Microbial enhancement of compost extracts based on cattle rumen content compost - characterisation of a system.

PubMed

Shrestha, Karuna; Shrestha, Pramod; Walsh, Kerry B; Harrower, Keith M; Midmore, David J

2011-09-01

Microbially enhanced compost extracts ('compost tea') are being used in commercial agriculture as a source of nutrients and for their perceived benefit to soil microbiology, including plant disease suppression. Rumen content material is a waste of cattle abattoirs, which can be value-added by conversion to compost and 'compost tea'. A system for compost extraction and microbial enhancement was characterised. Molasses amendment increased bacterial count 10-fold, while amendment based on molasses and 'fish and kelp hydrolysate' increased fungal count 10-fold. Compost extract incubated at 1:10 (w/v) dilution showed the highest microbial load, activity and humic/fulvic acid content compared to other dilutions. Aeration increased the extraction efficiency of soluble metabolites, and microbial growth rate, as did extraction of compost without the use of a constraining bag. A protocol of 1:10 dilution and aerated incubation with kelp and molasses amendments is recommended to optimise microbial load and fungal-to-bacterial ratio for this inoculum source. Copyright © 2011 Elsevier Ltd. All rights reserved.

Rheological Enhancement of Pork Myofibrillar Protein-Lipid Emulsion Composite Gels via Glucose Oxidase Oxidation/Transglutaminase Cross-Linking Pathway.

PubMed

Wang, Xu; Xiong, Youling L; Sato, Hiroaki

2017-09-27

Porcine myofibrillar protein (MP) was modified with glucose oxidase (GluOx)-iron that produces hydroxyl radicals then subjected to microbial transglutaminase (TGase) cross-linking in 0.6 M NaCl at 4 °C. The resulting aggregation and gel formation of MP were examined. The GluOx-mediated oxidation promoted the formation of both soluble and insoluble protein aggregates via disulfide bonds and occlusions of hydrophobic groups. The subsequent TGase treatment converted protein aggregates into highly cross-linked polymers. MP-lipid emulsion composite gels formed with such polymers exhibited markedly enhanced gelling capacity: up to 4.4-fold increases in gel firmness and 3.5-fold increases in gel elasticity over nontreated protein. Microstructural examination showed small oil droplets dispersed in a densely packed gel matrix when MP was oxidatively modified, and the TGase treatment further contributed to such packing. The enzymatic GluOx oxidation/TGase treatment shows promise to improve the textural properties of emulsified meat products.

Transglutaminase-mediated protein immobilization to casein nanolayers created on a plastic surface.

PubMed

Kamiya, Noriho; Doi, Satoshi; Tominaga, Jo; Ichinose, Hirofumi; Goto, Masahiro

2005-01-01

An enzymatic method for covalent and site-specific immobilization of recombinant proteins on a plastic surface was explored. Using Escherichia coli alkaline phosphatase (AP) with a specific peptide tag (MKHKGS) genetically incorporated at the N-terminus as a model (NK-AP), microbial transglutaminase (MTG)-mediated protein immobilization was demonstrated. To generate a reactive surface for MTG, a 96-well polystyrene microtiter plate was physically coated with casein, a good MTG substrate. Successful immobilization of recombinant AP to the nanolayer of casein on the surface of the microtiter plate was verified by the detection of enzymatic activity. Since little activity was observed when wild-type AP was used, immobilization of NK-AP was likely directed by the specific peptide tag. When polymeric casein prepared by MTG was used as a matrix on the plate, the loading capacity of AP was increased about 2-fold compared to when casein was used as the matrix. Transglutaminase-mediated site-specific posttranslational modification of proteins offers one way of generating a variety of protein-based solid formulations for biotechnological applications.

Chlorine stress mediates microbial surface attachment in drinking water systems.

PubMed

Liu, Li; Le, Yang; Jin, Juliang; Zhou, Yuliang; Chen, Guowei

2015-03-01

Microbial attachment to drinking water pipe surfaces facilitates pathogen survival and deteriorates disinfection performance, directly threatening the safety of drinking water. Notwithstanding that the formation of biofilm has been studied for decades, the underlying mechanisms for the origins of microbial surface attachment in biofilm development in drinking water pipelines remain largely elusive. We combined experimental and mathematical methods to investigate the role of environmental stress-mediated cell motility on microbial surface attachment in chlorination-stressed drinking water distribution systems. Results show that at low levels of disinfectant (0.0-1.0 mg/L), the presence of chlorine promotes initiation of microbial surface attachment, while higher amounts of disinfectant (>1.0 mg/L) inhibit microbial attachment. The proposed mathematical model further demonstrates that chlorination stress (0.0-5.0 mg/L)-mediated microbial cell motility regulates the frequency of cell-wall collision and thereby controls initial microbial surface attachment. The results reveal that transport processes and decay patterns of chlorine in drinking water pipelines regulate microbial cell motility and, thus, control initial surface cell attachment. It provides a mechanistic understanding of microbial attachment shaped by environmental disinfection stress and leads to new insights into microbial safety protocols in water distribution systems.

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

PubMed

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

2018-03-01

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

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities

PubMed Central

Avera, Bethany; Badgley, Brian; Barrett, John E.; Franklin, Josh; Knowlton, Katharine F.; Ray, Partha P.; Smitherman, Crystal

2017-01-01

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. PMID:28356447

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

PubMed

Wepking, Carl; Avera, Bethany; Badgley, Brian; Barrett, John E; Franklin, Josh; Knowlton, Katharine F; Ray, Partha P; Smitherman, Crystal; Strickland, Michael S

2017-03-29

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. © 2017 The Author(s).

Efficient chemo-enzymatic gluten detoxification: reducing toxic epitopes for celiac patients improving functional properties

PubMed Central

Ribeiro, Miguel; Nunes, Fernando M.; Guedes, Sofia; Domingues, Pedro; Silva, Amélia M.; Carrillo, Jose Maria; Rodriguez-Quijano, Marta; Branlard, Gérard; Igrejas, Gilberto

2015-01-01

Protein engineering of gluten, the exogenous effector in celiac disease, seeking its detoxification by selective chemical modification of toxic epitopes is a very attractive strategy and promising technology when compared to pharmacological treatment or genetic engineering of wheat. Here we present a simple and efficient chemo-enzymatic methodology that decreases celiac disease toxic epitopes of gluten proteins improving its technological value through microbial transglutaminase-mediated transamidation of glutamine with n-butylamine under reducing conditions. First, we found that using low concentrations of amine-nucleophile under non-reducing conditions, the decrease in toxic epitopes is mainly due to transglutaminase-mediated cross-linking. Second, using high amine nucleophile concentrations protein cross-linking is substantially reduced. Third, reducing conditions increase 7-fold the transamidation reaction further decreasing toxic epitopes amount. Fourth, using n-butylamine improves gluten hydrophobicity that strengthens the gluten network. These results open the possibility of tailoring gluten for producing hypoallergenic flours while still taking advantage of the unique viscoelastic properties of gluten. PMID:26691232

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants

PubMed Central

Gupta, Rashi; Bisaria, V. S.; Sharma, Shilpi

2015-01-01

Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However, effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. The ability of bioinoculants to reduce the application of chemicals for obtaining optimum yield of legume appears to be of great ecological and economic importance. In the present study, we compared the influence of seed inoculation of Cajanus cajan with a microbial consortium, comprising Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum, with that of application of chemical fertilizers on plant’s growth parameters and its rhizospheric microbial communities. Real-time PCR assay was carried out to target the structure (16S rRNA) and function (nitrogen cycle) of rhizospheric microbiota, using both DNA and RNA as markers. The results showed that the microbial consortium was the most efficient in increasing grain yield (2.5-fold), even better than the recommended dose of chemical fertilizers (by 1.2-fold) and showed enhancement in nifH and amoA transcripts by 2.7- and 2.0-fold, respectively. No adverse effects of bioinoculants' application were observed over the rhizospheric microbial community, rendering the consortium to be safe for release in agricultural fields. PMID:26231030

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities--A Comparison between Chemical Fertilizers and Bioinoculants.

PubMed

Gupta, Rashi; Bisaria, V S; Sharma, Shilpi

2015-01-01

Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However, effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. The ability of bioinoculants to reduce the application of chemicals for obtaining optimum yield of legume appears to be of great ecological and economic importance. In the present study, we compared the influence of seed inoculation of Cajanus cajan with a microbial consortium, comprising Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum, with that of application of chemical fertilizers on plant's growth parameters and its rhizospheric microbial communities. Real-time PCR assay was carried out to target the structure (16S rRNA) and function (nitrogen cycle) of rhizospheric microbiota, using both DNA and RNA as markers. The results showed that the microbial consortium was the most efficient in increasing grain yield (2.5-fold), even better than the recommended dose of chemical fertilizers (by 1.2-fold) and showed enhancement in nifH and amoA transcripts by 2.7- and 2.0-fold, respectively. No adverse effects of bioinoculants' application were observed over the rhizospheric microbial community, rendering the consortium to be safe for release in agricultural fields.

Microbially mediated alteration of crystalline basalts as identified from analogical reactive percolation experiments

NASA Astrophysics Data System (ADS)

Moore, Rachael; Ménez, Bénédicte; Stéphant, Sylvian; Dupraz, Sébastien; Ranchou-Peyruse, Magali; Ranchou-Peyruse, Anthony; Gérard, Emmanuelle

2017-04-01

Alteration in the ocean crust through fluid circulation is an ongoing process affecting the first kilometers and at low temperatures some alteration may be microbially mediated. Hydrothermal activity through the hard rock basement supports diverse microbial communities within the rock by providing nutrient and energy sources. Currently, the impact of basement hosted microbial communities on alteration is poorly understood. In order to identify and quantify the nature of microbially mediated alteration two reactive percolation experiments mimicking circulation of CO2 enriched ground water were performed at 35 °C and 30 bar for 21 days each. The experiments were performed using a crystalline basalt substrate from an earlier drilled deep Icelandic aquifer. One experiment was conducted on sterile rock while the other was conducted with the addition of a microbial inoculate derived from groundwater enrichment cultures obtained from the same aquifer. µCT on the experimental basaltic substrate before and after the reactive percolation experiment along with synchrotron radiation x-ray tomographic microscopy and the mineralogical characterization of resulting material allows for the comparative volumetric quantification of dissolution and precipitation. The unique design of this experiment allows for the identification of alteration which occurs solely abiotically and of microbially mediated alteration. Experimental results are compared to natural basaltic cores from Iceland retrieved following a large field CO2 injection experiment that stimulated microbial activity at depth.

Glyphosate toxicity and the effects of long-term vegetation control on soil microbial communities

Treesearch

Matt D. Busse; Alice W. Ratcliff; Carol J. Stestak; Robert F. Powers

2001-01-01

We assessed the direct and indirect effect of the herbicide glyphosate on soil microbial communities from soil bioassays at glyphosate concentrations up to 100-fold greater than expected following a single field application. Indirect effects on microbial biomass, respiration, and metabolic diversity (Biolog and catabolic response profile) were compared seasonally after...

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

Treesearch

Aimee T. Classen; Steven T. Overby; Stephen C. Hart; George W. Koch; Thomas G. Whitham

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality of an ecosystem or indirectly by shifting the composition of microbial communities that mediate nutrient processes. We examined the effects of tree susceptibility and resistance to herbivory on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore...

Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS.

PubMed

Bhagat, C; Dudhagara, P; Tank, S

2018-02-01

Growing industrialization and the desire for a better economy in countries has accelerated the emission of greenhouse gases (GHGs), by more than the buffering capacity of the earth's atmosphere. Among the various GHGs, carbon dioxide occupies the first position in the anthroposphere and has detrimental effects on the ecosystem. For decarbonization, several non-biological methods of carbon capture, utilization and storage (CCUS) have been in use for the past few decades, but they are suffering from narrow applicability. Recently, CO 2 emission and its disposal related problems have encouraged the implementation of bioprocessing to achieve a zero waste economy for a sustainable environment. Microbial carbonic anhydrase (CA) catalyses reversible CO 2 hydration and forms metal carbonates that mimic the natural phenomenon of weathering/carbonation and is gaining merit for CCUS. Thus, the diversity and specificity of CAs from different micro-organisms could be explored for CCUS. In the literature, more than 50 different microbial CAs have been explored for mineral carbonation. Further, microbial CAs can be engineered for the mineral carbonation process to develop new technology. CA driven carbonation is encouraging due to its large storage capacity and favourable chemistry, allowing site-specific sequestration and reusable product formation for other industries. Moreover, carbonation based CCUS holds five-fold more sequestration capacity over the next 100 years. Thus, it is an eco-friendly, feasible, viable option and believed to be the impending technology for CCUS. Here, we attempt to examine the distribution of various types of microbial CAs with their potential applications and future direction for carbon capture. Although there are few key challenges in bio-based technology, they need to be addressed in order to commercialize the technology. © 2017 The Society for Applied Microbiology.

Cu,Zn superoxide dismutase structure from a microbial pathogen establishes a class with a conserved dimer interface.

PubMed

Forest, K T; Langford, P R; Kroll, J S; Getzoff, E D

2000-02-11

Macrophages and neutrophils protect animals from microbial infection in part by issuing a burst of toxic superoxide radicals when challenged. To counteract this onslaught, many Gram-negative bacterial pathogens possess periplasmic Cu,Zn superoxide dismutases (SODs), which act on superoxide to yield molecular oxygen and hydrogen peroxide. We have solved the X-ray crystal structure of the Cu,Zn SOD from Actinobacillus pleuropneumoniae, a major porcine pathogen, by molecular replacement at 1.9 A resolution. The structure reveals that the dimeric bacterial enzymes form a structurally homologous class defined by a water-mediated dimer interface, and share with all Cu,Zn SODs the Greek-key beta-barrel subunit fold with copper and zinc ions located at the base of a deep loop-enclosed active-site channel. Our structure-based sequence alignment of the bacterial enzymes explains the monomeric nature of at least two of these, and suggests that there may be at least one additional structural class for the bacterial SODs. Two metal-mediated crystal contacts yielded our C222(1) crystals, and the geometry of these sites could be engineered into proteins recalcitrant to crystallization in their native form. This work highlights structural differences between eukaryotic and prokaryotic Cu,Zn SODs, as well as similarities and differences among prokaryotic SODs, and lays the groundwork for development of antimicrobial drugs that specifically target periplasmic Cu,Zn SODs of bacterial pathogens. Copyright 12000 Academic Press.

Effects of humic acid concentration on the microbially-mediated reductive solubilization of Pu(IV) polymers.

PubMed

Xie, Jinchuan; Han, Xiaoyuan; Wang, Weixian; Zhou, Xiaohua; Lin, Jianfeng

2017-10-05

The role of humic acid concentration in the microbially-mediated reductive solubilization of Pu(IV) polymers remains unclear until now. The effects of humic concentration (0-150.5mg/L) on the rate and extent of reduction of polymeric Pu(IV) were studied under anaerobic and pH 7.2 conditions. The results show that Shewanella putrefaciens, secreting flavins as endogenous electron shuttles, cannot notably stimulate the reduction of polymeric Pu(IV). In the presence of humic acids, the reduction rate of polymeric Pu(IV) increased with increasing humic concentrations (0-15.0mg/L): e.g., a 102-fold increase from 4.1×10 -15 (HA=0) to 4.2×10 -13 mol Pu(III) aq /h (HA=15.0mg/L). The bioreduced humic acids by S. putrefaciens facilitated the extracellular electron transfer to Pu(IV) polymers and thus the reduction of polymeric Pu(IV) to Pu(III) aq became thermodynamically favorable. However, the reduction rate did not increase but decrease with increasing humic concentrations from 15.0 to 150.5mg/L. Humic coatings formed on the polymer surfaces at relatively high humic concentrations limited the electron transfer to the polymers and thus decreased the reduction rate. The finding of the dynamic role of humic acids in the bioreductive solubilization may be helpful in evaluating Pu mobility in the geosphere. Copyright © 2017 Elsevier B.V. All rights reserved.

