(max) of cyanin at approximately 545 nm, the transmission spectra of live petals and of epidermal cells exhibit a second lambda(max) in the 620-625 nm range, the relative importance increasing with the presence of AVIs. In petals of fully opened flowers, the only pigmented structures in the vacuoles of epidermal cells are AVIs; their intense and massive absorption in the 520-640 nm area produces a much darker and bluer color than measured for the vacuolar solution present at the very first opening stage. Cyanin is probably "trapped" into AVIs at higher concentrations than would be possible in a vacuolar solution and in quinonoidal form, appearing purple-blue because of additional absorption in the 580-630 nm area. Quite similar pigmentation features were found in very ancient rose cultivars (cv. L'Evêque or Bleu Magenta), also displaying this type of so-called "blue" color.

[Study of androgen receptor and phosphoglycerate kinase gene polymorphism in major cellular components of the so-called pulmonary sclerosing hemangioma].

PubMed

Qi, Feng-jie; Zhang, Xiu-wei; Zhang, Yong-xing; Dai, Shun-dong; Wang, En-hua

2006-05-01

To study the clonality of polygonal cells and surface cuboidal cells in the so-called pulmonary sclerosing hemangioma (PSH). 17 female surgically resected PSH were found. The polygonal cells and surface cuboidal cells of the 17 PSH cases were microdissected from routine hematoxylin and eosin-stained sections. Genomic DNA was extracted, pretreated through incubation with methylation-sensitive restrictive endonuclease HhaI or HpaII, and amplified by nested polymerase chain reaction for X chromosome-linked androgen receptor (AR) and phosphoglycerate kinase (PGK) genes. The length polymorphism of AR gene was demonstrated by denaturing polyacrylamide gel electrophoresis and silver staining. The PGK gene products were treated with Bst XI and resolved on agarose gel. Amongst the 17 female cases of PSH, 15 samples were successfully amplified for AR and PGK genes. The rates of polymorphism were 53% (8/15) and 27% (4/15) for AR and PGK genes respectively. Polygonal cells and surface cuboidal cells of 10 cases which were suitable for clonality study, showed the same loss of alleles (clonality ratio = 0) or unbalanced methylation pattern (clonality ratio < 0.25). The polygonal cells and surface cuboidal cells in PSH demonstrate patterns of monoclonal proliferation, indicating that both represent true neoplastic cells.

Microbial seascapes revisited.

PubMed

DeLong, E F

2001-06-01

A remarkable array of new discoveries is emerging from studies of naturally occurring marine microbes. These discoveries originate from novel applications of evolving technologies, ranging from molecular phylogenetics to stable isotope analyses, to advanced microscopic techniques, to genomics. As a consequence, new perspectives on the natural history of marine microbes, the inseparable nature of the geological and biological worlds, and a plethora of unexpected new genotypes, phenotypes and physiologies are now being revealed. As our observations of naturally occurring microbes become increasingly more sophisticated, so will theory, technical applications and predictive capabilities in microbial ecology.

Pseudomonas putida as a platform for the synthesis of aromatic compounds.

PubMed

Molina-Santiago, Carlos; Cordero, Baldo F; Daddaoua, Abdelali; Udaondo, Zulema; Manzano, Javier; Valdivia, Miguel; Segura, Ana; Ramos, Juan-Luis; Duque, Estrella

2016-09-01

Aromatic compounds such as l-phenylalanine, 2-phenylethanol and trans-cinnamate are aromatic compounds of industrial interest. Current trends support replacement of chemical synthesis of these compounds by 'green' alternatives produced in microbial cell factories. The solvent-tolerant Pseudomonas putida DOT-T1E strain was genetically modified to produce up to 1 g l-1 of l-phenylalanine. In order to engineer this strain, we carried out the following stepwise process: (1) we selected random mutants that are resistant to toxic phenylalanine analogues; (2) we then deleted up to five genes belonging to phenylalanine metabolism pathways, which greatly diminished the internal metabolism of phenylalanine; and (3) in these mutants, we overexpressed the pheAfbr gene, which encodes a recombinant variant of PheA that is insensitive to feedback inhibition by phenylalanine. Furthermore, by introducing new genes, we were able to further extend the diversity of compounds produced. Introduction of histidinol phosphate transferase (PP_0967), phenylpyruvate decarboxylase (kdc) and an alcohol dehydrogenase (adh) enabled the strain to produce up to 180 mg l-1 2-phenylethanol. When phenylalanine ammonia lyase (pal) was introduced, the resulting strain produced up to 200 mg l-1 of trans-cinnamate. These results demonstrate that P. putida can serve as a promising microbial cell factory for the production of l-phenylalanine and related compounds.

Carbon input increases microbial nitrogen demand, but not microbial nitrogen mining in boreal forest soils

NASA Astrophysics Data System (ADS)

Wild, Birgit; Alaei, Saeed; Bengtson, Per; Bodé, Samuel; Boeckx, Pascal; Schnecker, Jörg; Mayerhofer, Werner; Rütting, Tobias

2016-04-01

Plant primary production at mid and high latitudes is often limited by low soil N availability. It has been hypothesized that plants can indirectly increase soil N availability via root exudation, i.e., via the release of easily degradable organic compounds such as sugars into the soil. These compounds can stimulate microbial activity and extracellular enzyme synthesis, and thus promote soil organic matter (SOM) decomposition ("priming effect"). Even more, increased C availability in the rhizosphere might specifically stimulate the synthesis of enzymes targeting N-rich polymers such as proteins that store most of the soil N, but are too large for immediate uptake ("N mining"). This effect might be particularly important in boreal forests, where plants often maintain high primary production in spite of low soil N availability. We here tested the hypothesis that increased C availability promotes protein depolymerization, and thus soil N availability. In a laboratory incubation experiment, we added 13C-labeled glucose to a range of soil samples derived from boreal forests across Sweden, and monitored the release of CO2 by C mineralization, distinguishing between CO2 from the added glucose and from the native, unlabeled soil organic C (SOC). Using a set of 15N pool dilution assays, we further measured gross rates of protein depolymerization (the breakdown of proteins into amino acids) and N mineralization (the microbial release of excess N as ammonium). Comparing unamended control samples, we found a high variability in C and N mineralization rates, even when normalized by SOC content. Both C and N mineralization were significantly correlated to SOM C/N ratios, with high C mineralization at high C/N and high N mineralization at low C/N, suggesting that microorganisms adjusted C and N mineralization rates to the C/N ratio of their substrate and released C or N that was in excess. The addition of glucose significantly stimulated the mineralization of native SOC in soils

Retardation of quality changes in camel meat sausages by phenolic compounds and phenolic extracts.

PubMed

Maqsood, Sajid; Manheem, Kusaimah; Abushelaibi, Aisha; Kadim, Isam Tawfik

2016-11-01

Impact of tannic acid (TA), date seed extract (DSE), catechin (CT) and green tea extract (GTE) on lipid oxidation, microbial load and textural properties of camel meat sausages during 12 days of refrigerated storage was investigated. TA and CT showed higher activities in all antioxidative assays compared to DSE and GTE. Lipid oxidation and microbial growth was higher for control sausages when compared to other samples. TA and CT at a level of 200 mg/kg were more effective in retarding lipid oxidation and lowering microbial count (P < 0.05). Sausages treated with TA and DSE were found to have higher hardness, gumminess and chewiness values compared to other treatments (P < 0.05). Addition of different phenolic compounds or extract did not influence the sensory color of sausages. Furthermore, sensory quality was also found to be superior in TA and CT treated sausages. Therefore, pure phenolic compounds (TA and CT) proved to be more effective in retaining microbial and sensorial qualities of camel meat sausages compared to phenolic extracts (GTE and DSE) over 12 days of storage at 4°C. © 2016 Japanese Society of Animal Science.

[Regarding respiration and the so-called "animal heat." An historical sketch].

PubMed

de Micheli, A

2001-01-01

According to Aristotle and Galen, the essential function of the respiration phenomenon was to cool the blood. Towards the middle of the XVI Century, Miguel Servet suggested, in his treatise Christianismi restitutio..., that the inspired air could have other functions besides cooling the blood. Later, Joseph Black thought that respiration was a combustion. In the light of the advances in chemistry achieved in the XVII Century, the English scientist Adair Crawford and the French chemist Antoine-Laurent Lavoisier conceived, in the second half of that century, the first general and quantitative theories on the origin of animal heat. Both these authors had the conviction that the "inflammable element", which will be called oxygen, was not formed in the pulmonary territory, but could be absorbed by the blood. Oxygen, foreseen by Mayow at the end of XVII Century, was discovered by Joseph Priestley in 1774. Lavoisier gave the name of oxygen to this gas and firmly established that the respiration phenomenon consists essentially in a process of combustion. The mathematician Joseph-Louis Lagrange, native of Turin, suggested that animal heat originates in all breathing tissues. This phenomenon was verified and described in detail by the biologist Lazzaro Spallanzani, professor at the University of Pavia. Dissemination, in the scientific world, of the new chemical nomenclature and of the respiratory theory, closely related to it, was based fundamentally on the works "Méthode de nomenclature chimique..." (1787) and "Traité élémentaire de chimie..." (1789). During the XIX Century, studies on the phenomenon of animal respiration continued and fundamental discoveries in this subject were attained, such as conversion of hemoglobin to oxyhemoglobin once oxygen had been fixed. Now it is possible to study the regulating mechanisms of the energetic metabolism of the myocardium in vivo, which allows decisive interventions in certain cardiopathies, such as in acute ischemic

A Call for Student Involvement in the Push for Assessment

ERIC Educational Resources Information Center

Rodgers, Megan

2011-01-01

As readers of "Assessment Update" know, the call for assessment is sweeping over the globe, so much so that faculty and administrators are finding it difficult to ignore it--though many may wish they could. Unfortunately, awareness does not lead to an increase in assessment implementation because fear of assessment is still widespread. The push…

Nitrogen cycle in microbial mats: completely unknown?