Response of the soil microbial community to imazethapyr application in a soybean field.

PubMed

Xu, Jun; Guo, Liqun; Dong, Fengshou; Liu, Xingang; Wu, Xiaohu; Sheng, Yu; Zhang, Ying; Zheng, Yongquan

2013-01-01

The objective of this study was to determine the effects of imazethapyr on soil microbial communities combined with its effect on soybean growth. A short-term field experiment was conducted, and imazethapyr was applied to the soil at three different doses [1-fold, 10-fold, and 50-fold of the recommended field rate (H1, H10, H50)] during the soybean seedling period (with two leaves). Soil sampling was performed after 1, 7, 30, 60, 90, and 120 days of application to determine the imazethapyr concentration and microbial community structure by investigating phospholipid fatty acids (PLFA) and microbial biomass carbon (MBC). The half-lives of the imazethapyr in the field soil varied from 30.1 to 43.3 days. Imazethapyr at H1 was innocuous to soybean plants, but imazethapyr at H10 and H50 led to a significant inhibition in soybean plant height and leaf number. The soil MBC, total PLFA, and bacterial PLFA were decreased by the application of imazethapyr during the initial period and could recover by the end of the experiment. The ratio of Gram-negative/Gram-positive (GN/GP) bacteria during the three treatments went through increases and decreases, and then recovered at the end of the experiment. The fungal PLFA of all three treatments increased during the initial period and then declined, and only the fungal PLFA at H50 recovered by the end of the treatment. A principal component analysis (PCA) of the PLFA clearly separated the treatments and sampling times, and the results demonstrate that imazethapyr alters the microbial community structure. This is the first systemic study reporting the effects of imazethapyr on the soil microbial community structure under soybean field conditions.

THE NEAR-EQUILIBRIUM OF MICROBIALLY MEDIATED REDOX COUPLES IN REDUCING GROUNDWATER ENVIRONMENTS

EPA Science Inventory

Redox couples are commonly held to be in disequilibrium among each other in most natural waters. To evaluate this view for microbially mediated, reducing, groundwater environments, monitoring data were examined for several couples under conditions ranging from nitrate-detectable...

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

PubMed

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

2013-10-15

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

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2016-08-15

Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm(-2) with ∼150 μg ml(-1) phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial community to access a solid electrode as an alternative electron acceptor. To better understand the ecological relationships between mediator producers and mediator utilizers, we here present a comparison of the phenazine-dependent electroactivities of three Pseudomonas strains. This work forms the foundation for more complex coculture investigations of mediated electron transfer in microbial fuel cells. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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

PubMed Central

Bosire, Erick M.; Blank, Lars M.

2016-01-01

ABSTRACT Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa. We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm−2 with ∼150 μg ml−1 phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. IMPORTANCE Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial community to access a solid electrode as an alternative electron acceptor. To better understand the ecological relationships between mediator producers and mediator utilizers, we here present a comparison of the phenazine-dependent electroactivities of three Pseudomonas strains. This work forms the foundation for more complex coculture investigations of mediated electron transfer in microbial fuel cells. PMID:27287325

Formation of novel hydrogel bio-anode by immobilization of biocatalyst in alginate/polyaniline/titanium-dioxide/graphite composites and its electrical performance.

PubMed

Szöllősi, Attila; Hoschke, Ágoston; Rezessy-Szabó, Judit M; Bujna, Erika; Kun, Szilárd; Nguyen, Quang D

2017-05-01

A new bio-anode containing gel-entrapped bacteria in alginate/polyaniline/TiO 2 /graphite composites was constructed and electrically investigated. Alginate as dopant and template as well as entrapped gel was used for immobilization of microorganism cells. Increase of polyaniline concentration resulted an increase in the conductivity in gels. Addition of 0.01 and 0.02 g/mL polyaniline caused 6-fold and 10-fold higher conductivity, respectively. Furthermore, addition of 0.05 g/mL graphite powder caused 10-fold higher conductivity and 4-fold higher power density, respectively. The combination of polyaniline and graphite resulted 105-fold higher conductivity and 7-fold higher power-density output. Optimized concentrations of polyaniline and graphite powder were determined to be 0.02 g/mL and 0.05 g/mL, respectively. Modified hydrogel anode was successfully used in microbial fuel cell systems both in semi- and continuous operations modes. In semi-continuous mode, about 7.88 W/m 3 power density was obtained after 13 h of fermentation. The glucose consumption rate was calculated to be about 7 mg glucose/h/1.2·10 7  CFU immobilized cells. Similar power density was observed in the continuous operation mode of the microbial fuel cell, and it was operated stably for more than 7 days. Our results are very promising for development of an improved microbial fuel cell with new type of bio-anode that have higher power density and can operate for long term. Copyright © 2017 Elsevier Ltd. All rights reserved.

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Microbial utilization of dissolved organic matter from leaves of the red mangrove, Rhizophora mangle, in the Fresh Creek estuary, Bahamas

NASA Astrophysics Data System (ADS)

Benner, Ronald; Peele, Emily R.; Hodson, Robert E.

1986-11-01

Dissolved organic matter was leached from [ 14C]labeled leaves of the red mangrove, Rhizophora mangle, and used in studies to determine the rates and efficiencies of microbial utilization of the water-soluble components of mangrove leaves in the Fresh Creek estuary, Bahamas. Rates of microbial utilization (assimilation plus mineralization) of mangrove leachate ranged from 0·022 to 4·675 μg ml -1 h -1 depending on the concentration of leachate and the size or diversity of microbial populations. Microflora associated with decaying mangrove leaves utilized mangrove leachate at rates up to 18-fold higher than rates of leachate utilization by planktonic microflora. Chemical analyses indicated that tannins and other potentially inhibitory phenolic compounds made up a major fraction (18%) of the dissolved organic matter in mangrove leachate. Mangrove leachate did not appear to be inhibitory to the microbial uptake of leachate or the microbial degradation of the lignocellulosic component of mangrove leaves except at high concentrations (mg ml -1). The availability of molecular oxygen also was an important parameter affecting rates of leachate utilization; rates of microbial utilization of leachate were up to 8-fold higher under aerobic rather than anaerobic conditions. The overall efficiency of conversion of mangrove leachate into microbial biomass was high and ranged from 64% to 94%. As much as 42% of the added leachate was utilized during 2 to 12 h incubations, indicating that a major fraction of the leachable material from mangrove leaves is incorporated into microbial biomass, and thus available to animals in the estuarine food web.

Overnight stagnation of drinking water in household taps induces microbial growth and changes in community composition.

PubMed

Lautenschlager, Karin; Boon, Nico; Wang, Yingying; Egli, Thomas; Hammes, Frederik

2010-09-01

Drinking water quality is routinely monitored in the distribution network but not inside households at the point of consumption. Fluctuating temperatures, residence times (stagnation), pipe materials and decreasing pipe diameters can promote bacterial growth in buildings. To test the influence of stagnation in households on the bacterial cell concentrations and composition, water was sampled from 10 separate households after overnight stagnation and after flushing the taps. Cell concentrations, measured by flow cytometry, increased (2-3-fold) in all water samples after stagnation. This increase was also observed in adenosine tri-phosphate (ATP) concentrations (2-18-fold) and heterotrophic plate counts (4-580-fold). An observed increase in cell biovolume and ATP-per-cell concentrations furthermore suggests that the increase in cell concentrations was due to microbial growth. After 5 min flushing of the taps, cell concentrations and water temperature decreased to the level generally found in the drinking water network. Denaturing gradient gel electrophoresis also showed a change in the microbial composition after stagnation. This study showed that water stagnation in household pipes results in considerable microbial changes. While hygienic risk was not directly assessed, it emphasizes the need for the development of good material validation methods, recommendations and spot tests for in-house water installations. However, a simple mitigation strategy would be a short flushing of taps prior to use. Copyright © 2010 Elsevier Ltd. All rights reserved.

The mechanism of neutral red-mediated microbial electrosynthesis in Escherichia coli: menaquinone reduction

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

Harrington, Timothy D.; Tran, Vi N.; Mohamed, Abdelrhman

The aim of this work was to elucidate the mechanism of mediated microbial electrosynthesis via neutral red from an electrode to fermenting Escherichia coli cultures in a bioelectrochemical system. Chemical reduction of NAD+ by reduced neutral red did not occur as predicted. Instead, neutral red was shown to reduce the menaquinone pool in the inner bacterial membrane. The reduced menaquinone pool altered fermentative metabolite production via the arcB redox-sensing cascade in the absence of terminal electron acceptors. When the acceptors DMSO, fumarate, or nitrate were provided, as many as 19% of the electrons trapped in the reduced acceptors were derivedmore » from the electrode. These results demonstrate the mechanism of neutral red-mediated microbial electrosynthesis during fermentation as well as how neutral red enables microbial electrosynthesis of reduced terminal electron acceptors.« less

Pilot scale biodiesel production from microbial oil of Rhodosporidium toruloides DEBB 5533 using sugarcane juice: Performance in diesel engine and preliminary economic study.

PubMed

Soccol, Carlos Ricardo; Dalmas Neto, Carlos José; Soccol, Vanete Thomaz; Sydney, Eduardo Bittencourt; da Costa, Eduardo Scopel Ferreira; Medeiros, Adriane Bianchi Pedroni; Vandenberghe, Luciana Porto de Souza

2017-01-01

A successful pilot-scale process for biodiesel production from microbial oil (Biooil) produced by Rhodosporidium toruloides DEBB 5533 is presented. Using fed-batch strategy (1000L working volume), a lipid productivity of 0.44g/L.h was obtained using a low-cost medium composed by sugarcane juice and urea. The microbial oil was used for biodiesel production and its performance was evaluated in diesel engine tests, showing very good performance, especially for the blend B20 SCO, when operating at 2500rpm with lower pollutant emissions (CO 2 - 220% less; CO - 7-fold less; NO X 50% less and no detectable HC emissions (<0.11ppm)) when compared with the blends of standard biofuel from soybean oil. A preliminary analysis showed that microbial biodiesel is economically competitive (US$ 0.76/L) when compared to the vegetable biodiesel (US$ 0.81/L). Besides, the yield of biodiesel from microbial oil is higher (4172L/ha of cultivated sugarcane) that represents 6.3-fold the yield of standard biodiesel (661L/ha of cultivated soybean). Copyright © 2016 Elsevier Ltd. All rights reserved.

A study of microbial communities on terracotta separator and on biocathode of air breathing microbial fuel cells.

PubMed

Rago, Laura; Zecchin, Sarah; Marzorati, Stefania; Goglio, Andrea; Cavalca, Lucia; Cristiani, Pierangela; Schievano, Andrea

2018-04-01

Recently, terracotta has attracted interest as low-cost and biocompatible material to build separators in microbial fuel cells (MFCs). However, the influence of a non-conductive material like terracotta on electroactive microbiological communities remains substantially unexplored. This study aims at describing the microbial pools developed from two different seed inocula (bovine and swine sewage) in terracotta-based air-breathing MFC. A statistical approach on microbiological data confirmed different community enrichment in the MFCs, depending mainly on the inoculum. Terracotta separators impeded the growth of electroactive communities in contact with cathodes (biocathodes), while a thick biofilm was observed on the surface (anolyte-side) of the terracotta separator. Terracotta-free MFCs, set as control experiments, showed a well-developed biocathode, Biocathode-MFCs resulted in 4 to 6-fold higher power densities. All biofilms were analyzed by high-throughput Illumina sequencing applied to 16S rRNA gene. The results showed more abundant (3- to 5-fold) electroactive genera (mainly Geobacter, Pseudomonas, Desulfuromonas and Clostridia MBA03) in terracotta-free biocathodes. Nevertheless, terracotta separators induced only slight changes in anodic microbial communities. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2017-01-15

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

Influence of porewater advection on denitrification in carbonate sands: Evidence from repacked sediment column experiments

NASA Astrophysics Data System (ADS)

Santos, Isaac R.; Eyre, Bradley D.; Glud, Ronnie N.

2012-11-01

Porewater flow enhances mineralization rates in organic-poor permeable sands. Here, a series of sediment column experiments were undertaken to assess the potential effect of advective porewater transport on denitrification in permeable carbonate sands collected from Heron Island (Great Barrier Reef). Experimental conditions (flow path length, advection rate, and temperature) were manipulated to represent conditions similar to near shore tropical environments. HgCl2-poisoned controls were used to assess whether reactions were microbially mediated. Overall, significant correlations were found between oxygen consumption and N2 production. The N:O2 slope of 0.114 implied that about 75% of all the nitrogen mineralized was denitrified. A 4-fold increase in sediment column length (from 10 to 40 cm) resulted in an overall increase in oxygen consumption (1.6-fold), TCO2 production (1.8-fold), and denitrification (1.9-fold). Oxic respiration increased quickly until advection reached 80 L m-2 h-1 and then plateaued at higher advection rates. Interestingly, denitrification peaked (up to 336 μmol N2 m-2 h-1) at intermediate advection rates (30-80 L m-2 h-1). We speculate that intermediate advection rates enhance the development of microniches (i.e., steep oxygen gradients) within porous carbonate sands, perhaps providing optimum conditions for denitrification. The denitrification peak fell within the broad range of advection rates (often on scales of 1-100 L m-2 h-1) typically found on continental shelves implying that carbonate sands may play a major, but as yet unquantified, role in oceanic nitrogen budgets.

MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection

PubMed Central

Kubinak, Jason L.; Stephens, W. Zac; Soto, Ray; Petersen, Charisse; Chiaro, Tyson; Gogokhia, Lasha; Bell, Rickesha; Ajami, Nadim J.; Petrosino, Joseph F.; Morrison, Linda; Potts, Wayne K.; Jensen, Peter E.; O'Connell, Ryan M.; Round, June L.

2015-01-01

The presentation of protein antigens on the cell surface by major histocompatibility complex (MHC) molecules coordinates vertebrate adaptive immune responses, thereby mediating susceptibility to a variety of autoimmune and infectious diseases. The composition of symbiotic microbial communities (the microbiota) is influenced by host immunity and can have a profound impact on host physiology. Here we use an MHC congenic mouse model to test the hypothesis that genetic variation at MHC genes among individuals mediates susceptibility to disease by controlling microbiota composition. We find that MHC genotype significantly influences antibody responses against commensals in the gut, and that these responses are correlated with the establishment of unique microbial communities. Transplantation experiments in germfree mice indicate that MHC-mediated differences in microbiota composition are sufficient to explain susceptibility to enteric infection. Our findings indicate that MHC polymorphisms contribute to defining an individual's unique microbial fingerprint that influences health. PMID:26494419

The Influence of Chitosan Substrate and Its Nanometric Form Toward the Green Power Generation in Sediment Microbial Fuel Cell.