NASA Astrophysics Data System (ADS)

Coban, O.; Bebout, B.

2015-12-01

Microbial mats are thought to have originated around 3.7 billion years ago, most likely in the areas around submarine hydrothermal vents, which supplied a source of energy in the form of reduced chemical species from the Earth's interior. Active hydrothermal vents are also believed to exist on Jupiter's moon Europa, Saturn's moon Enceladus, and on Mars, earlier in that planet's history. Microbial mats have been an important force in the maintenance of Earth's ecosystems and the first photosynthesis was also originated there. Microbial mats are believed to exhibit most, if not all, biogeochemical processes that exist in aquatic ecosystems, due to the presence of different physiological groups of microorganisms therein. While most microbially mediated biogeochemical transformations have been shown to occur within microbial mats, the nitrogen cycle in the microbial mats has received very little study in spite of the fact that nitrogen usually limits growth in marine environments. We will present the first results in the determination of a complete nitrogen budget for a photosynthetic microbial mat. Both in situ sources and sinks of nitrogen in photosynthetic microbial mats are being measured using stable isotope techniques. Our work has a particular focus on recently described, but poorly understood, processes, e.g., anammox and dissimilatory nitrate reduction, and an emphasis on understanding the role that nitrogen cycling may play in generating biogenic nitrogen isotopic signatures and biomarker molecules. Measurements of environmental controls on nitrogen cycling should offer insight into the nature of co-evolution of these microbial communities and their planets of origin. Identifying the spatial (microscale) as well as temporal (diel and seasonal) distribution of nitrogen transformations, e.g., rates of nitrification and denitrification, within mats, particularly with respect to the distribution of photosynthetically-produced oxygen, is anticipated. The results

Power management systems for sediment microbial fuel cells in high power and continuous power applications

NASA Astrophysics Data System (ADS)

Donovan, Conrad Koble

The objective of this dissertation was to develop power management systems (PMS) for sediment microbial fuel cells (SFMCs) for high power and continuous applications. The first part of this dissertation covers a new method for testing the performance of SMFCs. This device called the microbial fuel cell tester was developed to automatically test power generation of PMS. The second part focuses on a PMS capable of delivering high power in burst mode. This means that for a small amount of time a large amount of power up to 2.5 Watts can be delivered from a SMFC only generating mW level power. The third part is aimed at developing a multi-potentiostat laboratory tool that measures the performance at fixed cell potentials of microbial fuel cells so that I can optimize them for use with the PMS. This tool is capable of controlling the anode potential or cathode potential and measuring current of six separate SMFCs simultaneously. By operating multiple potentiostats, I was able to run experiments that find ideal operating conditions for the sediment microbial fuel cells, and also I can optimize the power management system for these conditions. The fourth part of the dissertation is targeting a PMS that was able to operate a sensor continuously which was powered by an SMFC. In pervious applications involving SMFCs, the PMS operated in batch mode. In this PMS, the firmware on the submersible ultrasonic receiver (SUR) was modified for use with my PMS. This integration of PMS and SUR allowed for the continuous operation of the SUR without using a battery. Finally, the last part of the dissertation recommends a scale-up power management system to overcome the linearity scale up issue of SMFCs as future work. Concluding remarks are also added to summarize the goal and focus of this dissertation.

The biodiversity of microbial cytochromes P450.

PubMed

Kelly, Steven L; Lamb, David C; Jackson, Colin J; Warrilow, Andrew G; Kelly, Diane E

2003-01-01

The cytochrome P450 (CYP) superfamily of genes and proteins are well known for their involvement in pharmacology and toxicology, but also increasingly for their importance and diversity in microbes. The extent of diversity has only recently become apparent with the emergence of data from whole genome sequencing projects and the coming years will reveal even more information on the diversity in microbial eukaryotes. This review seeks to describe the historical development of these studies and to highlight the importance of the genes and proteins. CYPs are deeply involved in the development of strategies for deterrence and attraction as well as detoxification. As such, there is intense interest in pathways of secondary metabolism that include CYPs in oxidative tailoring of antibiotics, sometimes influencing potency as bioactive compounds. Further to this is interest in CYPs in metabolism of xenobiotics for use as carbon sources for microbial growth and as biotransformation agents or in bioremediation. CYPs are also current and potential drug targets; compounds inhibiting CYP are antifungal and anti-protozoan agents, and potentially similar compounds may be useful against some bacterial diseases such as tuberculosis. Of note is the diversity of CYP requirements within an organism, ranging from Escherichia coli that has no CYPs as in many bacteria, to Mycobacterium smegmatis that has 40 representing 1% of coding genes. The basidiomycete fungus Phanerochaete chrysosporium surprised all when it was found to contain a hundred or more CYPs. The functional genomic investigation of these orphan CYPs is a major challenge for the future.

Acetobixan, an Inhibitor of Cellulose Synthesis Identified by Microbial Bioprospecting

PubMed Central

Xia, Ye; Lei, Lei; Brabham, Chad; Stork, Jozsef; Strickland, James; Ladak, Adam; Gu, Ying; Wallace, Ian; DeBolt, Seth

2014-01-01

In plants, cellulose biosynthesis is an essential process for anisotropic growth and therefore is an ideal target for inhibition. Based on the documented utility of small-molecule inhibitors to dissect complex cellular processes we identified a cellulose biosynthesis inhibitor (CBI), named acetobixan, by bio-prospecting among compounds secreted by endophytic microorganisms. Acetobixan was identified using a drug-gene interaction screen to sift through hundreds of endophytic microbial secretions for one that caused synergistic reduction in root expansion of the leaky AtcesA6prc1-1 mutant. We then mined this microbial secretion for compounds that were differentially abundant compared with Bacilli that failed to mimic CBI action to isolate a lead pharmacophore. Analogs of this lead compound were screened for CBI activity, and the most potent analog was named acetobixan. In living Arabidopsis cells visualized by confocal microscopy, acetobixan treatment caused CESA particles localized at the plasma membrane (PM) to rapidly re-localize to cytoplasmic vesicles. Acetobixan inhibited 14C-Glc uptake into crystalline cellulose. Moreover, cortical microtubule dynamics were not disrupted by acetobixan, suggesting specific activity towards cellulose synthesis. Previous CBI resistant mutants such as ixr1-2, ixr2-1 or aegeus were not cross resistant to acetobixan indicating that acetobixan targets a different aspect of cellulose biosynthesis. PMID:24748166

Encapsulation of a model compound in pectin delays its release from a biobased polymeric material

USDA-ARS?s Scientific Manuscript database

A model compound was encapsulated in pectin and then extruded with thermoplastic starch to form a composite. The intended product was a food-contact tray made of biobased polymers infused with an anti-microbial agent; however, caffeine was used as the model compound in the preliminary work. The mode...

Engineering microbial chemical factories to produce renewable "biomonomers".

PubMed

Adkins, Jake; Pugh, Shawn; McKenna, Rebekah; Nielsen, David R

2012-01-01

By applying metabolic engineering tools and strategies to engineer synthetic enzyme pathways, the number and diversity of commodity and specialty chemicals that can be derived directly from renewable feedstocks is rapidly and continually expanding. This of course includes a number of monomer building-block chemicals that can be used to produce replacements to many conventional plastic materials. This review aims to highlight numerous recent and important advancements in the microbial production of these so-called "biomonomers." Relative to naturally-occurring renewable bioplastics, biomonomers offer several important advantages, including improved control over the final polymer structure and purity, the ability to synthesize non-natural copolymers, and allowing products to be excreted from cells which ultimately streamlines downstream recovery and purification. To highlight these features, a handful of biomonomers have been selected as illustrative examples of recent works, including polyamide monomers, styrenic vinyls, hydroxyacids, and diols. Where appropriate, examples of their industrial penetration to date and end-product uses are also highlighted. Novel biomonomers such as these are ultimately paving the way toward new classes of renewable bioplastics that possess a broader diversity of properties than ever before possible.

Linkit: A CALL System for Learning Chinese Characters, Words, and Phrases

ERIC Educational Resources Information Center

Shei, Chris; Hsieh, Hsun-Ping

2012-01-01

Teaching Chinese as a foreign language (TCFL) is increasingly becoming a mainstream profession and an independent academic discipline. However, there is little research in CALL targeting the Chinese language to date. This research attempts to show how a CALL system can be constructed following the unique properties of the Chinese language so it…

Effect of sweating set rate on clothing real evaporative resistance determined on a sweating thermal manikin in a so-called isothermal condition (T manikin = T a = T r).

PubMed

Lu, Yehu; Wang, Faming; Peng, Hui; Shi, Wen; Song, Guowen

2016-04-01

The ASTM F2370 (2010) is the only standard with regard to measurement of clothing real evaporative resistance by means of a sweating manikin. However, the sweating set-point is not recommended in the standard. In this study, the effect of sweating rate on clothing real evaporative resistance was investigated on a 34-zone "Newton" sweating thermal manikin in a so-called isothermal condition (T manikin = T a = T r). Four different sweating set rates (i.e., all segments had a sweating rate of 400, 800, 1200 ml/hr ∙ m(2), respectively, and different sweating rates were assigned to different segments) were applied to determine the clothing real evaporative resistance of five clothing ensembles and the boundary air layer. The results indicated that the sweating rate did not affect the real evaporative resistance of clothing ensembles with the absence of strong moisture absorbent layers. For the clothing ensemble with tight cotton underwear, a sweating rate of lower than 400 ml/hr ∙ m(2) is not recommended. This is mainly because the wet fabric "skin" might not be fully saturated and thus led to a lower evaporative heat loss and thereby a higher real evaporative resistance. For vapor permeable clothing, the real evaporative resistance determined in the so-called isothermal condition should be corrected before being used in thermal comfort or heat strain models. However, the reduction of wet thermal insulation due to moisture absorption in different test scenarios had a limited contribution to the effect of sweating rate on the real evaporative resistance.

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.