PubMed

Karthikeyan, C; Sathishkumar, Y; Lee, Yang Soo; Kim, Ae Rhan; Yoo, Dong Jin; Kumar, G Gnana

2017-01-01

A simple, environmental friendly and biologically important sediment interfaced fuel cell was developed for the green energy generation. The soil sediment used for the study is enriched of rich anthropogenic free organic carbon, sufficient manganese and high level potassium contents as evidenced from the geochemical characterizations. The saccharides produced by the catalytic reaction of substrate chitosan were utilized for the growth of microorganisms and electron shuttling processes. Chitosan substrate influenced sediment microbial fuel cells exhibited the nearly two fold power increment over the substrate free fuel cells. The fuel cell efficiencies were further increased by bringing the substrate chitosan at nanometric level, which is nearly three and two fold higher than that of substrate free and chitosan influenced sediment microbial fuel cells, respectively, and the influential parameters involved in the power and longevity issues were addressed with different perspectives.

Bifurcations of a periodically forced microbial continuous culture model with restrained growth rate

NASA Astrophysics Data System (ADS)

Ren, Jingli; Yuan, Qigang

2017-08-01

A three dimensional microbial continuous culture model with a restrained microbial growth rate is studied in this paper. Two types of dilution rates are considered to investigate the dynamic behaviors of the model. For the unforced system, fold bifurcation and Hopf bifurcation are detected, and numerical simulations reveal that the system undergoes degenerate Hopf bifurcation. When the system is periodically forced, bifurcation diagrams for periodic solutions of period-one and period-two are given by researching the Poincaré map, corresponding to different bifurcation cases in the unforced system. Stable and unstable quasiperiodic solutions are obtained by Neimark-Sacker bifurcation with different parameter values. Periodic solutions of various periods can occur or disappear and even change their stability, when the Poincaré map of the forced system undergoes Neimark-Sacker bifurcation, flip bifurcation, and fold bifurcation. Chaotic attractors generated by a cascade of period doublings and some phase portraits are given at last.

Terreneuvian Orthothecid (Hyolitha) Digestive Tracts from Northern Montagne Noire, France; Taphonomic, Ontogenetic and Phylogenetic Implications

PubMed Central

Devaere, Léa; Clausen, Sébastien; Álvaro, J. Javier; Peel, John S.; Vachard, Daniel

2014-01-01

More than 285 specimens of Conotheca subcurvata with three-dimensionally preserved digestive tracts were recovered from the Terreneuvian (early Cambrian) Heraultia Limestone of the northern Montagne Noire, southern France. They represent one of the oldest occurrences of such preserved guts. The newly discovered operculum of some complete specimens provides additional data allowing emendation of the species diagnosis. Infestation of the U-shaped digestive tracts by smooth uniseriate, branching to anastomosing filaments along with isolated botryoidal coccoids attests to their early, microbially mediated phosphatisation. Apart from taphonomic deformation, C. subcurvata exhibits three different configurations of the digestive tract: (1) anal tube and gut parallel, straight to slightly undulating; (2) anal tube straight and loosely folded gut; and (3) anal tube straight and gut straight with local zigzag folds. The arrangement of the digestive tracts and its correlation with the mean apertural diameter of the specimens are interpreted as ontogenetically dependent. The simple U-shaped gut, usually considered as characteristic of the Hyolithida, developed in earlier stages of C. subcurvata, whereas the more complex orthothecid type-3 only appears in largest specimens. This growth pattern suggests a distinct phylogenetic relationship between these two hyolith orders through heterochronic processes. PMID:24533118

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

PubMed Central

Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

2014-01-01

Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2–1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2–1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms. PMID:24030599

The microbiota metabolite indole inhibits Salmonella virulence: Involvement of the PhoPQ two-component system.

PubMed

Kohli, Nandita; Crisp, Zeni; Riordan, Rebekah; Li, Michael; Alaniz, Robert C; Jayaraman, Arul

2018-01-01

The microbial community present in the gastrointestinal tract is an important component of the host defense against pathogen infections. We previously demonstrated that indole, a microbial metabolite of tryptophan, reduces enterohemorrhagic Escherichia coli O157:H7 attachment to intestinal epithelial cells and biofilm formation, suggesting that indole may be an effector/attenuator of colonization for a number of enteric pathogens. Here, we report that indole attenuates Salmonella Typhimurium (Salmonella) virulence and invasion as well as increases resistance to colonization in host cells. Indole-exposed Salmonella colonized mice less effectively compared to solvent-treated controls, as evident by competitive index values less than 1 in multiple organs. Indole-exposed Salmonella demonstrated 160-fold less invasion of HeLa epithelial cells and 2-fold less invasion of J774A.1 macrophages compared to solvent-treated controls. However, indole did not affect Salmonella intracellular survival in J774A.1 macrophages suggesting that indole primarily affects Salmonella invasion. The decrease in invasion was corroborated by a decrease in expression of multiple Salmonella Pathogenicity Island-1 (SPI-1) genes. We also identified that the effect of indole was mediated by both PhoPQ-dependent and independent mechanisms. Indole also synergistically enhanced the inhibitory effect of a short chain fatty acid cocktail on SPI-1 gene expression. Lastly, indole-treated HeLa cells were 70% more resistant to Salmonella invasion suggesting that indole also increases resistance of epithelial cells to colonization. Our results demonstrate that indole is an important microbiota metabolite that has direct anti-infective effects on Salmonella and host cells, revealing novel mechanisms of pathogen colonization resistance.

The microbiota metabolite indole inhibits Salmonella virulence: Involvement of the PhoPQ two-component system

PubMed Central

Kohli, Nandita; Crisp, Zeni; Riordan, Rebekah; Li, Michael; Alaniz, Robert C.

2018-01-01

The microbial community present in the gastrointestinal tract is an important component of the host defense against pathogen infections. We previously demonstrated that indole, a microbial metabolite of tryptophan, reduces enterohemorrhagic Escherichia coli O157:H7 attachment to intestinal epithelial cells and biofilm formation, suggesting that indole may be an effector/attenuator of colonization for a number of enteric pathogens. Here, we report that indole attenuates Salmonella Typhimurium (Salmonella) virulence and invasion as well as increases resistance to colonization in host cells. Indole-exposed Salmonella colonized mice less effectively compared to solvent-treated controls, as evident by competitive index values less than 1 in multiple organs. Indole-exposed Salmonella demonstrated 160-fold less invasion of HeLa epithelial cells and 2-fold less invasion of J774A.1 macrophages compared to solvent-treated controls. However, indole did not affect Salmonella intracellular survival in J774A.1 macrophages suggesting that indole primarily affects Salmonella invasion. The decrease in invasion was corroborated by a decrease in expression of multiple Salmonella Pathogenicity Island-1 (SPI-1) genes. We also identified that the effect of indole was mediated by both PhoPQ-dependent and independent mechanisms. Indole also synergistically enhanced the inhibitory effect of a short chain fatty acid cocktail on SPI-1 gene expression. Lastly, indole-treated HeLa cells were 70% more resistant to Salmonella invasion suggesting that indole also increases resistance of epithelial cells to colonization. Our results demonstrate that indole is an important microbiota metabolite that has direct anti-infective effects on Salmonella and host cells, revealing novel mechanisms of pathogen colonization resistance. PMID:29342189

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.

PubMed

Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

2014-01-01

Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.

Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii

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

Zurawski, Jeffrey V.; Khatibi, Piyum A.; Akinosho, Hannah O.

ABSTRACT Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates toC. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(–) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15%more » (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance.« less

Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii

DOE PAGES

Zurawski, Jeffrey V.; Khatibi, Piyum A.; Akinosho, Hannah O.; ...

2017-06-16

ABSTRACT Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates toC. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(–) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15%more » (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance.« less

Proteomic Characterization of Central Pacific Oxygen Minimum Zone Microbial Communities

NASA Astrophysics Data System (ADS)

Saunders, J. K.; McIlvin, M. M.; Moran, D.; Held, N.; Futrelle, J.; Webb, E.; Santoro, A.; Dupont, C.; Saito, M.

2018-05-01

Microbial proteomic profiles are excellent for surveying vast expanses of pelagic ecosystems for links between microbial communities and the biogeochemical cycles they mediate. Data from the ProteOMZ expedition supports the utility of this method.

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

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

Firestone, Mary

2015-03-31

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

Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction:Insight into "Redox mediator-Microbe-Iron oxide" Interaction Process.

PubMed

Zhu, Weihuang; Shi, Mengran; Yu, Dan; Liu, Chongxuan; Huang, Tinglin; Wu, Fengchang

2016-03-29

The characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into "redox mediator-iron oxide" interaction in the presence of DIRB. Two pre-incubation reaction systems of the "strain S12- goethite" and the "strain S12-AQS" were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of the redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for "Quinone-Iron" interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among "quinone-DIRB- goethite" under biotic/abiotic driven.

Microbial exopolysaccharide-mediated synthesis and stabilization of metal nanoparticles.

PubMed

Sathiyanarayanan, Ganesan; Dineshkumar, Krishnamoorthy; Yang, Yung-Hun

2017-11-01

Exopolysaccharides (EPSs) are structurally and functionally valuable biopolymer secreted by different prokaryotic and eukaryotic microorganisms in response to biotic/abiotic stresses and to survive in extreme environments. Microbial EPSs are fascinating in various industrial sectors due to their excellent material properties and less toxic, highly biodegradable, and biocompatible nature. Recently, microbial EPSs have been used as a potential template for the rapid synthesis of metallic nanoparticles and EPS-mediated metal reduction processes are emerging as simple, harmless, and environmentally benign green chemistry approaches. EPS-mediated synthesis of metal nanoparticles is a distinctive metabolism-independent bio-reduction process due to the formation of interfaces between metal cations and the polyanionic functional groups (i.e. hydroxyl, carboxyl and amino groups) of the EPS. In addition, the range of physicochemical features which facilitates the EPS as an efficient stabilizing or capping agents to protect the primary structure of the metal nanoparticles with an encapsulation film in order to separate the nanoparticle core from the mixture of composites. The EPS-capping also enables the further modification of metal nanoparticles with expected material properties for multifarious applications. The present review discusses the microbial EPS-mediated green synthesis/stabilization of metal nanoparticles, possible mechanisms involved in EPS-mediated metal reduction, and application prospects of EPS-based metal nanoparticles.

Extracellular Electron Uptake: Among Autotrophs and Mediated by Surfaces.

PubMed

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

2017-04-01

Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO 2 . Extracellular electron-transfer mechanisms involved in the acquisition of electrons from metals by electrical microbially influenced corrosion (EMIC), from other living cells by interspecies electron transfer (IET), or from an electrode during MES rely on: (i) mediators such as H 2 ; (ii) physical contact through electron-transfer proteins; or (iii) mediator-generating enzymes detached from cells. This review explores the interactions of autotrophs with solid electron donors and their importance in nature and for biosustainable technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effect of long-term fertilization on humic redox mediators in multiple microbial redox reactions.

PubMed

Guo, Peng; Zhang, Chunfang; Wang, Yi; Yu, Xinwei; Zhang, Zhichao; Zhang, Dongdong

2018-03-01

This study investigated the effects of different long-term fertilizations on humic substances (HSs), humic acids (HAs) and humins, functioning as redox mediators for various microbial redox biotransformations, including 2,2',4,4',5,5'- hexachlorobiphenyl (PCB 153 ) dechlorination, dissimilatory iron reduction, and nitrate reduction, and their electron-mediating natures. The redox activity of HSs for various microbial redox metabolisms was substantially enhanced by long-term application of organic fertilizer (pig manure). As a redox mediator, only humin extracted from soils with organic fertilizer amendment (OF-HM) maintained microbial PCB 153 dechlorination activity (1.03 μM PCB 153 removal), and corresponding HA (OF-HA) most effectively enhanced iron reduction and nitrate reduction by Shewanella putrefaciens. Electrochemical analysis confirmed the enhancement of their electron transfer capacity and redox properties. Fourier transform infrared analysis showed that C=C and C=O bonds, and carboxylic or phenolic groups in HSs might be the redox functional groups affected by fertilization. This research enhances our understanding of the influence of anthropogenic fertility on the biogeochemical cycling of elements and in situ remediation ability in agroecosystems through microorganisms' metabolisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial community variation and its relationship with nitrogen mineralization in historically altered forests

Treesearch

Jennifer M. Fraterrigo; Teri C. Balser; Monica g. Turner

2006-01-01

Past land use can impart soil legacies that have important implications for ecosystem function. Although these legacies have been linked with microbially mediated processes, little is known about the long-term influence of land use on soil microbial communities themselves. We examined whether historical land use affected soil microbial community composition (lipid...

Metagenomics analysis of gut microbiota and immune modulation in zebrafish (Danio rerio) fed chitosan silver nanocomposites.

PubMed

Udayangani, R M C; Dananjaya, S H S; Nikapitiya, Chamilani; Heo, Gang-Joon; Lee, Jehee; De Zoysa, Mahanama

2017-07-01

In this study, we evaluated the effects of chitosan silver nanocomposites (CAgNCs) supplemented diet on gut microbial community, goblet cell density, gut morphometry and mRNA expression of immune related and mucin encoding genes in zebrafish. Zebrafish gut microbiota analysis results clearly showed the reduction of phylum Proteobacteria. However, they remained as the major bacterial group in gut with CAgNCs supplemented diet, while the abundance of phylum Fusobacteria and phylum Bacteroidetes were increased notably compared to the control diet fed fish. Total goblet cell density was significantly increased at 30 and 60 days in CAgNCs supplemented group (1.6-fold and 2.0-fold, respectively) compared to the control group indicating enhanced immune function in the gut. CAgNCs supplementation has also increased villi height significantly in the zebrafish mid gut at the end of 30 (95.5 ± 3.7 μm) and 60 days (144.40 ± 4.8 μm) compared to control diet fed fish at 30 (86.90 ± 3.7 μm) and 60 days (96.2 ± 4.8 μm). Furthermore, mRNA expression of immune related genes such as TNF-α (6.2-fold), IL-10 (5.0-fold), IL-12 (9.2-fold), IRF-1 (5.2-fold), Defbl1 (3-fold), Lyz (5.1-fold) and mucin encoding genes were significantly upregulated (above 2-fold) compared to that of control group. The current study revealed that CAgNCs supplemented diet engenders promising effects on fish gut immunity by enhancing beneficial microbial populations, goblet cell density, villi length, and transcriptional regulation of immune related and mucin encoding genes. Copyright © 2017 Elsevier Ltd. All rights reserved.

MICROBIAL ENZYME ACTIVITY FOR CHARACTERIZING NUTRIENT LOADING TO GREAT LAKES COASTAL WETLANDS

EPA Science Inventory

Energy and material flows in aquatic ecosystems are mediated by microbial carbon and nutrient cycling. Extracellular enzymes produced by the microbial community aid in the degradation of organic matter and the resultant acquisition of limiting nutrients. Organic carbon sequestrat...

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

PubMed

Zhang, Yuguang; Liu, Xiao; Cong, Jing; Lu, Hui; Sheng, Yuyu; Wang, Xiulei; Li, Diqiang; Liu, Xueduan; Yin, Huaqun; Zhou, Jizhong; Deng, Ye

2017-07-01

Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p < .05) different between alpine meadow and alpine steppe meadow; the microbial ɑ-diversity in alpine steppe meadow was significantly (p < .01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition. © 2017 John Wiley & Sons Ltd.

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion.