PubMed

Bergauer, Kristin; Fernandez-Guerra, Antonio; Garcia, Juan A L; Sprenger, Richard R; Stepanauskas, Ramunas; Pachiadaki, Maria G; Jensen, Ole N; Herndl, Gerhard J

2018-01-16

The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm. Copyright © 2018 the Author(s). Published by PNAS.

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

PubMed Central

Bergauer, Kristin; Fernandez-Guerra, Antonio; Garcia, Juan A. L.; Sprenger, Richard R.; Stepanauskas, Ramunas; Pachiadaki, Maria G.; Herndl, Gerhard J.

2018-01-01

The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm. PMID:29255014

Microbial production of value-added nutraceuticals.

PubMed

Wang, Jian; Guleria, Sanjay; Koffas, Mattheos Ag; Yan, Yajun

2016-02-01

Nutraceuticals are important natural bioactive compounds that confer health-promoting and medical benefits to humans. Globally growing demands for value-added nutraceuticals for prevention and treatment of human diseases have rendered nutraceuticals a multi-billion dollar market. However, supply limitations and extraction difficulties from natural sources such as plants, animals or fungi, restrict the large-scale use of nutraceuticals. Metabolic engineering via microbial production platforms has been advanced as an eco-friendly alternative approach for production of value-added nutraceuticals from simple carbon sources. Microbial platforms like the most widely used Escherichia coli and Saccharomyces cerevisiae have been engineered as versatile cell factories for production of diverse and complex value-added chemicals such as phytochemicals, prebiotics, polysaccaharides and poly amino acids. This review highlights the recent progresses in biological production of value-added nutraceuticals via metabolic engineering approaches. Copyright © 2015 Elsevier Ltd. All rights reserved.

Relationships for the impact sensitivities of energetic C-nitro compounds based on bond dissociation energy.

PubMed

Li, Jinshan

2010-02-18

The ZPE-corrected C-NO(2) bond dissociation energies (BDEs(ZPE)) of a series of model C-nitro compounds and 26 energetic C-nitro compounds have been calculated using density functional theory methods. Computed results show that for C-nitro compounds the UB3LYP calculated BDE(ZPE) is less than the UB3P86 using the 6-31G** basis set, and the UB3P86 BDE(ZPE) changes slightly with the basis set varying from 6-31G** to 6-31++G**. For the series of model C-nitro compounds with different chemical skeletons, it is drawn from NBO analysis that the order of BDE(ZPE) is not only in line with that of the NAO bond order but also with that of the energy gap between C-NO(2) bonding and antibonding orbitals. It is found that for the energetic C-nitro compounds whose drop energies (Es(dr)) are below 24.5 J a good linear correlation exists between E(dr) and BDE(ZPE), implying that these compounds ignite through the C-NO(2) dissociation mechanism. After excluding the so-called trinitrotoluene mechanism compounds, a polynomial correlation of ln(E(dr)) with the BDE(ZPE) calculated at density functional theory levels has been established successfully for the 18 C-NO(2) dissociation energetic C-nitro compounds.

Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells

PubMed Central

Sorokin, Anatoly A.; Kiseleva, Larisa; Simpson, David J. W.; Fedorovich, V.; Sharipova, Margarita R.; Kainuma, Mami; Cohen, Michael F.; Goryanin, Igor

2017-01-01

Bioelectrochemical systems such as microbial fuel cells (MFCs) are promising new technologies for efficient removal of organic compounds from industrial wastewaters, including that generated from swine farming. We inoculated two pairs of laboratory-scale MFCs with sludge granules from a beer wastewater-treating anaerobic digester (IGBS) or from sludge taken from the bottom of a tank receiving swine wastewater (SS). The SS-inoculated MFC outperformed the IGBS-inoculated MFC with regard to COD and VFA removal and electricity production. Using a metagenomic approach, we describe the microbial diversity of the MFC planktonic and anodic communities derived from the different inocula. Proteobacteria (mostly Deltaproteobacteria) became the predominant phylum in both MFC anodic communities with amplification of the electrogenic genus Geobacter being the most pronounced. Eight dominant and three minor species of Geobacter were found in both MFC anodic communities. The anodic communities of the SS-inoculated MFCs had a higher proportion of Clostridium and Bacteroides relative to those of the IGBS-inoculated MFCs, which were enriched with Pelobacter. The archaeal populations of the SS- and IGBS-inoculated MFCs were dominated by Methanosarcina barkeri and Methanothermobacter thermautotrophicus, respectively. Our results show a long-term influence of inoculum type on the performance and microbial community composition of swine wastewater-treating MFCs. PMID:29158944

Determination of microbial phenolic acids in human faeces by UPLC-ESI-TQ MS.

PubMed

Sánchez-Patán, Fernando; Monagas, María; Moreno-Arribas, M Victoria; Bartolomé, Begoña

2011-03-23

The aim of the present work was to develop a reproducible, sensitive, and rapid UPLC-ESI-TQ MS analytical method for determination of microbial phenolic acids and other related compounds in faeces. A total of 47 phenolic compounds including hydroxyphenylpropionic, hydroxyphenylacetic, hydroxycinnamic, hydroxybenzoic, and hydroxymandelic acids and simple phenols were considered. To prepare an optimum pool standard solution, analytes were classified in 5 different groups with different starting concentrations according to their MS response. The developed UPLC method allowed a high resolution of the pool standard solution within an 18 min injection run time. The LOD of phenolic compounds ranged from 0.001 to 0.107 μg/mL and LOQ from 0.003 to 0.233 μg/mL. The method precision met acceptance criteria (<15% RSD) for all analytes, and accuracy was >80%. The method was applied to faecal samples collected before and after the intake of a flavan-3-ol supplement by a healthy volunteer. Both external and internal calibration methods were considered for quantification purposes, using 4-hydroxybenzoic-2,3,4,5-d4 acid as internal standard. For most analytes and samples, the level of microbial phenolic acids did not differ by using one or another calibration method. The results revealed an increase in protocatechuic, syringic, benzoic, p-coumaric, phenylpropionic, 3-hydroxyphenylacetic, and 3-hydroxyphenylpropionic acids, although differences due to the intake were only significant for the latter compound. In conclusion, the UPLC-DAD-ESI-TQ MS method developed is suitable for targeted analysis of microbial-derived phenolic metabolites in faecal samples from human intervention or in vitro fermentation studies, which requires high sensitivity and throughput.

Electron beam irradiation of Matricaria chamomilla L. for microbial decontamination

NASA Astrophysics Data System (ADS)

Nemţanu, Monica R.; Kikuchi, Irene Satiko; de Jesus Andreoli Pinto, Terezinha; Mazilu, Elena; Setnic, Silvia; Bucur, Marcela; Duliu, Octavian G.; Meltzer, Viorica; Pincu, Elena

2008-05-01

Wild chamomile (Matricaria chamomilla L.) is one of the most popular herbal materials with both internal and external use to cure different health disturbances. As a consequence of its origin, chamomile could carry various microbial contaminants which offer different hazards to the final consumer. Reduction of the microbial load to the in force regulation limits represents an important phase in the technological process of vegetal materials, and the electron beam treatment might be an efficient alternative to the classical methods of hygienic quality assurance. The purpose of the study was to analyze the potential application of the electron beam treatment in order to assure the microbial safety of the wild chamomile. Samples of chamomile dry inflorescences were treated in electron beam (e-beam) of 6 MeV mean energy, at room temperature and ambient pressure. Some loss of the chemical compounds with bioactive role could be noticed, but the number of microorganisms decreased as a function on the absorbed dose. Consequently, the microbial quality of studied vegetal material inflorescences was improved by e-beam irradiation.

Anti-Adhesive Activity of Cranberry Phenolic Compounds and Their Microbial-Derived Metabolites against Uropathogenic Escherichia coli in Bladder Epithelial Cell Cultures.

PubMed

de Llano, Dolores González; Esteban-Fernández, Adelaida; Sánchez-Patán, Fernando; Martínlvarez, Pedro J; Moreno-Arribas, Maria Victoria; Bartolomé, Begoña

2015-05-27

Cranberry consumption has shown prophylactic effects against urinary tract infections (UTI), although the mechanisms involved are not completely understood. In this paper, cranberry phenolic compounds and their potential microbial-derived metabolites (such as simple phenols and benzoic, phenylacetic and phenylpropionic acids) were tested for their capacity to inhibit the adherence of uropathogenic Escherichia coli (UPEC) ATCC®53503™ to T24 epithelial bladder cells. Catechol, benzoic acid, vanillic acid, phenylacetic acid and 3,4-dihydroxyphenylacetic acid showed anti-adhesive activity against UPEC in a concentration-dependent manner from 100-500 µM, whereas procyanidin A2, widely reported as an inhibitor of UPEC adherence on uroepithelium, was only statistically significant (p < 0.05) at 500 µM (51.3% inhibition). The results proved for the first time the anti-adhesive activity of some cranberry-derived phenolic metabolites against UPEC in vitro, suggesting that their presence in the urine could reduce bacterial colonization and progression of UTI.

REMOVAL OF SO2 FROM INDUSTRIAL WASTE GASES

EPA Science Inventory

The paper discusses technology for sulfur dioxide (SO2) pollution control by flue gas cleaning (called 'scrubbing') in the utility industry, a technology that has advanced significantly during the past 5 years. Federal Regulations are resulting in increasingly large-scale applica...

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells.

PubMed

Rago, Laura; Cristiani, Pierangela; Villa, Federica; Zecchin, Sarah; Colombo, Alessandra; Cavalca, Lucia; Schievano, Andrea

2017-08-01

Dissolved oxygen (DO) at cathodic interface is a critical factor influencing microbial fuel cells (MFC) performance. In this work, three MFCs were operated with cathode under different DO conditions: i) air-breathing (A-MFC); ii) water-submerged (W-MFC) and iii) assisted by photosynthetic microorganisms (P-MFC). A plateau of maximum current was reached at 1.06±0.03mA, 1.48±0.06mA and 1.66±0.04mA, increasing respectively for W-MFC, P-MFC and A-MFC. Electrochemical and microbiological tools (Illumina sequencing, confocal microscopy and biofilm cryosectioning) were used to explore anodic and cathodic biofilm in each MFC type. In all cases, biocathodes improved oxygen reduction reaction (ORR) as compared to abiotic condition and A-MFC was the best performing system. Photosynthetic cultures in the cathodic chamber supplied high DO level, up to 16mg O2 L -1 , which sustained aerobic microbial community in P-MFC biocathode. Halomonas, Pseudomonas and other microaerophilic genera reached >50% of the total OTUs. The presence of sulfur reducing bacteria (Desulfuromonas) and purple non-sulfur bacteria in A-MFC biocathode suggested that the recirculation of sulfur compounds could shuttle electrons to sustain the reduction of oxygen as final electron acceptor. The low DO concentration limited the cathode in W-MFC. A model of two different possible microbial mechanisms is proposed which can drive predominantly cathodic ORR. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial life in a liquid asphalt desert.

PubMed

Schulze-Makuch, Dirk; Haque, Shirin; de Sousa Antonio, Marina Resendes; Ali, Denzil; Hosein, Riad; Song, Young C; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M; Guinan, Edward; Lehto, Harry J; Hallam, Steven J

2011-04-01

Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 10(7) cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

Microbial Life in a Liquid Asphalt Desert

NASA Astrophysics Data System (ADS)

Schulze-Makuch, Dirk; Haque, Shirin; de Sousa Antonio, Marina Resendes; Ali, Denzil; Hosein, Riad; Song, Young C.; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M.; Guinan, Edward; Lehto, Harry J.; Hallam, Steven J.

2011-04-01

Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 107 cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

Construction of PAH-degrading mixed microbial consortia by induced selection in soil.

PubMed

Zafra, German; Absalón, Ángel E; Anducho-Reyes, Miguel Ángel; Fernandez, Francisco J; Cortés-Espinosa, Diana V

2017-04-01

Bioremediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soils through the biostimulation and bioaugmentation processes can be a strategy for the clean-up of oil spills and environmental accidents. In this work, an induced microbial selection method using PAH-polluted soils was successfully used to construct two microbial consortia exhibiting high degradation levels of low and high molecular weight PAHs. Six fungal and seven bacterial native strains were used to construct mixed consortia with the ability to tolerate high amounts of phenanthrene (Phe), pyrene (Pyr) and benzo(a)pyrene (BaP) and utilize these compounds as a sole carbon source. In addition, we used two engineered PAH-degrading fungal strains producing heterologous ligninolytic enzymes. After a previous selection using microbial antagonism tests, the selection was performed in microcosm systems and monitored using PCR-DGGE, CO 2 evolution and PAH quantitation. The resulting consortia (i.e., C1 and C2) were able to degrade up to 92% of Phe, 64% of Pyr and 65% of BaP out of 1000 mg kg -1 of a mixture of Phe, Pyr and BaP (1:1:1) after a two-week incubation. The results indicate that constructed microbial consortia have high potential for soil bioremediation by bioaugmentation and biostimulation and may be effective for the treatment of sites polluted with PAHs due to their elevated tolerance to aromatic compounds, their capacity to utilize them as energy source. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids

NASA Astrophysics Data System (ADS)

Purkamo, Lotta; Bomberg, Malin; Kietäväinen, Riikka; Salavirta, Heikki; Nyyssönen, Mari; Nuppunen-Puputti, Maija; Ahonen, Lasse; Kukkonen, Ilmo; Itävaara, Merja

2016-05-01

The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible "keystone" genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.

Spatio temporal analysis of microbial habitats in soil-root interfaces

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2017-04-01

Microbial habitats in soils are formed by the arrangement and availability of inorganic and organic compounds. They can be characterized by physico-chemical parameters and the resulting colonization by microorganisms. Areas being preferably colonized are known as microbial hot spots which can be found in (bio)pores within the aggregatusphere or in the rhizosphere. The latter is directly influenced by plants i.e. the growth and activity of plant roots which has an influence on physico-chemical dynamics in the rhizosphere and can even shape plants' root microbiome. As microbial communities play an important role in nutrient cycling their response in soil-root interfaces is of great importance. Especially in complex systems such as paddy soils used for the cultivation of wetland rice the analysis of spatio-temporal aspects is important to get knowledge about their influence on the microbial dynamics in the respective habitats. But also other spatial variations on larger scales up to landscape scale may have an impact on the soil microorganisms in their habitats. This PICO presentation will introduce a set of techniques which are useful to analyze both the physico-chemical characteristics of microbial habitats and the microbial colonization and dynamics in soil-root interfaces. Examples will be given on various studies from rice cultivation in different paddy soils up to an European transect representing rhizosphere soils of selected plant species.

So-called massive retinal gliosis: A critical review and reappraisal.

PubMed

Jakobiec, Frederick A; Thanos, Aristomenis; Stagner, Anna M; Grossniklaus, Hans E; Proia, Alan D

2016-01-01

most (an intermediate cytoplasmic filament typically restricted to embryonic and reparative neural tissue). The nonneoplastic nature of all categories of gliosis was confirmed by absent TP53 (tumor suppressor gene) dysregulation, Ki-67 negativity, and intact p16 expression (the protein product of the p16 tumor suppressor gene) in the overwhelming majority of cases. These findings indicate an intrinsic attempt to regulate and maintain a low level of glial cell proliferation that becomes unsuccessful as the disease evolves. The categories of tumoral proliferation appeared to constitute a spectrum. We conclude that focal nodular tumors encompass lesions previously called retinal vasoproliferative lesions, which display the same histopathologic and immunohistochemical findings as 3 major categories of retinal gliosis characterized herein. Copyright © 2016 Elsevier Inc. All rights reserved.

Biofilm-induced bioclogging produces sharp interfaces in hyporheic flow, redox conditions, and microbial community structure

NASA Astrophysics Data System (ADS)

Caruso, Alice; Boano, Fulvio; Ridolfi, Luca; Chopp, David L.; Packman, Aaron

2017-05-01

Riverbed sediments host important biogeochemical processes that play a key role in nutrient dynamics. Sedimentary nutrient transformations are mediated by bacteria in the form of attached biofilms. The influence of microbial metabolic activity on the hydrochemical conditions within the hyporheic zone is poorly understood. We present a hydrobiogeochemical model to assess how the growth of heterotrophic and autotrophic biomass affects the transport and transformation of dissolved nitrogen compounds in bed form-induced hyporheic zones. Coupling between hyporheic exchange, nitrogen metabolism, and biomass growth leads to an equilibrium between permeability reduction and microbial metabolism that yields shallow hyporheic flows in a region with low permeability and high rates of microbial metabolism near the stream-sediment interface. The results show that the bioclogging caused by microbial growth can constrain rates and patterns of hyporheic fluxes and microbial transformation rate in many streams.

Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score

PubMed Central

McDole, Tracey; Nulton, James; Barott, Katie L.; Felts, Ben; Hand, Carol; Hatay, Mark; Lee, Hochul; Nadon, Marc O.; Nosrat, Bahador; Salamon, Peter; Bailey, Barbara; Sandin, Stuart A.; Vargas-Angel, Bernardo; Youle, Merry; Zgliczynski, Brian J.; Brainard, Russell E.; Rohwer, Forest

2012-01-01

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing. PMID:22970122

Assessing coral reefs on a Pacific-wide scale using the microbialization score.

PubMed

McDole, Tracey; Nulton, James; Barott, Katie L; Felts, Ben; Hand, Carol; Hatay, Mark; Lee, Hochul; Nadon, Marc O; Nosrat, Bahador; Salamon, Peter; Bailey, Barbara; Sandin, Stuart A; Vargas-Angel, Bernardo; Youle, Merry; Zgliczynski, Brian J; Brainard, Russell E; Rohwer, Forest

2012-01-01

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing.

Microbial Transformation of Biomacromolecules in a Membrane Bioreactor: Implications for Membrane Fouling Investigation

PubMed Central

Zhou, Zhongbo; Meng, Fangang; Chae, So-Ryong; Huang, Guocheng; Fu, Wenjie; Jia, Xiaoshan; Li, Shiyu; Chen, Guang-Hao

2012-01-01

Background The complex characteristics and unclear biological fate of biomacromolecules (BMM), including colloidal and soluble microbial products (SMP), extracellular polymeric substances (EPS) and membrane surface foulants (MSF), are crucial factors that limit our understanding of membrane fouling in membrane bioreactors (MBRs). Findings In this study, the microbial transformation of BMM was investigated in a lab-scale MBR by well-controlled bioassay tests. The results of experimental measurements and mathematical modeling show that SMP, EPS, and MSF had different biodegradation behaviors and kinetic models. Based on the multi-exponential G models, SMP were mainly composed of slowly biodegradable polysaccharides (PS), proteins (PN), and non-biodegradable humic substances (HS). In contrast, EPS contained a large number of readily biodegradable PN, slowly biodegradable PS and HS. MSF were dominated by slowly biodegradable PS, which had a degradation rate constant similar to that of SMP-PS, while degradation behaviors of MSF-PN and MSF-HS were much more similar to those of EPS-PN and EPS-HS, respectively. In addition, the large-molecular weight (MW) compounds (>100 kDa) in BMM were found to have a faster microbial transformation rate compared to the small-MW compounds (<5 kDa). The parallel factor (PARAFAC) modeling of three-dimensional fluorescence excitation-emission matrix (EEM) spectra showed that the tryptophan-like PN were one of the major fractions in the BMM and they were more readily biodegradable than the HS. Besides microbial mineralization, humification and hydrolysis could be viewed as two important biotransformation mechanisms of large-MW compounds during the biodegradation process. Significance The results of this work can aid in tracking the origin of membrane foulants from the perspective of the biotransformation behaviors of SMP, EPS, and MSF. PMID:22912694

Potential Impact of Microbial Activity on the Oxidant Capacity and the Organic Carbon Budget in Clouds (Invited)

NASA Astrophysics Data System (ADS)

Delort, A.