PubMed

Peterson, Robyn A; Gueniche, Audrey; Adam de Beaumais, Ségolène; Breton, Lionel; Dalko-Csiba, Maria; Packer, Nicolle H

2016-03-01

There is increasing evidence that secretory fluids such as tears, saliva and milk play an important role in protecting the human body from infection via a washing mechanism involving glycan-mediated adhesion of potential pathogens to secretory glycoproteins. Interaction of sweat with bacteria is well established as the cause of sweat-associated malodor. However, the role of sweat glycoproteins in microbial attachment has received little, if any, research interest in the past. In this review, we demonstrate how recent published studies involving high-throughput proteomic analysis have inadvertently, and fortuitously, exposed an abundance of glycoproteins in sweat, many of which have also been identified in other secretory fluids. We bring together research demonstrating microbial adhesion to these secretory glycoproteins in tears, saliva and milk and suggest a similar role of the sweat glycoproteins in mediating microbial attachment to sweat and/or skin. The contribution of glycan-mediated microbial adhesion to sweat glycoproteins, and the associated impact on sweat derived malodor and pathogenic skin infections are unchartered new research areas that we are beginning to explore. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Characteristics and kinetic analysis of AQS transformation and microbial goethite reduction: Insight into “redox mediator-microbe-iron oxide” interaction process

DOE PAGES

Zhu, Weihuang; Shi, Mengran; Yu, Dan; ...

2016-03-29

Here, the characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into “redox mediator-iron oxide” interaction in the presence of DIRB. Two pre-incubation reaction systems of the “strain S12-goethite” and the “strain S12-AQS” were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of themore » redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for “Quinone-Iron” interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among “quinone-DIRB- goethite” under biotic/abiotic driven.« less

The human laryngeal microbiome: effects of cigarette smoke and reflux.

PubMed

Jetté, Marie E; Dill-McFarland, Kimberly A; Hanshew, Alissa S; Suen, Garret; Thibeault, Susan L

2016-10-24

Prolonged diffuse laryngeal inflammation from smoking and/or reflux is commonly diagnosed as chronic laryngitis and treated empirically with expensive drugs that have not proven effective. Shifts in microbiota have been associated with many inflammatory diseases, though little is known about how resident microbes may contribute to chronic laryngitis. We sought to characterize the core microbiota of disease-free human laryngeal tissue and to investigate shifts in microbial community membership associated with exposure to cigarette smoke and reflux. Using 454 pyrosequencing of the 16S rRNA gene, we compared bacterial communities of laryngeal tissue biopsies collected from 97 non-treatment-seeking volunteers based on reflux and smoking status. The core community was characterized by a highly abundant OTU within the family Comamonadaceae found in all laryngeal tissues. Smokers demonstrated less microbial diversity than nonsmokers, with differences in relative abundances of OTUs classified as Streptococcus, unclassified Comamonadaceae, Cloacibacterium, and Helicobacter. Reflux status did not affect microbial diversity nor community structure nor composition. Comparison of healthy laryngeal microbial communities to benign vocal fold disease samples revealed greater abundance of Streptococcus in benign vocal fold disease suggesting that mucosal dominance by Streptococcus may be a factor in disease etiology.

Metabolic Response of Soil Microorganisms to Frost: A New Perspective from Position-specific 13C Labeling

NASA Astrophysics Data System (ADS)

Bore, E. K.; Apostel, C.; Halicki, S.; Dippold, M. A.; Kuzyakov, Y.

2016-12-01

Cold adapted organisms and their biomolecules have received considerable attention in the last few decades, particularly in light of the perceived biotechnological potential. Mostly, these studies are based on pure isolated cultures from permafrost or permafrost samples with inherently adapted microbes. However, microbial activities in agricultural soils that are predominantly exposed to freeze conditions during winter in temperate ecosystems remain unclear. To analyze microbial metabolism at low soil temperatures, isotopomeres of position-specifically 13C labeled glucose were incubated at three temperature; 5 (control), -5 -20 oC. Soils were sampled after 1, 3 and 10 days (and after 30 days for samples at -20 °C). 13C was quantifed in CO2, bulk soil, microbial biomass and dissolved organic carbon (DOC). Highest 13C recovery in CO2 was obtained from C-1 position in control soil. Consequently, metabolic activity was dominated by pentose phosphate pathway at 5 °C. In contrast, metabolic behaviors switched towards a preferential respiration of the glucose C-4 position at -5 and -20 °C. High 13C recovery from C-4 position confirms previous studies suggesting that fermentation increases at subzero temperature. A 3-fold higher 13C recovery in microbial biomass at -5 °C than under control conditions points towards synthesis of intracellular antifreeze metabolites such as glycerol and ethanol and it is consistent with fermentative metabolism. A 5-fold higher 13C in bulk soil than microbial biomass at -20 °C does not reflect non-metabolized glucose because 13C recovery in DOC was less than 0.4% at day 1. Therefore, high 13C recovery in bulk soil at -20 °C was attributed to extracellular metabolites secreted to overcome frost. The shift in antifreeze mechanisms with temperature was brought about by shift in microbial community structure as indicated by incorporation into 13C into PLFA which was 2-fold higher in gram negative bacteria under control than frozen conditions, but inverted in gram positives. The results confirm that catabolic and anabolic processes continue under frozen conditions, but, mechanisms differ with temperature. This information is not only useful in modelling C dynamics in permafrost, but also in food industry where shelf-life depends on frozen conditions. Cold adapted organisms and their biomolecules have received considerable attention in the last few decades, particularly in light of the perceived biotechnological potential. Mostly, these studies are based on pure isolated cultures from permafrost or permafrost samples with inherently adapted microbes. However, microbial activities in agricultural soils that are predominantly exposed to freeze conditions during winter in temperate ecosystems remain unclear. To analyze microbial metabolism at low soil temperatures, isotopomeres of position-specifically 13C labeled glucose were incubated at three temperature; 5 (control), -5 -20 oC. Soils were sampled after 1, 3 and 10 days (and after 30 days for samples at -20 °C). 13C was quantifed in CO2, bulk soil, microbial biomass and dissolved organic carbon (DOC). Highest 13C recovery in CO2 was obtained from C-1 position in control soil. Consequently, metabolic activity was dominated by pentose phosphate pathway at 5 °C. In contrast, metabolic behaviors switched towards a preferential respiration of the glucose C-4 position at -5 and -20 °C. High 13C recovery from C-4 position confirms previous studies suggesting that fermentation increases at subzero temperature. A 3-fold higher 13C recovery in microbial biomass at -5 °C than under control conditions points towards synthesis of intracellular antifreeze metabolites such as glycerol and ethanol and it is consistent with fermentative metabolism. A 5-fold higher 13C in bulk soil than microbial biomass at -20 °C does not reflect non-metabolized glucose because 13C recovery in DOC was less than 0.4% at day 1. Therefore, high 13C recovery in bulk soil at -20 °C was attributed to extracellular metabolites secreted to overcome frost. The shift in antifreeze mechanisms with temperature was brought about by shift in microbial community structure as indicated by incorporation into 13C into PLFA which was 2-fold higher in gram negative bacteria under control than frozen conditions, but inverted in gram positives. The results confirm that catabolic and anabolic processes continue under frozen conditions, but, mechanisms differ with temperature. This information is not only useful in modelling C dynamics in permafrost, but also in food industry where shelf-life depends on frozen conditions.

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

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

Classen, Aimee T; Overby, Stephen; Hart, Stephen C

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality entering an ecosystem or indirectly by affecting a shift in the microbial community that mediate nutrient processes. We examine herbivore susceptibility and resistance effects on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore driven changes in litter inputs will feedback to the microbial community. Our study population consisted of individual trees that are susceptible or resistant to the stem-boring moth (Dioryctria albovittella) and trees that herbivores have been manually removed since 1982. Moth herbivory increased pi on litter nitrogen concentrations (16%) and canopy precipitation infiltrationmore » (28%), both significant factors influencing litter and soil microbial populations. Our research resulted in three major conclusions: 1) In spite of an increase in litter quality, herbivory does not change litter microarthropod abundance or species richness. 2) Herbivore susceptibility alters bulk soil microbial communities, but not soil properties. 3) Season has a strong influence on microbial communities, and their response to herbivore inputs, in this semi-arid ecosystem.« less

ATF4, A Novel Mediator of the Anabolic Actions of PTH on Bone

DTIC Science & Technology

2010-07-01

increased the expression of genes known to be associated with osteoblast differentiation including osteocalcin (Ocn), bone sialoprotein (Bsp...differentiation including osteocalcin (Ocn) (2.2-fold), bone sialoprotein (Bsp) (4.2-fold), alkaline phosphatase (Alp) (3.2-fold), a1(I) collagen (Col1... sialoprotein (BSP) gene transcription is mediated through a pituitary-specific transcription factor-1 (Pit-1) motif in the rat BSP gene promoter. Matrix Biol

Development of a Loop Mediated Isothermal Amplification (LAMP) - Surface Enhanced Raman spectroscopy (SERS) Assay for the Detection of Salmonella Enterica Serotype Enteritidis.

PubMed

Draz, Mohamed Shehata; Lu, Xiaonan

2016-01-01

As a major foodborne pathogen, Salmonella enterica serotype Enteritidis is increasingly rising as a global health concern. Here, we developed an integrated assay that combines loop mediated isothermal amplification (LAMP) and surface enhanced Raman spectroscopy (SERS) for DNA detection of S. Enteritidis using specifically designed Raman active Au-nanoprobes. The target DNA was amplified by LAMP and then labeled with Au-nanoprobes comprised of gold nanoparticle-modified with specific cy5/DNA probes to allow the detection by SERS. The sensitivity of the developed LAMP-SERS detection assay (66 CFU/mL) was ~100-fold higher than the conventional polymerase chain reaction (PCR) method. Significantly, this technique allowed highly specific detection of the target DNA of S. Enteritidis and could differentiate it from the DNA of closely related bacterial species or non-specific contamination, making it more accurate and reliable than the standard LAMP technique. The applicability of detection of S. Enteritidis in milk samples using LAMP-SERS assay was validated as well. In sum, the developed LAMP-SERS assay is highly specific and sensitive, and has the potential to be applied for rapid detection of different foodborne pathogens and other microbial contaminants.

Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation

PubMed Central

Meng, Guoyu; Spahich, Nicole; Kenjale, Roma; Waksman, Gabriel; St Geme, Joseph W

2011-01-01

Bacterial biofilms are complex microbial communities that are common in nature and are being recognized increasingly as an important determinant of bacterial virulence. However, the structural determinants of bacterial aggregation and eventual biofilm formation have been poorly defined. In Gram-negative bacteria, a major subgroup of extracellular proteins called self-associating autotransporters (SAATs) can mediate cell–cell adhesion and facilitate biofilm formation. In this study, we used the Haemophilus influenzae Hap autotransporter as a prototype SAAT to understand how bacteria associate with each other. The crystal structure of the H. influenzae HapS passenger domain (harbouring the SAAT domain) was determined to 2.2 Å by X-ray crystallography, revealing an unprecedented intercellular oligomerization mechanism for cell–cell interaction. The C-terminal SAAT domain folds into a triangular-prism-like structure that can mediate Hap–Hap dimerization and higher degrees of multimerization through its F1–F2 edge and F2 face. The intercellular multimerization can give rise to massive buried surfaces that are required for overcoming the repulsive force between cells, leading to bacterial cell–cell interaction and formation of complex microcolonies. PMID:21841773

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

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

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Increased Levels of Markers of Microbial Exposure in Homes with Indoor Storage of Organic Household Waste

PubMed Central

Wouters, Inge M.; Douwes, Jeroen; Doekes, Gert; Thorne, Peter S.; Brunekreef, Bert; Heederik, Dick J. J.

2000-01-01

As part of environmental management policies in Europe, separate collection of organic household waste and nonorganic household waste has become increasingly common. As waste is often stored indoors, this policy might increase microbial exposure in the home environment. In this study we evaluated the association between indoor storage of organic waste and levels of microbial agents in house dust. The levels of bacterial endotoxins, mold β(1→3)-glucans, and fungal extracullar polysaccharides (EPS) of Aspergillus and Penicillium species were determined in house dust extracts as markers of microbial exposure. House dust samples were collected in 99 homes in The Netherlands selected on the basis of whether separated organic waste was present in the house. In homes in which separated organic waste was stored indoors for 1 week or more the levels of endotoxin, EPS, and glucan were 3.2-, 7.6-, and 4.6-fold higher, respectively (all P < 0.05), on both living room and kitchen floors than the levels in homes in which only nonorganic residual waste was stored indoors. Increased levels of endotoxin and EPS were observed, 2.6- and 2.1-fold (P < 0.1), respectively, when separated organic waste was stored indoors for 1 week or less, whereas storage of nonseparated waste indoors had no effect on microbial agent levels (P > 0.2). The presence of textile floor covering was another major determinant of microbial levels (P < 0.05). Our results indicate that increased microbial contaminant levels in homes are associated with indoor storage of separated organic waste. These increased levels might increase the risk of bioaerosol-related respiratory symptoms in susceptible people. PMID:10653727

Models of microbiome evolution incorporating host and microbial selection.

PubMed

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

2017-09-25

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

The effect of peroxiredoxin 4 on fly physiology is a complex interplay of antioxidant and signaling functions

PubMed Central

Radyuk, Svetlana N.; Klichko, Vladimir I.; Michalak, Katarzyna; Orr, William C.

2013-01-01

Peroxiredoxin 4 (Prx4) has been implicated in a wide variety of biological processes, including development, progression of cancer, inflammation, and antioxidant function. The purpose of this study was to provide further insight into its multiple roles at the whole-animal level, using Drosophila. Reduced expression of dPrx4 (up to 90%) resulted in greater sensitivity to oxidative stress, an elevated H2O2 flux, and increases in lipid peroxidation, but no effect on longevity. Overexpression at low levels (<2-fold) gave reduced levels of oxidative damage and tended to show an increase in longevity. Flies expressing dPrx4 globally at high levels (>5-fold) had a dramatically reduced life span (by 20–80%) and increased apoptosis. Analysis of these overexpressors revealed an aberrant redistribution of the dPrx4 protein from the endoplasmic reticulum (ER) to cytosol and hemolymph. In addition to the known proapoptotic effects of the cytosolic form of dPrx4, dPrx4 overexpression triggered an NF-κB-mediated proinflammatory response, similar to that observed in cells under ER stress or when microbially challenged. Finally, we provide the first evidence that dPrx4, on secretion into the hemolymph, elicits a JAK/STAT-mediated response. The effects on fly survival and homeostasis appear to represent a combination of differential effects dictated in large part by dPrx4 subcellular and tissue-specific localization.—Radyuk, S. N., Klichko, V. I., Michalak, K., Orr, W. C. The effect of peroxiredoxin 4 on fly physiology is a complex interplay of antioxidant and signaling functions. PMID:23271054

An EXAFS study of zinc coordination in microbial cells.

PubMed

Webb, S M; Gaillard, J F; Jackson, B E; Stahl, D A

2001-03-01

Five microbes were isolated from metal amended enrichment cultures derived from the sediments of a lake contaminated by a zinc smelter. Each of these organisms was grown in pure culture in the presence of zinc. Quick Extended X-ray Absorption Fine Structure (QEXAFS) spectroscopy was used to investigate the average coordination environment of the zinc associated with the microbial biomass. Fitting of the first coordination shell of zinc shows that significant differences exist for each microbial species examined. The coordination environment of zinc varies between sulfurs to six-fold nitrogen/oxygen. with two microbial strains showing mixed coordination shells. Further study is required in order to characterize these sites and their locations within the cell.