2013-12-01

Within cloud water, microorganisms are metabolically active; so they are suspected to contribute to atmospheric chemistry. This paper is focused on the interactions between microorganisms and Reactive Oxygenated Species present in cloud water since these chemical compounds are driving the oxidant capacity of the cloud system. For this, real cloud waters with contrasting features (marine, continental, urban) were sampled at the puy de Dôme mountain (France). They exhibit high microbial biodiversity and complex chemical composition. These media were incubated in the dark and subjected to UV-light radiation in specifically designed photo-bio-reactors. The concentrations of hydrogen peroxide (H2O2), organic compounds and the ATP/ADP ratio were monitored during the incubation period. Microorganisms remained metabolically active in the presence of hydroxyl radicals photo-produced from H2O2. This oxidant and major carbon compounds (formaldehyde and carboxylic acids) were biodegraded by the endogenous microflora. This work suggests that microorganisms could play a double role in atmospheric chemistry: first, they could directly metabolize organic carbon species; second they could reduce the available source of radicals due to their oxidative metabolism. Consequently, molecules such as H2O2 would be no longer available for photochemical or other chemical reactions, decreasing the cloud oxidant capacity.

Dynamics of soil organic carbon and microbial activity in treated wastewater irrigated agricultural soils along soil profiles

NASA Astrophysics Data System (ADS)

Jüschke, Elisabeth; Marschner, Bernd; Chen, Yona; Tarchitzky, Jorge

2010-05-01

Treated wastewater (TWW) is an important source for irrigation water in arid and semiarid regions and already serves as an important water source in Jordan, the Palestinian Territories and Israel. Reclaimed water still contains organic matter (OM) and various compounds that may effect microbial activity and soil quality (Feigin et al. 1991). Natural soil organic carbon (SOC) may be altered by interactions between these compounds and the soil microorganisms. This study evaluates the effects of TWW irrigation on the quality, dynamics and microbial transformations of natural SOC. Priming effects (PE) and SOC mineralization were determined to estimate the influence of TWW irrigation on SOC along soil profiles of agricultural soils in Israel and the Westbank. The used soil material derived from three different sampling sites allocated in Israel and The Palestinian Authority. Soil samples were taken always from TWW irrigated sites and control fields from 6 different depths (0-10, 10-20, 20-30, 30-50, 50-70, 70-100 cm). Soil carbon content and microbiological parameters (microbial biomass, microbial activities and enzyme activities) were investigated. In several sites, subsoils (50-160 cm) from TWW irrigated plots were depleted in soil organic matter with the largest differences occurring in sites with the longest TWW irrigation history. Laboratory incubation experiments with additions of 14C-labelled compounds to the soils showed that microbial activity in freshwater irrigated soils was much more stimulated by sugars or amino acids than in TWW irrigated soils. The lack of such "priming effects" (Hamer & Marschner 2005) in the TWW irrigated soils indicates that here the microorganisms are already operating at their optimal metabolic activity due to the continuous substrate inputs with soluble organic compounds from the TWW. The fact that PE are triggered continuously due to TWW irrigation may result in a decrease of SOC over long term irrigation. Already now this could be

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

PubMed Central

Walsh, Aaron M.; Crispie, Fiona; Kilcawley, Kieran; O’Sullivan, Orla; O’Sullivan, Maurice G.; Claesson, Marcus J.

2016-01-01

ABSTRACT Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to

Microbial Murders Crime Scene Investigation: An Active Team-Based Learning Project that Enhances Student Enthusiasm and Comprehension of Clinical Microbial Pathogens.

PubMed

Steel, J Jordan

2017-01-01

Microbial disease knowledge is a critical component of microbiology courses and is beneficial for many students' future careers. Microbiology courses traditionally cover core concepts through lectures and labs, but specific instruction on microbial diseases varies greatly depending on the instructor and course. A common project involves students researching and presenting a disease to the class. This method alone is not very effective, and course evaluations have consistently indicated that students felt they lacked adequate disease knowledge; therefore, a more hands-on and interactive disease project was developed called Microbial Murders. For this team-based project, a group of students chooses a pathogen, researches the disease, creates a "mugshot" of the pathogen, and develops a corresponding "crime scene," where a hypothetical patient has died from the microbe. Each group gives a presentation introducing the microbial pathogen, signs/symptoms, treatments, and overall characteristics. The students then visit each other's crime scenes to match the pathogen with the correct crime scene by critically thinking through the clues. This project has shown remarkable success. Surveys indicate that 73% of students thought the project helped them understand the material and 84% said it was worth their time. Student participation, excitement, understanding, and application of microbial disease knowledge have increased and are evident through an increase in course evaluations and in student assessment scores. This project is easy to implement and can be used in a wide variety of biology, microbiology, or health classes for any level (middle school through college).

SEE: improving nurse-patient communications and preventing software piracy in nurse call applications.

PubMed

Unluturk, Mehmet S

2012-06-01

Nurse call system is an electrically functioning system by which patients can call upon from a bedside station or from a duty station. An intermittent tone shall be heard and a corridor lamp located outside the room starts blinking with a slow or a faster rate depending on the call origination. It is essential to alert nurses on time so that they can offer care and comfort without any delay. There are currently many devices available for a nurse call system to improve communication between nurses and patients such as pagers, RFID (radio frequency identification) badges, wireless phones and so on. To integrate all these devices into an existing nurse call system and make they communicate with each other, we propose software client applications called bridges in this paper. We also propose a window server application called SEE (Supervised Event Executive) that delivers messages among these devices. A single hardware dongle is utilized for authentication and copy protection for SEE. Protecting SEE with securities provided by dongle only is a weak defense against hackers. In this paper, we develop some defense patterns for hackers such as calculating checksums in runtime, making calls to dongle from multiple places in code and handling errors properly by logging them into database.

Synthesis and biological evaluation of (E)-1-(substituted)-3-phenylprop-2-en-1-ones bearing rhodanines as potent anti-microbial agents.

PubMed

Song, Ming-Xia; Deng, Xian-Qing; Li, Ya-Ru; Zheng, Chang-Ji; Hong, Lan; Piao, Hu-Ri

2014-10-01

Herein, we report the design, syntheses and in vitro anti-microbial activity of two series of rhodanines with chalcone moiety. Anti-microbial tests showed that some of the synthesized compounds exhibited good inhibition (MIC = 1-8 µg/mL) against multi-drug-resistant Gram-positive organisms, including methicillin resistant and quinolone-resistant Staphylococcus aureus, in which the compound 4g was found to be the most potent with minimum inhibitory concentration (MIC) value of 1 µg/mL against two methicillin-resistant S. aureus.

Research progress of microbial corrosion of reinforced concrete structure

NASA Astrophysics Data System (ADS)

Li, Shengli; Li, Dawang; Jiang, Nan; Wang, Dongwei

2011-04-01

Microbial corrosion of reinforce concrete structure is a new branch of learning. This branch deals with civil engineering , environment engineering, biology, chemistry, materials science and so on and is a interdisciplinary area. Research progress of the causes, research methods and contents of microbial corrosion of reinforced concrete structure is described. The research in the field is just beginning and concerted effort is needed to go further into the mechanism of reinforce concrete structure and assess the security and natural life of reinforce concrete structure under the special condition and put forward the protective methods.

Influence of Pig Slurry on Microbial and Biochemical Characteristics of Soil in Albacete Region, SE Spain

NASA Astrophysics Data System (ADS)

Halil Yanardaǧ, Ibrahim

2013-04-01

Soil quality is very important in terms of agricultural sustainability, ecosystem and terrestrial carbon (C) cycle. In turn, soil microbial and biochemical characteristics are indicative of nutrient cycling and soil organic matter dynamics. We investigated the effects of the pig slurries (raw pig slurry (RPS) and treated pig slurry (TPS) from liquid and solid feeding diets) on microbial and biochemical characteristics of soil under barley cropping system. Application doses of slurries are identified with legal doses of Castilla La Mancha Region, which is 210 kg N ha-1 year-1. Microbial biomass C, soluble C, black C and three soil enzymes (β-Glucosidase, β-galactosidase and Arylesterase enzymes) are studied to determine effect slurry on soil biochemical characteristics, which are very important in terms of C cycle in soil. Black carbon content and β-Glucosidase enzyme activities are increased with all pig slurry applications from liquid and traditional feeding diet, as well as microbial biomass and organic carbon content and β-galactosidase enzyme activities are increased with slurry from liquid feeding diet doses. However, pig slurry application from liquid feeding diet doses have increased yield, quality, length and total biomass content of barley. Bioavailable metal contents are increased with all slurry application and with using high doses of slurry can be caused soil pollution. Pig slurries from liquid feeding diet had positive impacts on microbial and biochemical characteristics in terms of soil quality in comparison to the different feeding diets. PS addition to soil had a very significant stimulating effect on the enzyme activities, microbial biomass, soluble and black C compared with different kind of PS and control plots on Mediterranean soil in barley monoculture. This effect may originate from the organic C, N, P and S compounds added with PS. The highest enzyme activity and microbial biomass were observed on the soil samples from the RPS treatment

Microbial volatile organic compound emissions from Stachybotrys chartarum growing on gypsum wallboard and ceiling tile