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

PubMed

Barrick, Jeffrey E; Colburn, Geoffrey; Deatherage, Daniel E; Traverse, Charles C; Strand, Matthew D; Borges, Jordan J; Knoester, David B; Reba, Aaron; Meyer, Austin G

2014-11-29

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.

Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation.

PubMed

Button, Mark; Weber, Kela; Nivala, Jaime; Aubron, Thomas; Müller, Roland Arno

2016-03-01

Community-level physiological profiling (CLPP) using BIOLOG® EcoPlates™ has become a popular method for characterizing and comparing the functional diversity, functional potential, and metabolic activity of heterotrophic microbial communities. The method was originally developed for profiling soil communities; however, its usage has expanded into the fields of ecotoxicology, agronomy, and the monitoring and profiling of microbial communities in various wastewater treatment systems, including constructed wetlands for water pollution control. When performing CLPP on aqueous samples from constructed wetlands, a wide variety of sample characteristics can be encountered and challenges may arise due to excessive solids, color, or turbidity. The aim of this study was to investigate the impacts of different sample preparation methods on CLPP performed on a variety of aqueous samples covering a broad range of physical and chemical characteristics. The results show that using filter paper, centrifugation, or settling helped clarify samples for subsequent CLPP analysis, however did not do so as effectively as dilution for the darkest samples. Dilution was able to provide suitable clarity for the darkest samples; however, 100-fold dilution significantly affected the carbon source utilization patterns (CSUPs), particularly with samples that were already partially or fully clear. Ten-fold dilution also had some effect on the CSUPs of samples which were originally clear; however, the effect was minimal. Based on these findings, for this specific set of samples, a 10-fold dilution provided a good balance between ease of use, sufficient clarity (for dark samples), and limited effect on CSUPs. The process and findings outlined here can hopefully serve future studies looking to utilize CLPP for functional analysis of microbial communities and also assist in comparing data from studies where different sample preparation methods were utilized.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Specificity of marine microbial surface interactions.

PubMed Central

Imam, S H; Bard, R F; Tosteson, T R

1984-01-01

The macromolecular surface components involved in intraspecific cell surface interactions of the green microalga Chlorella vulgaris and closely associated bacteria were investigated. The specific surface attachment between this alga and its associated bacteria is mediated by lectin-like macromolecules associated with the surfaces of these cells. The binding activity of these surface polymers was inhibited by specific simple sugars; this suggests the involvement of specific receptor-ligand binding sites on the interactive surfaces. Epifluorescent microscopic evaluation of bacteria-alga interactions in the presence and absence of the macromolecules that mediate these interactions showed that the glycoproteins active in these processes were specific to the microbial sources from which they were obtained. The demonstration and definition of the specificity of these interactions in mixed microbial populations may play an important role in our understanding of the dynamics of marine microbial populations in the sea. PMID:6508293

Removal of heavy metal cations by biogenic magnetite nanoparticles produced in Fe(III)-reducing microbial enrichment cultures.

PubMed

Iwahori, Keisuke; Watanabe, Jun-ichi; Tani, Yukinori; Seyama, Haruhiko; Miyata, Naoyuki

2014-03-01

The biogenic magnetite nanoparticles presented here had a high capacity of adsorbing metal cations, which was approximately 30- to 40-fold greater than commercially available magnetite. These results suggest the potential application of microbial magnetite formation in the removal of toxic metal cations from water. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Humic substances-mediated microbial reductive dehalogenation of triclosan

NASA Astrophysics Data System (ADS)

Wang, L.; Xu, S.; Yang, Y.

2015-12-01

The role of natural organic matter in regulating the redox reactions as an electron shuttle has received lots of attention, because it can significantly affect the environmental degradation of contaminants and biogeochemical cycles of major elements. However, up to date, limited studies examined the role of natural organic matter in affecting the microbial dehalogenation of emergent organohalides, a critical detoxification process. In this study, we investigated the humic substance (HS)-mediated microbial dehalogenation of triclosan, a widely used antimicrobial agent. We found that the presence of HS stimulated the microbial degradation of triclosan by Shewanella putrefaciens CN-32. In the absence of HS, the triclosan was degraded gradually, achieving 8.6% residual at 8 days. With HS, the residual triclosan was below 2% after 4 days. Cl- was confirmed by ion chromatography analysis, but the dehalogenation processes and other byproducts warrant further investigations. The impact of HS on the degradation of triclosan was highly dependent on the concentration of HS. When the HS was below 15 mg/L, the degradation rate constant for triclosan increased with the organic carbon concentration. Beyond that point, the increased organic carbon concentration decreased the degradation of triclosan. Microbially pre-reduced HS abiotically reduced triclosan, testifying the electron shuttling processes. These results indicate that dissolved organic matter plays a dual role in regulating the degradation of triclosan: it mediates electron transport and inhibits the bioavailability through complexation. Such novel organic matter-mediated reactions for organohalides are important for evaluating the natural attenuation of emergent contaminants and designing cost-effective engineering treatment.

Construction Biotechnology: a new area of biotechnological research and applications.

PubMed

Stabnikov, Viktor; Ivanov, Volodymyr; Chu, Jian

2015-09-01

A new scientific and engineering discipline, Construction Biotechnology, is developing exponentially during the last decade. The major directions of this discipline are selection of microorganisms and development of the microbially-mediated construction processes and biotechnologies for the production of construction biomaterials. The products of construction biotechnologies are low cost, sustainable, and environmentally friendly microbial biocements and biogrouts for the construction ground improvement. The microbial polysaccharides are used as admixtures for cement. Microbially produced biodegradable bioplastics can be used for the temporarily constructions. The bioagents that are used in construction biotechnologies are either pure or enrichment cultures of microorganisms or activated indigenous microorganisms of soil. The applications of microorganisms in the construction processes are bioaggregation, biocementation, bioclogging, and biodesaturation of soil. The biotechnologically produced construction materials and the microbially-mediated construction technologies have a lot of advantages in comparison with the conventional construction materials and processes. Proper practical implementations of construction biotechnologies could give significant economic and environmental benefits.

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

PubMed

Silveira, Gustavo; Schneedorf, José Maurício

2018-02-21

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

An Overview of Electron Acceptors in Microbial Fuel Cells

PubMed Central

Ucar, Deniz; Zhang, Yifeng; Angelidaki, Irini

2017-01-01

Microbial fuel cells (MFC) have recently received increasing attention due to their promising potential in sustainable wastewater treatment and contaminant removal. In general, contaminants can be removed either as an electron donor via microbial catalyzed oxidization at the anode or removed at the cathode as electron acceptors through reduction. Some contaminants can also function as electron mediators at the anode or cathode. While previous studies have done a thorough assessment of electron donors, cathodic electron acceptors and mediators have not been as well described. Oxygen is widely used as an electron acceptor due to its high oxidation potential and ready availability. Recent studies, however, have begun to assess the use of different electron acceptors because of the (1) diversity of redox potential, (2) needs of alternative and more efficient cathode reaction, and (3) expanding of MFC based technologies in different areas. The aim of this review was to evaluate the performance and applicability of various electron acceptors and mediators used in MFCs. This review also evaluated the corresponding performance, advantages and disadvantages, and future potential applications of select electron acceptors (e.g., nitrate, iron, copper, perchlorate) and mediators. PMID:28469607

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer.

PubMed

Alcamán-Arias, María E; Farías, Laura; Verdugo, Josefa; Alarcón-Schumacher, Tomás; Díez, Beatriz

2018-05-01

Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.

Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

PubMed Central

Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

2015-01-01

Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

Microbial Community Response during the Iron Fertilization Experiment LOHAFEX

PubMed Central

Thiele, Stefan; Ramaiah, Nagappa; Amann, Rudolf

2012-01-01

Iron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean, Bacteria and Archaea were monitored within and outside an induced bloom, dominated by Phaeocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescence in situ hybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such as Roseobacter and Gammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers. PMID:23064339

Macrophage genetic reprogramming during chronic peritonitis is augmented by LPS pretreatment.

PubMed

Kanaan, Ziad; Gardner, Sarah; Carruba, Christopher; Mattingly, Jameson; Druen, Devin; Cheadle, William G

2012-06-15

Persistent and tertiary chronic peritonitis is a clinically challenging problem especially in those who are critically ill. This could be attributed to a state of immune-paralysis, known as microbial tolerance. Microbial tolerance is the diminished pro-inflammatory protein response following repeated stimulation by numerous pathogen-associated molecular patterns (PAMPs) of varying origins, which we have shown in this novel model of chronic peritonitis. We aimed in this study to investigate the molecular mechanisms behind microbial tolerance and the early innate immune response resolution in this model. C57BL/6 mice were pretreated intra-peritoneally (IP) with saline or endotoxin LPS 10 mg/kg (LPS 10). Following pretreatment, peritonitis was induced 24 h later injecting 10(3)Klebsiella pneumonia CFU IP. Gentamicin was administered 4 h prior to infection and BID thereafter. Peritoneal exudate cells (PEC) were obtained through peritoneal lavage and RNA was isolated (n = 3) at 4, 24, and 48 h following infection. SA Biosciences© RT2-Profiler PCR array mouse Toll-like receptor signaling pathway (PAMM_018A) data were further analyzed by Ingenuity Pathway Inc. analysis (IPA). Of the 89 genes studied, 26 were significantly up-regulated (fold change > 1.2 and P value < 0.05) in the saline pretreated group at 4, 24, and 48 h after infection. There were no down-regulated genes. In the LPS-pretreated group, 35 genes were significantly up-regulated; of these genes, 13 were not increased in the saline pretreated infected mice. This left 22 up-regulated genes in both infected groups. At 4 h, 6 of these 22 genes (CHUK, HMGB1, HSPD1, IRAK2, LY96, and TLR4) were further 2-fold increased in the LPS pretreatment group compared with the saline pretreatment group. Only IRAK2 was 2-fold increased at 24 h. By 48 h, no LPS effect was seen. When applying IPA analysis, six main canonical pathways were constantly dysregulated in the same significance order in both the saline and LPS group at 4, 24, and 48 h. These were: Toll-like receptor and NF-κB signaling, hepatic cholestasis, interleukin-6, and LPS-mediated MAPK signaling pathways, and pattern recognition receptors of bacterial pathway. Peritonitis increased PEC gene expression associated with sepsis and a pro-inflammatory response, which was further augmented by LPS pretreatment over 24 h only. Prior exposure to LPS did not induce PEC gene tolerance to subsequent infection with Klebsiella at the mRNA level. Post-transcriptional modification as microRNA down-regulation of inflammatory cytokines could possibly explain such phenomena. Published by Elsevier Inc.

Methane oxidation and abundance of methane oxidizers in tropical agricultural soil (vertisol) in response to CuO and ZnO nanoparticles contamination.

PubMed

Mohanty, Santosh Ranjan; Rajput, Parul; Kollah, Bharati; Chourasiya, Dipanti; Tiwari, Archana; Singh, Muneshwar; Rao, A Subba

2014-06-01

There is worldwide concern over the increase use of nanoparticles (NPs) and their ecotoxicological effect. It is not known if the annual production of tons of industrial nanoparticles (NPs) has the potential to impact terrestrial microbial communities, which are so necessary for ecosystem functioning. Here, we have examined the consequences of adding the NPs particularly the metal oxide (CuO, ZnO) on CH4 oxidation activity in vertisol and the abundance of heterotrophs, methane oxidizers, and ammonium oxidizers. Soil samples collected from the agricultural field located at Madhya Pradesh, India, were incubated with either CuO and ZnO NPs or ionic heavy metals (CuCl2, ZnCl2) separately at 0, 10, and 20 μg g(-1) soil. CH4 oxidation activity in the soil samples was estimated at 60 and 100 % moisture holding capacity (MHC) in order to link soil moisture regime with impact of NPs. NPs amended to soil were highly toxic for the microbial-mediated CH4 oxidation, compared with the ionic form. The trend of inhibition was Zn 20 > Zn 10 > Cu 20 > Cu 10. NPs delayed the lag phase of CH4 oxidation to a maximum of 4-fold and also decreased the apparent rate constant k up to 50 % over control. ANOVA and Pearson correlation analysis (α = 0.01) revealed significant impact of NPs on the CH4 oxidation activity and microbial abundance (p < 0.0001, and high F statistics). Principal component analysis (PCA) revealed that PC1 (metal concentration) rendered 76.06 % of the total variance, while 18.17 % of variance accounted by second component (MHC). Biplot indicated negative impact of NPs on CH4 oxidation and microbial abundance. Our result also confirmed that higher soil moisture regime alleviates toxicity of NPs and opens new avenues of research to manage ecotoxicity and environmental hazard of NPs.

Microbially enhanced dissolution and reductive dechlorination of PCE by a mixed culture: Model validation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Chen, Mingjie; Abriola, Linda M.; Amos, Benjamin K.; Suchomel, Eric J.; Pennell, Kurt D.; Löffler, Frank E.; Christ, John A.

2013-08-01

Reductive dechlorination catalyzed by organohalide-respiring bacteria is often considered for remediation of non-aqueous phase liquid (NAPL) source zones due to cost savings, ease of implementation, regulatory acceptance, and sustainability. Despite knowledge of the key dechlorinators, an understanding of the processes and factors that control NAPL dissolution rates and detoxification (i.e., ethene formation) is lacking. A recent column study demonstrated a 5-fold cumulative enhancement in tetrachloroethene (PCE) dissolution and ethene formation (Amos et al., 2009). Spatial and temporal monitoring of key geochemical and microbial (i.e., Geobacter lovleyi and Dehalococcoides mccartyi strains) parameters in the column generated a data set used herein as the basis for refinement and testing of a multiphase, compositional transport model. The refined model is capable of simulating the reactive transport of multiple chemical constituents produced and consumed by organohalide-respiring bacteria and accounts for substrate limitations and competitive inhibition. Parameter estimation techniques were used to optimize the values of sensitive microbial kinetic parameters, including maximum utilization rates, biomass yield coefficients, and endogenous decay rates. Comparison and calibration of model simulations with the experimental data demonstrate that the model is able to accurately reproduce measured effluent concentrations, while delineating trends in dechlorinator growth and reductive dechlorination kinetics along the column. Sensitivity analyses performed on the optimized model parameters indicate that the rates of PCE and cis-1,2-dichloroethene (cis-DCE) transformation and Dehalococcoides growth govern bioenhanced dissolution, as long as electron donor (i.e., hydrogen flux) is not limiting. Dissolution enhancements were shown to be independent of cis-DCE accumulation; however, accumulation of cis-DCE, as well as column length and flow rate (i.e., column residence time), strongly influenced the extent of reductive dechlorination. When cis-DCE inhibition was neglected, the model over-predicted ethene production ten-fold, while reductions in residence time (i.e., a two-fold decrease in column length or two-fold increase in flow rate) resulted in a more than 70% decline in ethene production. These results suggest that spatial and temporal variations in microbial community composition and activity must be understood to model, predict, and manage bioenhanced NAPL dissolution.

Beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra.