PubMed Central

2013-01-01

Background Stachybotrys chartarum is a filamentous mold frequently identified among the mycobiota of water-damaged building materials. Growth of S. chartarum on suitable substrates and under favorable environmental conditions leads to the production of secondary metabolites such as mycotoxins and microbial volatile organic compounds (MVOCs). The aim of this study was to characterize MVOC emission profiles of seven toxigenic strains of S. chartarum, isolated from water-damaged buildings, in order to identify unique MVOCs generated during growth on gypsum wallboard and ceiling tile coupons. Inoculated coupons were incubated and monitored for emissions and growth using a closed glass environmental growth chamber maintained at a constant room temperature. Gas samples were collected from the headspace for three to four weeks using Tenax TA tubes. Results Most of the MVOCs identified were alcohols, ketones, ethers and esters. The data showed that anisole (methoxybenzene) was emitted from all of the S. chartarum strains tested on both types of substrates. Maximum anisole concentration was detected after seven days of incubation. Conclusions MVOCs are suitable markers for fungal identification because they easily diffuse through weak barriers like wallpaper, and could be used for early detection of mold growth in hidden cavities. This study identifies the production of anisole by seven toxigenic strains of Stachybotrys chartarum within a period of one week of growth on gypsum wallboard and ceiling tiles. These data could provide useful information for the future construction of a robust MVOC library for the early detection of this mold. PMID:24308451

Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems

PubMed Central

Decho, Alan W.; Gutierrez, Tony

2017-01-01

Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured ‘biofilm’ communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called ‘marine snow.’ Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range of molecular sizes, conformations and physical/chemical properties, and polysaccharides, proteins, lipids, and even nucleic acids are actively secreted components. Interestingly, however, the physical ultrastructure of how individual EPS interact with each other is poorly understood. Together, the EPS matrix molecules form a three-dimensional architecture from which cells may localize extracellular activities and conduct cooperative/antagonistic interactions that cannot be accomplished efficiently by free-living cells. EPS alter optical signatures of sediments and seawater, and are involved in biogeomineral precipitation and the construction of microbial macrostructures, and horizontal-transfers of genetic information. In the water-column, they contribute to the formation of marine snow, transparent exopolymer particles (TEPs), sea-surface microlayer biofilm, and marine oil snow. Excessive production of EPS occurs during later-stages of phytoplankton blooms as an excess metabolic by product and releases a carbon pool that transitions among dissolved-, colloidal-, and gel-states. Some EPS are highly labile carbon forms, while other forms appear quite refractory to degradation. Emerging studies suggest that EPS contribute to

Bioactive natural products from novel microbial sources.

PubMed

Challinor, Victoria L; Bode, Helge B

2015-09-01

Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics. © 2015 New York Academy of Sciences.

Therapeutic Potential of Plants as Anti-microbials for Drug Discovery

PubMed Central

Perumal Samy, Ramar

2010-01-01

The uses of traditional medicinal plants for primary health care have steadily increased worldwide in recent years. Scientists are in search of new phytochemicals that could be developed as useful anti-microbials for treatment of infectious diseases. Currently, out of 80% of pharmaceuticals derived from plants, very few are now being used as anti-microbials. Plants are rich in a wide variety of secondary metabolites that have found anti-microbial properties. This review highlights the current status of traditional medicine, its contribution to modern medicine, recent trends in the evaluation of anti-microbials with a special emphasis upon some tribal medicine, in vitro and in vivo experimental design for screening, and therapeutic efficacy in safety and human clinical trails for commercial outlet. Many of these commercially available compounds are crude preparations administered without performing human clinical trials. Recent methods are useful to standardize the extraction for scientific investigation of new phytochemicals and anti-microbials of traditionally used plants. It is concluded that once the local ethnomedical preparations of traditional sources are scientifically evaluated before dispensing they should replace existing drugs commonly used for the therapeutic treatment of infection. This method should be put into practice for future investigations in the field of ethnopharmacology, phytochemistry, ethnobotany and other biological fields for drug discovery. PMID:18955349

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract

NASA Astrophysics Data System (ADS)

Li, Dongyao; Chen, Haiqin; Mao, Bingyong; Yang, Qin; Zhao, Jianxin; Gu, Zhennan; Zhang, Hao; Chen, Yong Q.; Chen, Wei

2017-04-01

As a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities.

Microbial Metabolism in Serpentinite Fluids

NASA Astrophysics Data System (ADS)

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

Harmonisation of microbial sampling and testing methods for distillate fuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, G.C.; Hill, E.C.

1995-05-01

Increased incidence of microbial infection in distillate fuels has led to a demand for organisations such as the Institute of Petroleum to propose standards for microbiological quality, based on numbers of viable microbial colony forming units. Variations in quality requirements, and in the spoilage significance of contaminating microbes plus a tendency for temporal and spatial changes in the distribution of microbes, makes such standards difficult to implement. The problem is compounded by a diversity in the procedures employed for sampling and testing for microbial contamination and in the interpretation of the data obtained. The following paper reviews these problems andmore » describes the efforts of The Institute of Petroleum Microbiology Fuels Group to address these issues and in particular to bring about harmonisation of sampling and testing methods. The benefits and drawbacks of available test methods, both laboratory based and on-site, are discussed.« less

Population density controls on microbial pollution across the Ganga catchment.

PubMed

Milledge, D G; Gurjar, S K; Bunce, J T; Tare, V; Sinha, R; Carbonneau, P E

2018-01-01

For millions of people worldwide, sewage-polluted surface waters threaten water security, food security and human health. Yet the extent of the problem and its causes are poorly understood. Given rapid widespread global urbanisation, the impact of urban versus rural populations is particularly important but unknown. Exploiting previously unpublished archival data for the Ganga (Ganges) catchment, we find a strong non-linear relationship between upstream population density and microbial pollution, and predict that these river systems would fail faecal coliform standards for irrigation waters available to 79% of the catchment's 500 million inhabitants. Overall, this work shows that microbial pollution is conditioned by the continental-scale network structure of rivers, compounded by the location of cities whose growing populations contribute c. 100 times more microbial pollutants per capita than their rural counterparts. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

13C-DEPLETED MICROBIAL LIPIDS INDICATE SEASONAL METHANOTROPHIC ACTIVITY IN SHALLOW ESTUARINE SEDIMENTS

EPA Science Inventory

Compound specific isotope analysis was combined with phospholipid fatty acid (PLFA) analysis to identify methanotrophic activity in members of the sedimentary microbial community in the Altamaha and Savannah River estuaries in Georgia. 13C-depleted PLFAs indicate methane utilizat...

Antimicrobial Compounds from Eukaryotic Microalgae against Human Pathogens and Diseases in Aquaculture

PubMed Central

Falaise, Charlotte; François, Cyrille; Travers, Marie-Agnès; Morga, Benjamin; Haure, Joël; Tremblay, Réjean; Turcotte, François; Pasetto, Pamela; Gastineau, Romain; Hardivillier, Yann; Leignel, Vincent; Mouget, Jean-Luc

2016-01-01

The search for novel compounds of marine origin has increased in the last decades for their application in various areas such as pharmaceutical, human or animal nutrition, cosmetics or bioenergy. In this context of blue technology development, microalgae are of particular interest due to their immense biodiversity and their relatively simple growth needs. In this review, we discuss about the promising use of microalgae and microalgal compounds as sources of natural antibiotics against human pathogens but also about their potential to limit microbial infections in aquaculture. An alternative to conventional antibiotics is needed as the microbial resistance to these drugs is increasing in humans and animals. Furthermore, using natural antibiotics for livestock could meet the consumer demand to avoid chemicals in food, would support a sustainable aquaculture and present the advantage of being environmentally friendly. Using natural and renewable microalgal compounds is still in its early days, but considering the important research development and rapid improvement in culture, extraction and purification processes, the valorization of microalgae will surely extend in the future. PMID:27598176

Geobacter strains that use alternate organic compounds, methods of making, and methods of use thereof

DOEpatents

Lovley, Derek R.; Summers, Zarath Morgan; Haveman, Shelley Annette; Izallalen, Mounir

2016-03-01

In preferred embodiments, the present invention provides new isolated strains of a Geobacter species that are capable of using a carbon source that is selected from C.sub.3 to C.sub.12 organic compounds selected from pyruvate or metabolic precursors of pyruvate as an electron donor in metabolism and in subsequent energy production. The wild type strain of the microorganisms has been shown to be unable to use these C.sub.3 to C.sub.12 organic compounds as electron donors. The inventive strains of microorganisms are useful for improving bioremediation applications, including in situ bioremediation (including uranium bioremediation and halogenated solvent bioremediation), microbial fuel cells, power generation from small and large-scale waste facilities (e.g., biomass waste from dairy, agriculture, food processing, brewery, or vintner industries, etc.) using microbial fuel cells, and other applications of microbial fuel cells, including, but not limited to, improved electrical power supplies for environmental sensors, electronic devices, and electric vehicles.

A review on the applications of microbial electrolysis cells in anaerobic digestion.

PubMed

Yu, Zhengsheng; Leng, Xiaoyun; Zhao, Shuai; Ji, Jing; Zhou, Tuoyu; Khan, Aman; Kakde, Apurva; Liu, Pu; Li, Xiangkai

2018-05-01

Anaerobic digestion (AD) has been widely used for biogas or biofuel generation from waste treatment. Because a low production rate and instability of AD occur frequently, various technologies have been applied to improvement of AD. Microbial electrolysis cells (MECs), an emerging technology, can convert organic matter into hydrogen, methane, and other value-added products. Recent studies showed that application of MEC to AD (MEC-AD) can accelerate degradation of a substrate (including recalcitrant compounds) and alter AD microbial community by enriching exoelectrogens and methanogens thus increasing biogas production. With stable microbial communities established, improvement of MEC-AD for methane production was achieved. MEC-AD process can be monitored in real-time by detecting electric signals, which linearly correlate with substrate concentrations. This review attempts to evaluate interactions among the decomposition of substrates, MEC-AD system, and the microbial community. This analysis should provide useful insights into the improvement of methane production and the performance of MEC-AD. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hydrolytic microbial communities in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Manucharova, Natalia; Chernov, Timofey; Kolcova, Ekaterina; Zelezova, Alena; Lukacheva, Euhenia; Zenova, Galina

2014-05-01

Hydrolytic microbial communities in terrestrial ecosystems Manucharova N.A., Chernov T.I., Kolcova E.M., Zelezova A.D., Lukacheva E.G. Lomonosov Moscow State University, Russia Vertical differentiation of terrestrial biogeocenoses is conditioned by the formation of vertical tiers that differ considerably in the composition and structure of microbial communities. All the three tiers, phylloplane, litter and soil, are united by a single flow of organic matter, and are spatially separated successional stages of decomposition of organic substances. Decomposition of organic matter is mainly due to the activity of microorganisms producing enzymes - hydrolase and lyase - which destroy complex organic compounds. Application of molecular biological techniques (FISH) in environmental studies provides a more complete information concerning the taxonomic diversity and potential hydrolytic activity of microbial complexes of terrestrial ecosystems that exist in a wide range of environmental factors (moisture, temperature, redox potential, organic matter). The combination of two molecular biological techniques (FISH and DGGE-analysis of fragments of gene 16S rRNA total amplificate) enables an informative assessment of the differences in the structure of dominant and minor components of hydrolytic complexes formed in different tiers of terrestrial ecosystems. The functional activity of hydrolytic microbial complexes of terrestrial ecosystems is determined by the activity of dominant and minor components, which also have a high gross enzymatic activity. Degradation of biopolymers in the phylloplane is mainly due to the representatives of the Proteobacteria phylogenetic group (classes alpha and beta). In mineral soil horizons, the role of hydrolytic representatives of Firmicutes and Actinobacteria increases. Among the key environmental parameters that determine the functional activity of the hydrolytic (chitinolytic) complex of soil layer (moisture, nutrient supply, successional

Microbial transformation of ginsenoside Rb1 to compound K by Lactobacillus paralimentarius.

PubMed

Quan, Lin-Hu; Kim, Yeon-Ju; Li, Guan Hao; Choi, Kwang-Tea; Yang, Deok-Chun

2013-06-01

In this study, the major ginsenoside Rb1 was transformed into the more pharmacologically active minor compound K by food grade Lactobacillus paralimentarius LH4, which was isolated from kimchi, a traditional Korean fermented food. The enzymatic reaction was analyzed by TLC, HPLC, and NMR. Using the cell-free enzyme of Lactobacillus paralimentarius LH4 at optimal conditions for 30 °C at pH 6.0, 1.0 mg ml(-1) ginsenoside Rb1 was transformed into 0.52 mg ml(-1) compound K within 72 h, with a corresponding molar conversion yield of 88 %. The cell-free enzyme hydrolyzed the two glucose moieties attached to the C-3 position and the outer glucose moiety attached to the C-20 position of the ginsenoside Rb1. The cell-free enzyme hydrolyzed the ginsenoside Rb1 along the following pathway: ginsenoside Rb1 → gypenoside XVII and ginsenoside Rd → ginsenoside F2 → compound K. Our results indicate that Lactobacillus paralimentarius LH4 has the potential to be applied for the preparation of compound K in the food industry.

The role of microbial reductive dechlorination of TCE at a phytoremediation site

USGS Publications Warehouse

Godsy, E.M.; Warren, E.; Paganelli, V.V.

2003-01-01

In April 1996, a phytoremediation field demonstration site at the Naval Air Station, Fort Worth, Texas, was developed to remediate shallow oxic ground water (< 3.7 m deep) contaminated with chlorinated ethenes. Microbial populations were sampled in February and June 1998. The populations under the newly planted cottonwood trees had not yet matured to an anaerobic community that could dechlorinate trichloroethene (TCE) to cis-1,2-dichloroethene (DCE); however, the microbial population under a mature (???22-year-old) cottonwood tree about 30 m southwest of the plantings had a mature anaerobic population capable of dechlorinating TCE to DCE, and DCE to vinyl chloride (VC). Oxygen-free sediment incubations with contaminated groundwater also demonstrated that resident microorganisms were capable of the dechlorination of TCE to DCE. This suggests that a sufficient amount of organic material is present for microbial dechlorination in aquifer microniches where dissolved O2 concentrations are low. Phenol, benzoic acid, acetic acid, and a cyclic hydrocarbon, compounds consistent with the degradation of root exudates and complex aromatic compounds, were identified by gas chromatography/mass spectrometry (GC/MS) in sediment samples under the mature cottonwood tree. Elsewhere at the site, transpiration and degradation by the cottonwood trees appears to be responsible for loss of chlorinated ethenes.

A fungal metallo-beta-lactamase necessary for biotransformation of maize phytoprotectant compounds

USDA-ARS?s Scientific Manuscript database

Xenobiotic compounds such as phytochemicals, microbial metabolites, and agrochemicals can impact the diversity and frequency of fungal species occurring in agricultural environments. Resistance to xenobiotics may allow plant pathogenic fungi to dominate the overall fungal community, with potential ...

Biodiversity of genes encoding anti-microbial traits within plant associated microbes

PubMed Central

Mousa, Walaa K.; Raizada, Manish N.

2015-01-01

The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters. PMID:25914708

The importance of anabolism in microbial control over soil carbon storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 catabolismmore » 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.« less

Acetogenic microbial degradation of vinyl chloride

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.

2000-01-01

Under methanogenic conditions, microbial degradation of [1,2-14C]vinyl chloride (VC) resulted in significant (14 ?? 3% maximum recovery) but transient recovery of radioactivity as 14C-acetate. Subsequently, 14C- acetate was degraded to 14CH4 and 14CO2 (18 ?? 2% and 54 ?? 3% final recoveries, respectively). In contrast, under 2-bromoethanesulfonic acid (BES) amended conditions, 14C-acetate recovery remained high (27 ?? 1% maximum recovery) throughout the study, no 14CH4 was produced, and the final recovery of 14CO2 was only 35 ?? 4%. These results demonstrate that oxidative acetogenesis may be an important mechanism for anaerobic VC biodegradation. Moreover, these results (1) demonstrate that microbial degradation of VC to CH4 and CO2 may involve oxidative acetogenesis followed by acetotrophic methanogenesis and (2) suggest that oxidative acetogenesis may be the initial step in the net oxidation of VC to CO2 reported previously under Fe(III)-reducing, SO4-reducing, and humic acids- reducing conditions.Under methanogenic conditions, microbial degradation of [1,2-14C]vinyl chloride (VC) resulted in significant (14 ?? 3% maximum recovery) but transient recovery of radioactivity as 14C-acetate. Subsequently, 14C-acetate was degraded to 14CH4 and 14CO2 (18 ?? 2% and 54 ?? 3% final recoveries respectively). In contrast, under 2-bromoethanesulfonic acid (BES) amended conditions, 14C-acetate recovery remained high (27 ?? 1% maximum recovery) throughout the study, no 14CH4 was produced, and the final recovery of 14CO2 was only 35 ?? 4%. These results demonstrate that oxidative acetogenesis may be an important mechanism for anaerobic VC biodegradation. Moreover, these results (1) demonstrate that microbial degradation of VC to CH4 and CO2 may involve oxidative acetogenesis followed by acetotrophic methanogenesis and (2) suggest that oxidative acetogenesis may be the initial step in the net oxidation of VC to CO2 reported previously under Fe(III)-reducing, SO4-reducing, and

Effects of Ga substitution on the structural and magnetic properties of half metallic Fe{sub 2}MnSi Heusler compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pedro, S. S., E-mail: sandrapedro@uerj.br; Caraballo Vivas, R. J.; Andrade, V. M.

2015-01-07

The so-called half-metallic magnets have been proposed as good candidates for spintronic applications due to the feature of exhibiting a hundred percent spin polarization at the Fermi level. Such materials follow the Slater-Pauling rule, which relates the magnetic moment with the valence electrons in the system. In this paper, we study the bulk polycrystalline half-metallic Fe{sub 2}MnSi Heusler compound replacing Si by Ga to determine how the Ga addition changes the magnetic, the structural, and the half-metal properties of this compound. The material does not follow the Slater-Pauling rule, probably due to a minor structural disorder degree in the system,more » but a linear dependence on the magnetic transition temperature with the valence electron number points to the half-metallic behavior of this compound.« less

Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure.

PubMed

Aydin, Sevcan

2016-06-01

As a result of developments in molecular technologies and the use of sequencing technologies, the analyses of the anaerobic microbial community in biological treatment process has become increasingly prevalent. This review examines the ways in which microbial sequencing methods can be applied to achieve an extensive understanding of the phylogenetic and functional characteristics of microbial assemblages in anaerobic reactor if the substrate is contaminated by antibiotics which is one of the most important toxic compounds. It will discuss some of the advantages and disadvantages associated with microbial sequencing techniques that are more commonly employed and will assess how a combination of the existing methods may be applied to develop a more comprehensive understanding of microbial communities and improve the validity and depth of the results for the enhancement of the stability of anaerobic reactors.

Designing the Microbial Research Commons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uhlir, Paul F.

Recent decades have witnessed an ever-increasing range and volume of digital data. All elements of the pillars of science--whether observation, experiment, or theory and modeling--are being transformed by the continuous cycle of generation, dissemination, and use of factual information. This is even more so in terms of the re-using and re-purposing of digital scientific data beyond the original intent of the data collectors, often with dramatic results. We all know about the potential benefits and impacts of digital data, but we are also aware of the barriers, the challenges in maximizing the access, and use of such data. There ismore » thus a need to think about how a data infrastructure can enhance capabilities for finding, using, and integrating information to accelerate discovery and innovation. How can we best implement an accessible, interoperable digital environment so that the data can be repeatedly used by a wide variety of users in different settings and with different applications? With this objective: to use the microbial communities and microbial data, literature, and the research materials themselves as a test case, the Board on Research Data and Information held an International Symposium on Designing the Microbial Research Commons at the National Academy of Sciences in Washington, DC on 8-9 October 2009. The symposium addressed topics such as models to lower the transaction costs and support access to and use of microbiological materials and digital resources from the perspective of publicly funded research, public-private interactions, and developing country concerns. The overall goal of the symposium was to stimulate more research and implementation of improved legal and institutional models for publicly funded research in microbiology.« less

Hailstones: a window into the microbial and chemical inventory of a storm cloud.