PubMed

Manjunath, Mallappa; Kanchan, Amrita; Ranjan, Kunal; Venkatachalam, Siddarthan; Prasanna, Radha; Ramakrishnan, Balasubramanian; Hossain, Firoz; Nain, Lata; Shivay, Yashbir Singh; Rai, Awadhesh Bahadur; Singh, Bijendra

2016-02-01

Microorganisms in the rhizosphere mediate the cycling of nutrients, their enhanced mobilisation and facilitate their uptake, leading to increased root growth, biomass and yield of plants. We examined the promise of beneficial cyanobacteria and eubacteria as microbial inoculants, applied singly or in combination as consortia or biofilms, to improve growth and yields of okra. Interrelationships among the microbial activities and the micro/macro nutrient dynamics in soils and okra yield characteristics were assessed along with the changes in the soil microbiome. A significant effect of microbial inoculation on alkaline phosphatase activity was recorded both at the mid-crop and harvest stages. Microbial biomass carbon values were highest due to the Anabaena sp. - Providencia sp. (CR1 + PR3) application. The yield of okra ranged from 444.6-478.4 g(-1) plant and a positive correlation (0.69) recorded between yield and root weight. The application of Azotobacter led to the highest root weight and yield. The concentration of Zn at mid-crop stage was 60-70% higher in the Azotobacter sp. and Calothrix sp. inoculated soils, as compared to uninoculated control. Iron concentration in soil was more than 2-3 folds higher than control at the mid-crop stage, especially due to the application of Anabaena-Azotobacter biofilm and Azotobacter sp. Both at the mid-crop and harvest stages, the PCR-DGGE profiles of eubacterial communities were similar among the uninoculated control, the Anabaena sp. - Providencia sp. (CW1 + PW5) and the Anabaena-Azotobacter biofilm treatments. Although the profiles of the Azotobacter, Calothrix and CR1 + PR3 treatments were identical at these stages of growth, the profile of CR1 + PR3 was clearly distinguishable. The performance of the inoculants, particularly Calothrix (T6) and consortium of Anabaena and Providencia (CR1 + PR3; T5), in terms of microbiological and nutrient data, along with generation of distinct PCR-DGGE profiles suggested their superiority and emphasized the utility of combining microbiological and molecular tools in the selection of effective microbial inoculants.

Adaptation of Aquatic Microbial Communities to Hg2+ Stress †

PubMed Central

Barkay, Tamar

1987-01-01

The mechanism of adaptation to Hg2+ in four aquatic habitats was studied by correlating microbially mediated Hg2+ volatilization with the adaptive state of the exposed communities. Community diversity, heterotrophic activity, and Hg2+ resistance measurements indicated that adaptation of all four communities was stimulated by preexposure to Hg2+. In saline water communities, adaptation was associated with rapid volatilization after an initial lag period. This mechanism, however, did not promote adaptation in a freshwater sample, in which Hg2+ was volatilized slowly, regardless of the resistance level of the microbial community. Distribution of the mer operon among representative colonies of the communities was not related to adaptation to Hg2+. Thus, although volatilization enabled some microbial communities to sustain their functions in Hg2+-stressed environments, it was not mediated by the genes that serve as a model system in molecular studies of bacterial resistance to mercurials. PMID:16347488

Needles in the blue sea: sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome.

PubMed

Saito, Mak A; Dorsk, Alexander; Post, Anton F; McIlvin, Matthew R; Rappé, Michael S; DiTullio, Giacomo R; Moran, Dawn M

2015-10-01

Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P-II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open-source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8 ± 1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13 ± 15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P-II peptide showed specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ∼4 × 10(7) , 1000-fold larger than an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

Malla, Muneer A; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd Allah, Elsayed Fathi

2018-01-01

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

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

PubMed Central

Malla, Muneer A.; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd_Allah, Elsayed Fathi

2018-01-01

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches. PMID:29915565

Interaction intensity and pollinator-mediated selection.

PubMed

Trunschke, Judith; Sletvold, Nina; Ågren, Jon

2017-05-01

In animal-pollinated plants, the opportunity for selection and the strength of pollinator-mediated selection are expected to increase with the degree of pollen limitation. However, whether differences in pollen limitation can explain variation in pollinator-mediated and net selection among animal-pollinated species is poorly understood. In the present study, we quantified pollen limitation, variance in relative fitness and pollinator-mediated selection on five traits important for pollinator attraction (flowering start, plant height, flower number, flower size) and pollination efficiency (spur length) in natural populations of 12 orchid species. Pollinator-mediated selection was quantified by subtracting estimates of selection gradients for plants receiving supplemental hand-pollination from estimates obtained for open-pollinated control plants. Mean pollen limitation ranged from zero to 0.96. Opportunity for selection, pollinator-mediated selection and net selection were all positively related to pollen limitation, whereas nonpollinator-mediated selection was not. Opportunity for selection varied five-fold, strength of pollinator-mediated selection varied three-fold and net selection varied 1.5-fold among species. Supplemental hand-pollination reduced both opportunity for selection and selection on floral traits. The results show that the intensity of biotic interactions is an important determinant of the selection regime, and indicate that the potential for pollinator-mediated selection and divergence in floral traits is particularly high in species that are strongly pollen-limited. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Role of Neurochemicals in the Interaction between the Microbiota and the Immune and the Nervous System of the Host Organism.

PubMed

Oleskin, Alexander V; Shenderov, Boris A; Rogovsky, Vladimir S

2017-09-01

This work is concerned with the role of evolutionary conserved substances, neurotransmitters, and neurohormones, within the complex framework of the microbial consortium-immune system-nervous system axis in the human or animal organism. Although the operation of each of these systems per se is relatively well understood, their combined effects on the host organism still await further research. Drawing on recent research on host-produced and microbial low-molecular-weight neurochemicals such as biogenic amines, amino acids, and short-chain fatty acids (SCFAs), we suggest that these mediators form a part of a universal neurochemical "language." It mediates the whole gamut of harmonious and disharmonious interactions between (a) the intestinal microbial consortium, (b) local and systemic immune cells, and (c) the central and peripheral nervous system. Importantly, the ongoing microbiota-host interactivity is bidirectional. We present evidence that a large number of microbially produced low-molecular-weight compounds are identical or homologous to mediators that are synthesized by immune or nervous cells and, therefore, can bind to the corresponding host receptors. In addition, microbial cells specifically respond to host-produced neuromediators/neurohormones because they have adapted to them during the course of many millions of years of microbiota-host coevolution. We emphasize that the terms "microbiota" and "microbial consortium" are to be used in the broadest sense, so as to include, apart from bacteria, also eukaryotic microorganisms. These are exemplified by the mycobiota whose role in the microbial consortium-immune system-nervous system axis researchers are only beginning to elucidate. In light of the above, it is imperative to reform the current strategies of using probiotic microorganisms and their metabolites for treating and preventing dysbiosis-related diseases. The review demonstrates, in the example of novel probiotics (psychobiotics), that many target-oriented probiotic preparations produce important side effects on a wide variety of processes in the host organism. In particular, we should take into account probiotics' capacity to produce mediators that can considerably modify the operation of the microecological, immune, and nervous system of the human organism.

Chitin degradation and electricity generation by Aeromonas hydrophila in microbial fuel cells.

PubMed

Li, Shan-Wei; He, Hui; Zeng, Raymond J; Sheng, Guo-Ping

2017-02-01

Chitin is one of the most abundant biopolymers in nature and the main composition of shrimp and crab shells (usually as food wastes). Thus it is essential to investigate the potential of degrading chitin for energy recovery. This study investigated the anaerobic degradation of chitin by Aeromonas hydrophila, a chitinolytic and popular electroactive bacterium, in both fermentation and microbial fuel cell (MFC) systems. The primary chitin metabolites produced in MFC were succinate, lactate, acetate, formate, and ethanol. The total metabolite concentration from chitin degradation increased seven-fold in MFC compared to the fermentation system, as well as additional electricity generation. Moreover, A. hydrophila degraded GlcNAc (the intermediate of chitin hydrolysis) significantly faster (0.97 and 0.94 mM C/d/mM-GlcNAc) than chitin (0.13 and 0.03 mM C/d/mM-GlcNAc) in MFC and fermentation systems, indicating that extracellular hydrolysis of chitin was the rate-limiting step and this step could be accelerated in MFC. Furthermore, more chemicals produced by the addition of exogenous mediators in MFC. This study proves that the chitin could be degraded effectively by an electroactive bacterium in MFC, and our results suggest that this bioelectrochemical system might be useful for the degradation of recalcitrant biomass to recover energy. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2013-02-01

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

Periodontitis: from microbial immune subversion to systemic inflammation

PubMed Central

Hajishengallis, George

2014-01-01

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

Dietary influence of kefir on microbial activities in the mouse bowel.

PubMed

Marquina, Domingo; Santos, A; Corpas, I; Muñoz, J; Zazo, J; Peinado, J M

2002-01-01

In this work the microflora present in kefir, a fermented milk product, was studied together with the effect of kefir administration on different groups of indigenous bacteria of mouse bowel. Kefir microflora was composed of lactic acid bacteria, acetic acid bacteria and yeasts. Yeast population was composed of Saccharomyces cerevisiae, S. unisporus, Candida kefir, Kluyveromyces marxianus and K. lactis. The streptococci levels in kefir treated mice increased by 10-fold and the levels of sulfite-reducing clostridia decreased by 100-fold. The number of lactic acid bacteria increased significantly. The administration of kefir significantly increased the lactic acid bacteria counts in the mucosa of the bowel. Ingestion of kefir specifically lowered microbial populations of Enterobacteriaceae and clostridia. This is the first long-term study about the effects of the kefir administration on the intestinal microflora of mice.

A Theoretical Lower Bound for Selection on the Expression Levels of Proteins

DOE PAGES

Price, Morgan N.; Arkin, Adam P.

2016-06-11

We use simple models of the costs and benefits of microbial gene expression to show that changing a protein's expression away from its optimum by 2-fold should reduce fitness by at least [Formula: see text], where P is the fraction the cell's protein that the gene accounts for. As microbial genes are usually expressed at above 5 parts per million, and effective population sizes are likely to be above 10(6), this implies that 2-fold changes to gene expression levels are under strong selection, as [Formula: see text], where Ne is the effective population size and s is the selection coefficient.more » Thus, most gene duplications should be selected against. On the other hand, we predict that for most genes, small changes in the expression will be effectively neutral.« less

A Theoretical Lower Bound for Selection on the Expression Levels of Proteins

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

Price, Morgan N.; Arkin, Adam P.

We use simple models of the costs and benefits of microbial gene expression to show that changing a protein's expression away from its optimum by 2-fold should reduce fitness by at least [Formula: see text], where P is the fraction the cell's protein that the gene accounts for. As microbial genes are usually expressed at above 5 parts per million, and effective population sizes are likely to be above 10(6), this implies that 2-fold changes to gene expression levels are under strong selection, as [Formula: see text], where Ne is the effective population size and s is the selection coefficient.more » Thus, most gene duplications should be selected against. On the other hand, we predict that for most genes, small changes in the expression will be effectively neutral.« less

Linking genes to ecosystem trace gas fluxes in a large-scale model system

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Cueva, A.; Volkmann, T. H. M.; Sengupta, A.; Troch, P. A.

2017-12-01

Soil microorganisms mediate biogeochemical cycles through biosphere-atmosphere gas exchange with significant impact on atmospheric trace gas composition. Improving process-based understanding of these microbial populations and linking their genomic potential to the ecosystem-scale is a challenge, particularly in soil systems, which are heterogeneous in biodiversity, chemistry, and structure. In oligotrophic systems, such as the Landscape Evolution Observatory (LEO) at Biosphere 2, atmospheric trace gas scavenging may supply critical metabolic needs to microbial communities, thereby promoting tight linkages between microbial genomics and trace gas utilization. This large-scale model system of three initially homogenous and highly instrumented hillslopes facilitates high temporal resolution characterization of subsurface trace gas fluxes at hundreds of sampling points, making LEO an ideal location to study microbe-mediated trace gas fluxes from the gene to ecosystem scales. Specifically, we focus on the metabolism of ubiquitous atmospheric reduced trace gases hydrogen (H2), carbon monoxide (CO), and methane (CH4), which may have wide-reaching impacts on microbial community establishment, survival, and function. Additionally, microbial activity on LEO may facilitate weathering of the basalt matrix, which can be studied with trace gas measurements of carbonyl sulfide (COS/OCS) and carbon dioxide (O-isotopes in CO2), and presents an additional opportunity for gene to ecosystem study. This work will present initial measurements of this suite of trace gases to characterize soil microbial metabolic activity, as well as links between spatial and temporal variability of microbe-mediated trace gas fluxes in LEO and their relation to genomic-based characterization of microbial community structure (phylogenetic amplicons) and genetic potential (metagenomics). Results from the LEO model system will help build understanding of the importance of atmospheric inputs to microorganisms pioneering fresh mineral matrix. Additionally, the measurement and modeling techniques that will be developed at LEO will be relevant for other investigators linking microbial genomics to ecosystem function in more well-developed soils with greater complexity.

A Profile of an Endosymbiont-enriched Fraction of the Coral Stylophora pistillata Reveals Proteins Relevant to Microbial-Host Interactions*

PubMed Central

Weston, Andrew J.; Dunlap, Walter C.; Shick, J. Malcolm; Klueter, Anke; Iglic, Katrina; Vukelic, Ana; Starcevic, Antonio; Ward, Malcolm; Wells, Mark L.; Trick, Charles G.; Long, Paul F.

2012-01-01

This study examines the response of Symbiodinium sp. endosymbionts from the coral Stylophora pistillata to moderate levels of thermal “bleaching” stress, with and without trace metal limitation. Using quantitative high throughput proteomics, we identified 8098 MS/MS events relating to individual peptides from the endosymbiont-enriched fraction, including 109 peptides meeting stringent criteria for quantification, of which only 26 showed significant change in our experimental treatments; 12 of 26 increased expression in response to thermal stress with little difference affected by iron limitation. Surprisingly, there were no significant increases in antioxidant or heat stress proteins; those induced to higher expression were generally involved in protein biosynthesis. An outstanding exception was a massive 114-fold increase of a viral replication protein indicating that thermal stress may substantially increase viral load and thereby contribute to the etiology of coral bleaching and disease. In the absence of a sequenced genome for Symbiodinium or other photosymbiotic dinoflagellate, this proteome reveals a plethora of proteins potentially involved in microbial-host interactions. This includes photosystem proteins, DNA repair enzymes, antioxidant enzymes, metabolic redox enzymes, heat shock proteins, globin hemoproteins, proteins of nitrogen metabolism, and a wide range of viral proteins associated with these endosymbiont-enriched samples. Also present were 21 unusual peptide/protein toxins thought to originate from either microbial consorts or from contamination by coral nematocysts. Of particular interest are the proteins of apoptosis, vesicular transport, and endo/exocytosis, which are discussed in context of the cellular processes of coral bleaching. Notably, the protein complement provides evidence that, rather than being expelled by the host, stressed endosymbionts may mediate their own departure. PMID:22351649

Nano-sized Fe2O3/Fe3O4 facilitate anaerobic transformation of hexavalent chromium in soil-water systems.