PubMed

Šantl-Temkiv, Tina; Finster, Kai; Dittmar, Thorsten; Hansen, Bjarne Munk; Thyrhaug, Runar; Nielsen, Niels Woetmann; Karlson, Ulrich Gosewinkel

2013-01-01

Storm clouds frequently form in the summer period in temperate climate zones. Studies on these inaccessible and short-lived atmospheric habitats have been scarce. We report here on the first comprehensive biogeochemical investigation of a storm cloud using hailstones as a natural stochastic sampling tool. A detailed molecular analysis of the dissolved organic matter in individual hailstones via ultra-high resolution mass spectrometry revealed the molecular formulae of almost 3000 different compounds. Only a small fraction of these compounds were rapidly biodegradable carbohydrates and lipids, suitable for microbial consumption during the lifetime of cloud droplets. However, as the cloud environment was characterized by a low bacterial density (Me = 1973 cells/ml) as well as high concentrations of both dissolved organic carbon (Me = 179 µM) and total dissolved nitrogen (Me = 30 µM), already trace amounts of easily degradable organic compounds suffice to support bacterial growth. The molecular fingerprints revealed a mainly soil origin of dissolved organic matter and a minor contribution of plant-surface compounds. In contrast, both the total and the cultivable bacterial community were skewed by bacterial groups (γ-Proteobacteria, Sphingobacteriales and Methylobacterium) that indicated the dominance of plant-surface bacteria. The enrichment of plant-associated bacterial groups points at a selection process of microbial genera in the course of cloud formation, which could affect the long-distance transport and spatial distribution of bacteria on Earth. Based on our results we hypothesize that plant-associated bacteria were more likely than soil bacteria (i) to survive the airborne state due to adaptations to life in the phyllosphere, which in many respects matches the demands encountered in the atmosphere and (ii) to grow on the suitable fraction of dissolved organic matter in clouds due to their ecological strategy. We conclude that storm clouds are

Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud

PubMed Central

Šantl-Temkiv, Tina; Finster, Kai; Dittmar, Thorsten; Hansen, Bjarne Munk; Nielsen, Niels Woetmann; Karlson, Ulrich Gosewinkel

2013-01-01

Storm clouds frequently form in the summer period in temperate climate zones. Studies on these inaccessible and short-lived atmospheric habitats have been scarce. We report here on the first comprehensive biogeochemical investigation of a storm cloud using hailstones as a natural stochastic sampling tool. A detailed molecular analysis of the dissolved organic matter in individual hailstones via ultra-high resolution mass spectrometry revealed the molecular formulae of almost 3000 different compounds. Only a small fraction of these compounds were rapidly biodegradable carbohydrates and lipids, suitable for microbial consumption during the lifetime of cloud droplets. However, as the cloud environment was characterized by a low bacterial density (Me = 1973 cells/ml) as well as high concentrations of both dissolved organic carbon (Me = 179 µM) and total dissolved nitrogen (Me = 30 µM), already trace amounts of easily degradable organic compounds suffice to support bacterial growth. The molecular fingerprints revealed a mainly soil origin of dissolved organic matter and a minor contribution of plant-surface compounds. In contrast, both the total and the cultivable bacterial community were skewed by bacterial groups (γ-Proteobacteria, Sphingobacteriales and Methylobacterium) that indicated the dominance of plant-surface bacteria. The enrichment of plant-associated bacterial groups points at a selection process of microbial genera in the course of cloud formation, which could affect the long-distance transport and spatial distribution of bacteria on Earth. Based on our results we hypothesize that plant-associated bacteria were more likely than soil bacteria (i) to survive the airborne state due to adaptations to life in the phyllosphere, which in many respects matches the demands encountered in the atmosphere and (ii) to grow on the suitable fraction of dissolved organic matter in clouds due to their ecological strategy. We conclude that storm clouds are

Biodegradable alternative for removing toxic compounds from sugarcane bagasse hemicellulosic hydrolysates for valorization in biorefineries.

PubMed

Silva-Fernandes, T; Santos, J C; Hasmann, F; Rodrigues, R C L B; Izario Filho, H J; Felipe, M G A

2017-11-01

Among the major challenges for hemicellulosic hydrolysate application in fermentative processes, there is the presence of toxic compounds generated during the pretreatment of the biomass, which can inhibit microbial growth. Therefore, the development of efficient, biodegradable and cost-effective detoxification methods for lignocellulosic hydrolysates is crucial. In this work, two tannin-based biopolymers (called A and B) were tested in the detoxification of sugarcane bagasse hydrolysate for subsequent fermentation by Candida guilliermondii. The effects of biopolymer concentration, pH, temperature, and contact time were studied using a 2 4 experimental design for both biopolymers. Results revealed that the biopolymer concentration and the pH were the most significant factors in the detoxification step. Biopolymer A removed phenolics, 5-hydroxymethylfurfural, and nickel from the hydrolysate more efficiently than biopolymer B, while biopolymer B was efficient to remove chromium at 15% (v/v). Detoxification enhanced the fermentation of sugarcane bagasse hydrolysate, and the biopolymers showed different influences on the process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diagnosing gastrointestinal illnesses using fecal headspace volatile organic compounds

PubMed Central

Chan, Daniel K; Leggett, Cadman L; Wang, Kenneth K

2016-01-01

Volatile organic compounds (VOCs) emitted from stool are the components of the smell of stool representing the end products of microbial activity and metabolism that can be used to diagnose disease. Despite the abundance of hydrogen, carbon dioxide, and methane that have already been identified in human flatus, the small portion of trace gases making up the VOCs emitted from stool include organic acids, alcohols, esters, heterocyclic compounds, aldehydes, ketones, and alkanes, among others. These are the gases that vary among individuals in sickness and in health, in dietary changes, and in gut microbial activity. Electronic nose devices are analytical and pattern recognition platforms that can utilize mass spectrometry or electrochemical sensors to detect these VOCs in gas samples. When paired with machine-learning and pattern recognition algorithms, this can identify patterns of VOCs, and thus patterns of smell, that can be used to identify disease states. In this review, we provide a clinical background of VOC identification, electronic nose development, and review gastroenterology applications toward diagnosing disease by the volatile headspace analysis of stool. PMID:26819529

Microbial chemical factories: recent advances in pathway engineering for synthesis of value added chemicals.

PubMed

Dhamankar, Himanshu; Prather, Kristala L J

2011-08-01

The dwindling nature of petroleum and other fossil reserves has provided impetus towards microbial synthesis of fuels and value added chemicals from biomass-derived sugars as a renewable resource. Microbes have naturally evolved enzymes and pathways that can convert biomass into hundreds of unique chemical structures, a property that can be effectively exploited for their engineering into Microbial Chemical Factories (MCFs). De novo pathway engineering facilitates expansion of the repertoire of microbially synthesized compounds beyond natural products. In this review, we visit some recent successes in such novel pathway engineering and optimization, with particular emphasis on the selection and engineering of pathway enzymes and balancing of their accessory cofactors. Copyright © 2011 Elsevier Ltd. All rights reserved.

Microbial carbon pump and its significance for carbon sequestration in soils

NASA Astrophysics Data System (ADS)

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.

Is artificial recharge promoting microbial activity and biodegradation processes in groundwater systems?

NASA Astrophysics Data System (ADS)

Barba Ferrer, Carme; Folch, Albert; Gaju, Núria; Martínez-Alonso, Maira; Carrasquilla, Marc; Grau-Martínez, Alba; Sanchez-Vila, Xavier

2016-04-01

Managed Artificial Recharge (MAR) represents a strategic tool for managing water resources, especially during scarce periods. On one hand, it can increase water stored in aquifers and extract it when weather conditions do not permit exclusive exploitation of surface resources. On the other, it allows improve water quality due the processes occurring into the soil whereas water crosses vadose zone. Barcelona (Catalonia, Spain) conurbation is suffering significant quantitative and qualitative groundwater disturbances. For this reason, Sant Vicenç MAR system, constituted by a sedimentation and an infiltration pond, was constructed in 2009 as the strategic water management infrastructure. Compared with other MAR facilities, this infiltration pond has a reactive bed formed by organic compost and local material. The objective is to promote different redox states allowing more and different degradation of chemical compounds than regular MAR systems. In previous studies in the site, physical and hydrochemical parameters demonstrated that there was indeed a degradation of different pollutants. However, to go a step further understanding the different biogeochemical processes and the related degradation processes occurring in the system, we studied the existing microbial communities. So, molecular techniques were applied in water and soil samples in two different scenarios; the first one, when the system was fully operating and the second when the system was not operating during some months. We have specifically compared microbial diversity and richness indexes and both cluster dendrograms obtained from DGGEs analysis made in each sampling campaign.

Nitrogen Deposition Reduces Decomposition Rates Through Shifts in Microbial Community Composition and Function

NASA Astrophysics Data System (ADS)

Waldrop, M.; Zak, D.; Sinsabaugh, R.

2002-12-01

Atmospheric nitrogen (N) deposition may alter soil biological activity in northern hardwood forests by repressing phenol oxidase enzyme activity and altering microbial community composition, thereby slowing decomposition and increasing the export of phenolic compounds. We tested this hypothesis by adding 13C-labelled cellobiose, vanillin, and catechol to control and N fertilized soils (30 and 80 kg ha-1) collected from three forests; two dominated by Acer Saccharum and one dominated by Quercus Alba and Quercus Velutina. While N deposition increased total microbial respiration, it decreased soil oxidative enzyme activities, resulting in slower degradation rates of all compounds, and larger DOC pools. This effect was larger in the oak forest, where fungi dominate C-cycling processes. DNA and 13C-phospolipid analyses showed that N addition altered the fungal community and reduced the activity of fungal and bacterial populations in soil, potentially explaining reduced soil enzyme activities and incomplete decomposition.

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

PubMed Central

Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C.; Mackie, Roderick I.

2014-01-01

Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds. PMID:25383887