PubMed

Zhang, Yaxian; Li, Hua; Gong, Libo; Dong, Guowen; Shen, Liang; Wang, Yuanpeng; Li, Qingbiao

2017-07-01

The purpose of this study is to investigate the effects of nano-sized or submicro Fe 2 O 3 /Fe 3 O 4 on the bioreduction of hexavalent chromium (Cr(VI)) and to evaluate the effects of nano-sized Fe 2 O 3 /Fe 3 O 4 on the microbial communities from the anaerobic flooding soil. The results indicated that the net decreases upon Cr(VI) concentration from biotic soil samples amended with nano-sized Fe 2 O 3 (317.1±2.1mg/L) and Fe 3 O 4 (324.0±22.2mg/L) within 21days, which were approximately 2-fold of Cr(VI) concentration released from blank control assays (117.1±5.6mg/L). Furthermore, the results of denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing indicated a greater variety of microbes within the microbial community in amendments with nano-sized Fe 2 O 3 /Fe 3 O 4 than the control assays. Especially, Proteobacteria occupied a predominant status on the phylum level within the indigenous microbial communities from chromium-contaminated soils. Besides, some partial decrease of soluble Cr(VI) in abiotic nano-sized Fe 2 O 3 /Fe 3 O 4 amendments was responsible for the adsorption of nano-sized Fe 2 O 3 /Fe 3 O 4 to soluble Cr(VI). Hence, the presence of nano-sized Fe 2 O 3 /Fe 3 O 4 could largely facilitate the mobilization and biotransformation of Cr(VI) from flooding soils by adsorption and bio-mediated processes. Copyright © 2017. Published by Elsevier B.V.

Protective role of glycerol against benzene stress: insights from the Pseudomonas putida proteome.

PubMed

Bhaganna, Prashanth; Bielecka, Agata; Molinari, Gabriella; Hallsworth, John E

2016-05-01

Chemical activities of hydrophobic substances can determine the windows of environmental conditions over which microbial systems function and the metabolic inhibition of microorganisms by benzene and other hydrophobes can, paradoxically, be reduced by compounds that protect against cellular water stress (Bhaganna et al. in Microb Biotechnol 3:701-716, 2010; Cray et al. in Curr Opin Biotechnol 33:228-259, 2015a). We hypothesized that this protective effect operates at the macromolecule structure-function level and is facilitated, in part at least, by genome-mediated adaptations. Based on proteome profiling of the soil bacterium Pseudomonas putida, we present evidence that (1) benzene induces a chaotrope-stress response, whereas (2) cells cultured in media supplemented with benzene plus glycerol were protected against chaotrope stress. Chaotrope-stress response proteins, such as those involved in lipid and compatible-solute metabolism and removal of reactive oxygen species, were increased by up to 15-fold in benzene-stressed cells relative to those of control cultures (no benzene added). By contrast, cells grown in the presence of benzene + glycerol, even though the latter grew more slowly, exhibited only a weak chaotrope-stress response. These findings provide evidence to support the hypothesis that hydrophobic substances induce a chaotropicity-mediated water stress, that cells respond via genome-mediated adaptations, and that glycerol protects the cell's macromolecular systems. We discuss the possibility of using compatible solutes to mitigate hydrocarbon-induced stresses in lignocellulosic biofuel fermentations and for industrial and environmental applications.

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling.

PubMed

Piao, Hailan; Lachman, Medora; Malfatti, Stephanie; Sczyrba, Alexander; Knierim, Bernhard; Auer, Manfred; Tringe, Susannah G; Mackie, Roderick I; Yeoman, Carl J; Hess, Matthias

2014-01-01

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome-both microbially facilitated processes with global significance.

Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing.

PubMed

Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

2011-09-01

Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species--the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E-9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E-14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356-896 OTUs) was >2-fold higher than in the MI (112-567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that can effectively breakdown a wide variety of complex polysaccharides.

Diflerent formulations of microbial respiratory losses and microbial efficiency have pronounced short and long term consequences for soil C dynamics and soil respiration

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Billings, S. A.

2016-12-01

Much of the variability in projections of Earth's future C balance derives from uncertainty in how to formulate and parameterize models of biologically mediated transformations of soil organic C (SOC). Over the past decade, models of belowground decomposition have incorporated more realism, namely microbial biomass and exoenzyme pools, but it remains unclear whether microbially mediated decomposition is accurately formulated. Different models and different assumptions about how microbial efficiency, defined in terms of respiratory losses, varies with temperature exert great influence on SOC and CO2 flux projections for the future. Here, we incorporate a physiologically realistic formulation of CO2 loss from microbes, distinct from extant formulations and logically consistent with microbial C uptake and losses, into belowground dynamics and contrast its projections for SOC pools and CO2 flux from soils to those from the phenomenological formulations of efficiency in current models. We quantitatively describe how short and long term SOC dynamics are influenced by different mathematical formulations of efficiency, and that our lack of knowledge regarding loss rates from SOC and microbial biomass pools, specific respiration rate and maximum substrate uptake rate severely constrains our ability to confidently parameterize microbial SOC modules in Earth System Models. Both steady-state SOC and microbial biomass C pools, as well as transient responses to perturbations, can differ substantially depending on how microbial efficiency is derived. In particular, the discrepancy between SOC stocks for different formulations of efficiency varies from negligible to more than two orders of magnitude, depending on the relative values of respiratory versus non-respiratory losses from microbial biomass. Mass-specific respiration and proportional loss rates from soil microbes emerge as key determinants of the consequences of different formulations of efficiency for C flux in soils.

Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii

PubMed Central

Zurawski, Jeffrey V.; Khatibi, Piyum A.; Akinosho, Hannah O.; Straub, Christopher T.; Compton, Scott H.; Conway, Jonathan M.; Lee, Laura L.; Ragauskas, Arthur J.; Davison, Brian H.; Adams, Michael W. W.

2017-01-01

ABSTRACT Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates to C. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(−) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15% (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance. IMPORTANCE Key to a microbial process for solubilization of plant biomass is the organism's access to the carbohydrate content of lignocellulose. Economically viable routes will characteristically minimize physical, chemical, and biological pretreatment such that microbial steps contribute to the greatest extent possible. Recently, transgenic versions of plants and trees have been developed with the intention of lowering the barrier to lignocellulose conversion, with particular focus on lignin content and composition. Here, the extremely thermophilic bacterium Caldicellulosiruptor bescii was used to solubilize natural and genetically modified switchgrass lines, with and without the aid of hydrothermal treatment. For lignocellulose conversion, it is clear that the microorganism, plant biomass substrate, and processing steps must all be considered simultaneously to achieve optimal results. Whether switchgrass lines engineered for low lignin or natural variants with desirable properties are used, conversion will depend on microbial access to crystalline cellulose in the plant cell wall. PMID:28625990

Microbial communities in bulk fluids and biofilms of an oil facility have similar composition but different structure.

PubMed

Stevenson, Bradley S; Drilling, Heather S; Lawson, Paul A; Duncan, Kathleen E; Parisi, Victoria A; Suflita, Joseph M

2011-04-01

The oil-water-gas environments of oil production facilities harbour abundant and diverse microbial communities that can participate in deleterious processes such as biocorrosion. Several molecular methods, including pyrosequencing of 16S rRNA libraries, were used to characterize the microbial communities from an oil production facility on the Alaskan North Slope. The communities in produced water and a sample from a 'pig envelope' were compared in order to identify specific populations or communities associated with biocorrosion. The 'pigs' are used for physical mitigation of pipeline corrosion and fouling and the samples are enriched in surface-associated solids (i.e. paraffins, minerals and biofilm) and coincidentally, microorganisms (over 10(5) -fold). Throughout the oil production facility, bacteria were more abundant (10- to 150-fold) than archaea, with thermophilic members of the phyla Firmicutes (Thermoanaerobacter and Thermacetogenium) and Synergistes (Thermovirga) dominating the community. However, the structure (relative abundances of taxa) of the microbial community in the pig envelope was distinct due to the increased relative abundances of the genera Thermacetogenium and Thermovirga. The data presented here suggest that bulk fluid is representative of the biofilm communities associated with biocorrosion but that certain populations are more abundant in biofilms, which should be the focus of monitoring and mitigation strategies. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Expression, purification, and breast cancer cell inhibiting effect of recombinant human lactoferrin C-lobe.

PubMed

Hu, Lulu; Gao, Chen-Hui; Hong, Chao; Zhong, Qiao; Dong, Hong-Liang; Gao, Xiao-Ming

2016-01-01

Lactoferrin (LTF), a multifunctional glycoprotein of the transferrin family mainly found in exotic secretions in mammals, is an important defense molecule against not only microbial invasion but also tumors. It folds into two globular domains (N- and C-lobes) each containing an iron-binding site. The cationic antimicrobial peptide in N-lobe is known to exert anti-tumor effect via a non-receptor-mediated pathway. However, whether LTF C-lobe also contributes to its anti-tumor activity remains to be investigated. In this study, a human LTF fragment (amino acid residues 343-682) covering the C-lobe was expressed with a histidine tag in E. coli and the purified polypeptide refolded through a series of buffer changing procedure. The resultant recombinant protein caused significant growth arrest of breast carcinoma cells MDA-MB-231 in a dose- and time-dependent manner, evidently via induction of apoptosis of the cell. Our data suggest a positive role for the C-lobe of human LTF in controlling tumors in vitro.

Anticorrosive Microbial Polysaccharides: Structure-Function Relationships

USDA-ARS?s Scientific Manuscript database

Water-soluble microbial polysaccharides are often implicated in biofilm formation and are believed to mediate cell-cell aggregation and adhesion to surfaces. Generally, biofilm formation is considered harmful or undesirable, as it leads to increased drag, plugging of pores, dimished heat transfer, ...

Effects of positive results for Mycobacterium avium subsp paratuberculosis as determined by microbial culture of feces or antibody ELISA on results of caudal fold tuberculin test and interferon-gamma assay for tuberculosis in cattle.

PubMed

Dunn, John R; Kaneene, John B; Grooms, Daniel L; Bolin, Steven R; Bolin, Carole A; Bruning-Fann, Colleen S

2005-02-01

To determine whether cattle testing positive for Mycobacterium avium subsp paratuberculosis as determined by microbial culture of feces or antibody ELISA were more likely to have false-positive responses on the caudal fold tuberculin (CFT) test or interferon-gamma (IFN-gamma) assay for Mycobacterium bovis than cattle testing negative for M paratuberculosis. 1043 cattle from 10 herds in Michigan. Feces and blood samples for plasma were collected from cattle > or =24 months old on the day the CFT test was read. Fecal samples were submitted for microbial culture for M paratuberculosis. Plasma samples were tested for antibody against M paratuberculosis, and IFN-gamma after stimulation with purified protein derivative tuberculin from M bovis or M avium. Of 1043 cattle, 180 (17.3%) had positive CFT test results (suspects) and 8 (0.8%) had positive IFN-gamma assay results after stimulation with purified protein derivative tuberculin from M bovis. Forty-five (4.3%) and 115 (11.0%) cattle tested positive for M paratuberculosis as determined by microbial culture of feces and antibody ELISA, respectively. Cattle with positive responses for M paratuberculosis appeared to have an increased likelihood of false-positive results on the CFT test, although this association was not significant. No significant association was detected among cattle testing positive for M paratuberculosis as determined by microbial culture of feces and antibody ELISA and positive CFT test and IFN-gamma assay results for M bovis.

Effects of Non-Indigenous Oysters on Microbial Diversity and Ecosystem Functioning

PubMed Central

Green, Dannielle S.; Boots, Bas; Crowe, Tasman P.

2012-01-01

Invasive ecosystem engineers can physically and chemically alter the receiving environment, thereby affecting biodiversity and ecosystem functioning. The Pacific oyster, Crassostrea gigas, invasive throughout much of the world, can establish dense populations monopolising shorelines and possibly altering ecosystem processes including decomposition and nutrient cycling. The effects of increasing cover of invasive C. gigas on ecosystem processes and associated microbial assemblages in mud-flats were tested experimentally in the field. Pore-water nutrients (NH4 + and total oxidised nitrogen), sediment chlorophyll content, microbial activity, total carbon and nitrogen, and community respiration (CO2 and CH4) were measured to assess changes in ecosystem functioning. Assemblages of bacteria and functionally important microbes, including methanogens, methylotrophs and ammonia-oxidisers were assessed in the oxic and anoxic layers of sediment using terminal restriction length polymorphism of the bacterial 16S rRNA, mxaF, amoA and archaeal mcrA genes respectively. At higher covers (40 and 80%) of oysters there was significantly greater microbial activity, increased chlorophyll content, CO2 (13 fold greater) and CH4 (6 fold greater) emission from the sediment compared to mud-flats without C. gigas. At 10% cover, C. gigas increased the concentration of total oxidised nitrogen and altered the assemblage structure of ammonia-oxidisers and methanogens. Concentrations of pore-water NH4 + were increased by C. gigas regardless of cover. Invasive species can alter ecosystem functioning not only directly, but also indirectly, by affecting microbial communities vital for the maintenance of ecosystem processes, but the nature and magnitude of these effects can be non-linear, depending on invader abundance. PMID:23144762

Cytokine profile in severe gram-positive and gram-negative abdominal sepsis

PubMed Central

Surbatovic, Maja; Popovic, Nada; Vojvodic, Danilo; Milosevic, Ivan; Acimovic, Gordana; Stojicic, Milan; Veljovic, Milic; Jevdjic, Jasna; Djordjevic, Dragan; Radakovic, Sonja

2015-01-01

Sepsis is a principal cause of death in critical care units worldwide and consumes considerable healthcare resources. The aim of our study was to determine whether the early cytokine profile can discriminate between Gram-positive and Gram-negative bacteraemia (GPB and GNB, respectively) and to assess the prognostic value regarding outcome in critically ill patients with severe abdominal sepsis. The outcome measure was hospital mortality. Blood samples were obtained from 165 adult patients with confirmed severe abdominal sepsis. Levels of the proinflammatory mediators TNF-α, IL-8, IL-12 and IFN-γ and the anti-inflammatory mediators IL-1ra, IL-4, IL-10 and TGF-β1 were determined and correlated with the nature of the bacteria isolated from the blood culture and outcome. The cytokine profile in our study indicated that the TNF-α levels were 2-fold, IL-8 were 3.3-fold, IFN-γ were 13-fold, IL-1ra were 1.05-fold, IL-4 were 1.4-fold and IL-10 were 1.83-fold higher in the GNB group compared with the GPB group. The TNF-α levels were 4.7-fold, IL-8 were 4.6-fold, IL-1ra were 1.5-fold and IL-10 were 3.3-fold higher in the non-survivors compared with the survivors. PMID:26079127

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

PubMed

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

2006-03-15

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

Effect of structural modification of α-aminoxy peptides on their intestinal absorption and transport mechanism.

PubMed

Ma, Bin; Zha, Huiyan; Li, Na; Yang, Dan; Lin, Ge

2011-08-01

A representative α-aminoxy peptide 1 has been demonstrated to have a potential for the treatment of human diseases associated with Cl(-) channel dysfunctions. However, its poor intestinal absorption was determined. The purpose of this study was to delineate the transport mechanism responsible for its poor absorption and also to prepare peptide analogues by structural modifications of 1 at its isobutyl side chains without changing the α-aminoxy core for retaining biological activity to improve the intestinal absorption. The poor intestinal absorption of 1 was proved to be due to the P-glycoprotein (P-gp) mediated efflux transport in Caco-2 cell monolayer, intestinal segments in Ussing chamber and rat single pass intestinal perfusion models. Four analogues with propionic acid (2), butanamine (3), methyl (4) and hydroxymethyl side chains (5) were synthesized and tested using the same models. Except for the permeability of 2, the absorbable permeability of the modified peptides in Caco-2 cell monolayer and their intestinal absorption in rats were significantly improved to 7-fold (3), 4-fold (4), 11-fold (5) and 36-fold (2), 42-fold (3), 55-fold (4), 102-fold (5), respectively, compared with 1 (P(app), 0.034 ± 0.003 × 10(-6) cm/s; P(blood), 1.61 ± 0.807 × 10(-6) cm/s). More interestingly, the structural modification remarkably altered transport mechanism of the peptides, leading to the conversion of the active transport via P-gp mediation (1, 2), to MRP mediation (3), MRP plus BCRP mediation (4) or a passive diffusion (5). Furthermore, P-gp mediated efflux transport of 1 and 2 was demonstrated to not alter the P-gp expression, while 1 but not 2 exhibited uncompetitive inhibitory effect on P-gp ATPase. The results demonstrated that intestinal absorption and transport mechanism of the α-aminoxy peptides varied significantly with different structures, and their absorption can be dramatically improved by structural modifications, which allow us to further design and prepare better α-aminoxy peptide candidates with appropriate pharmacokinetic fates, including intestinal absorption, for potential clinical use.

Homochiral stereochemistry: the missing link of structure to energetics in protein folding.

PubMed

Kumar, Anil; Ramakrishnan, Vibin; Ranbhor, Ranjit; Patel, Kirti; Durani, Susheel

2009-12-24

The notion is tested that homochiral stereochemistry being ubiquitous to protein structure could be critical to protein folding as well, causing it to become frustrated energetically providing the basis for its solvent- and sequence-mediated control. The proof in support of the notion is found in a consensus of experiment and computation according to which suitable oligopeptides are in their folding-unfolding equilibria, at both macrostate and microstate levels, susceptible to dielectric because of the conflict of peptide-chain electrostatics with interpeptide hydrogen bonds when the structure is poly-L but not when it is alternating-L,D. The argument is thus made that homochiral stereochemistry may in protein folding provide the unifying basis for its solvent- and sequence-mediated control based on screening of peptide-chain electrostatics under conflict with folding of the chain due to homochiral stereochemistry. Dielectric is brought into spotlight as the effect comparatively obscure but presumably critical to the folding in protein structure for its control.

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe.

PubMed

Purahong, Witoon; Schloter, Michael; Pecyna, Marek J; Kapturska, Danuta; Däumlich, Veronika; Mital, Sanchit; Buscot, François; Hofrichter, Martin; Gutknecht, Jessica L M; Krüger, Dirk

2014-11-12

The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

Microbial enzyme activities of peatland soils in south central Alaska lowlands

EPA Science Inventory

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

MICROBIAL TRANSFORMATION RATE CONSTANTS OF STRUCTURALLY DIVERSE MAN-MADE CHEMICALS

EPA Science Inventory

To assist in estimating microbially mediated transformation rates of man-made chemicals from their chemical structures, all second order rate constants that have been measured under conditions that make the values comparable have been extracted from the literature and combined wi...

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Mechanism of Flavoprotein l-6-Hydroxynicotine Oxidase: pH and Solvent Isotope Effects and Identification of Key Active Site Residues.

PubMed

Fitzpatrick, Paul F; Chadegani, Fatemeh; Zhang, Shengnan; Dougherty, Vi

2017-02-14

The flavoenzyme l-6-hydroxynicotine oxidase is a member of the monoamine oxidase family that catalyzes the oxidation of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during microbial catabolism of nicotine. While the enzyme has long been understood to catalyze oxidation of the carbon-carbon bond, it has recently been shown to catalyze oxidation of a carbon-nitrogen bond [Fitzpatrick, P. F., et al. (2016) Biochemistry 55, 697-703]. The effects of pH and mutagenesis of active site residues have now been utilized to study the mechanism and roles of active site residues. Asn166 and Tyr311 bind the substrate, while Lys287 forms a water-mediated hydrogen bond with flavin N5. The N166A and Y311F mutations result in ∼30- and ∼4-fold decreases in k cat /K m and k red for (S)-6-hydroxynicotine, respectively, with larger effects on the k cat /K m value for (S)-6-hydroxynornicotine. The K287M mutation results in ∼10-fold decreases in these parameters and a 6000-fold decrease in the k cat /K m value for oxygen. The shapes of the pH profiles are not altered by the N166A and Y311F mutations. There is no solvent isotope effect on the k cat /K m value for amines. The results are consistent with a model in which both the charged and neutral forms of the amine can bind, with the former rapidly losing a proton to a hydrogen bond network of water and amino acids in the active site prior to the transfer of hydride to the flavin.

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

A simple microbial fuel cell model for improvement of biomedical device powering times.

PubMed

Roxby, Daniel N; Tran, Nham; Nguyen, Hung T

2014-01-01

This study describes a Matlab based Microbial Fuel Cell (MFC) model for a suspended microbial population, in the anode chamber for the use of the MFC in powering biomedical devices. The model contains three main sections including microbial growth, microbial chemical uptake and secretion and electrochemical modeling. The microbial growth portion is based on a Continuously Stirred Tank Reactor (CSTR) model for the microbial growth with substrate and electron acceptors. Microbial stoichiometry is used to determine chemical concentrations and their rates of change and transfer within the MFC. These parameters are then used in the electrochemical modeling for calculating current, voltage and power. The model was tested for typically exhibited MFC characteristics including increased electrode distances and surface areas, overpotentials and operating temperatures. Implantable biomedical devices require long term powering which is the main objective for MFCs. Towards this end, our model was tested with different initial substrate and electron acceptor concentrations, revealing a four-fold increase in concentrations decreased the power output time by 50%. Additionally, the model also predicts that for a 35.7% decrease in specific growth rate, a 50% increase in power longevity is possible.

Electricity generation from acetate and glucose by sedimentary bacterium attached to electrode in microbial-anode fuel cells

NASA Astrophysics Data System (ADS)

Zhang, Enren; Xu, Wei; Diao, Guowang; Shuang, Chendong

Microbial-anode fuel cells (MAFCs) with high electron recovery (>50%) from acetate and glucose have been constructed in this study. By inoculating fresh sedimentary microorganisms into anaerobic anode compartments, a stable current (∼0.42 mA for acetate-fed MAFCs; ∼0.35 mA for glucose-fed MAFCs) is generated from the oxidation of the added organic matter until its concentration decreases to a low level. SEM micrographs indicate that thick biofilms of microbial communities (coccoid cells with a diameter of ∼0.5 μm in acetate-fed MAFCs; rod-shaped cells with a length of 2.0-4.0 μm and a width of 0.5-0.7 μm in glucose-fed MAFCs) completely cover the anode electrodes. These anodophillic biofilms are thought to be responsible for the current generation, and make these microbial-anode fuel cells exhibit good performance even when the growth medium is replaced by a salt buffer without any growth factor. In comparison with those microbial fuel cells that require the addition of artificial electron transfer-mediating compounds, the findings in this study imply a potential way to develop excellent mediator-less MAFCs for electricity generation from organic matter by using substrate-induced anodophillic microbial species.

Inhibition of the receptor for advanced glycation end-products (RAGE) protects from secondhand smoke (SHS)-induced intrauterine growth restriction IUGR in mice.

PubMed

Lewis, Joshua B; Mejia, Camilo; Jordan, Clinton; Monson, Troy D; Bodine, Jared S; Dunaway, Todd M; Egbert, Kaleb M; Lewis, Adam L; Wright, Tanner J; Ogden, K Connor; Broberg, Dallin S; Hall, Parker D; Nelson, Shawn M; Hirschi, Kelsey M; Reynolds, Paul R; Arroyo, Juan A

2017-12-01

Intrauterine growth restriction (IUGR) is a disease affecting 10% of all pregnancies. IUGR is associated with maternal, fetal, or placental abnormalities. Studies investigating the effects of secondhand smoke (SHS) exposure and IUGR are limited. The receptor for advanced glycation end-products (RAGE) is a pro-inflammatory transmembrane receptor increased by SHS in the placenta. We tested the hypothesis that inhibition of RAGE during SHS exposure protects from smoke-induced IUGR. C57BL/6 mice were exposed to SHS or SHS + semi-synthetic glycosaminoglycan ethers (SAGEs) known to inhibit RAGE signaling. Trophoblast cells were treated with cigarette smoke extract (CSE) with or without SAGEs in order to address the effects of RAGE inhibition during trophoblast invasion in vitro. SHS-treated mice demonstrated a significant reduction in fetal weight (7.35-fold, P ≤ 0.0001) and placental weight (1.13-fold, P ≤ 0.0001) compared with controls. Mice co-treated with SHS and SAGEs were protected from SHS-induced fetal weights decreases. SHS treatment of C57BL/6 mice activated placental extracellular signal-regulated kinase (ERK) (3.0-fold, P ≤ 0.05), JNK (2.4-fold, P ≤ 0.05) and p38 (2.1-fold, P ≤ 0.05) and the expression of inflammatory mediators including TNF-α (1.34-fold, P ≤ 0.05) and IL-1β (1.03-fold, P ≤ 0.05). SHS-mediated activation of these molecules was reduced to basal levels when SAGE was co-administered. Invasion of trophoblast cells decreased 92% (P < 0.002) when treated with CSE and CSE-mediated invasion was completely reversed by SAGEs. We conclude that RAGE inhibition protects against fetal weight loss during SHS-induced IUGR. These studies provide insight into tobacco-mediated IUGR development and clarify avenues that may be helpful in the alleviation of placental complications.

Borneol Dehydrogenase from Pseudomonas sp. Strain TCU-HL1 Catalyzes the Oxidation of (+)-Borneol and Its Isomers to Camphor

PubMed Central

Tsang, Hoi-Lung; Huang, Jui-Lin; Lin, Yu-Hsuan; Huang, Kai-Fa; Lu, Pei-Luen; Lin, Guang-Huey; Khine, Aye Aye; Hu, Anren

2016-01-01

ABSTRACT Most plant-produced monoterpenes can be degraded by soil microorganisms. Borneol is a plant terpene that is widely used in traditional Chinese medicine. Neither microbial borneol dehydrogenase (BDH) nor a microbial borneol degradation pathway has been reported previously. One borneol-degrading strain, Pseudomonas sp. strain TCU-HL1, was isolated by our group. Its genome was sequenced and annotated. The genome of TCU-HL1 consists of a 6.2-Mbp circular chromosome and one circular plasmid, pTHL1 (12.6 kbp). Our results suggest that borneol is first converted into camphor by BDH in TCU-HL1 and is further decomposed through a camphor degradation pathway. The recombinant BDH was produced in the form of inclusion bodies. The apparent Km values of refolded recombinant BDH for (+)-borneol and (−)-borneol were 0.20 ± 0.01 and 0.16 ± 0.01 mM, respectively, and the kcat values for (+)-borneol and (−)-borneol were 0.75 ± 0.01 and 0.53 ± 0.01 s−1, respectively. Two plant BDH genes have been reported previously. The kcat and kcat/Km values of lavender BDH are about 1,800-fold and 500-fold lower, respectively, than those of TCU-HL1 BDH. IMPORTANCE The degradation of borneol in a soil microorganism through a camphor degradation pathway is reported in this study. We also report a microbial borneol dehydrogenase. The kcat and kcat/Km values of lavender BDH are about 1,800-fold and 500-fold lower, respectively, than those of TCU-HL1 BDH. The indigenous borneol- and camphor-degrading strain isolated, Pseudomonas sp. strain TCU-HL1, reminds us of the time 100 years ago when Taiwan was the major producer of natural camphor in the world. PMID:27542933

Investigating Transporter‐Mediated Drug‐Drug Interactions Using a Physiologically Based Pharmacokinetic Model of Rosuvastatin

PubMed Central

Wang, Q; Leil, T

2017-01-01

Rosuvastatin is a frequently used probe in transporter‐mediated drug‐drug interaction (DDI) studies. This report describes the development of a physiologically based pharmacokinetic (PBPK) model of rosuvastatin for prediction of pharmacokinetic (PK) DDIs. The rosuvastatin model predicted the observed single (i.v. and oral) and multiple dose PK profiles, as well as the impact of coadministration with transporter inhibitors. The predicted effects of rifampin and cyclosporine (6.58‐fold and 5.07‐fold increase in rosuvastatin area under the curve (AUC), respectively) were mediated primarily via inhibition of hepatic organic anion‐transporting polypeptide (OATP)1B1 (Inhibition constant (Ki) ∼1.1 and 0.014 µM, respectively) and OATP1B3 (Ki ∼0.3 and 0.007 µM, respectively), with cyclosporine also inhibiting intestinal breast cancer resistance protein (BCRP; Ki ∼0.07 µM). The predicted effects of gemfibrozil and its metabolite were moderate (1.88‐fold increase in rosuvastatin AUC) and mediated primarily via inhibition of hepatic OATP1B1 and renal organic cation transporter 3. This model of rosuvastatin will be useful in prospectively predicting transporter‐mediated DDIs with novel pharmaceutical agents in development. PMID:28296193

β-Arrestin-1 mediates thyrotropin-enhanced osteoblast differentiation.

PubMed

Boutin, Alisa; Eliseeva, Elena; Gershengorn, Marvin C; Neumann, Susanne

2014-08-01

Thyrotropin (TSH) activation of the TSH receptor (TSHR), a 7-transmembrane-spanning receptor (7TMR), may have osteoprotective properties by direct effects on bone. TSHR activation by TSH phosphorylates protein kinases AKT1, p38α, and ERK1/2 in some cells. We found TSH-induced phosphorylation of these kinases in 2 cell lines engineered to express TSHRs, human embryonic kidney HEK-TSHR cells and human osteoblastic U2OS-TSHR cells. In U2OS-TSHR cells, TSH up-regulated pAKT1 (7.1±0.5-fold), p38α (2.9±0.4-fold), and pERK1/2 (3.1±0.2-fold), whereas small molecule TSHR agonist C2 had no or little effect on pAKT1 (1.8±0.08-fold), p38α (1.2±0.09-fold), and pERK1/2 (1.6±0.19-fold). Furthermore, TSH increased expression of osteoblast marker genes ALPL (8.2±4.6-fold), RANKL (21±5.9-fold), and osteopontin (OPN; 17±5.3-fold), whereas C2 had little effect (ALPL, 1.7±0.5-fold; RANKL, 1.3±0.6-fold; and OPN, 2.2±0.7-fold). β-Arrestin-1 and -2 can mediate activatory signals by 7TMRs. TSH stimulated translocation of β-arrestin-1 and -2 to TSHR, whereas C2 failed to translocate either β-arrestin. Down-regulation of β-arrestin-1 by siRNA inhibited TSH-stimulated phosphorylation of ERK1/2, p38α, and AKT1, whereas down-regulation of β-arrestin-2 increased phosphorylation of AKT1 in both cell types and of ERK1/2 in HEK-TSHR cells. Knockdown of β-arrestin-1 inhibited TSH-stimulated up-regulation of mRNAs for OPN by 87 ± 1.7% and RANKL by 73 ± 2.4%, and OPN secretion by 74 ± 10%. We conclude that TSH enhances osteoblast differentiation in U2OS cells that is, in part, caused by activatory signals mediated by β-arrestin-1. © FASEB.

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

PubMed

Saleem, Muhammad; Moe, Luke A

2014-10-01

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

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

PubMed

Rautava, S

2016-02-01

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

Development of mediated BOD biosensor system of flow injection mode for shochu distillery wastewater.

PubMed

Oota, Shinichi; Hatae, Yuta; Amada, Kei; Koya, Hidekazu; Kawakami, Mitsuyasu

2010-09-15

Although microbial biochemical oxygen demand (BOD) sensors utilizing redox mediators have attracted much attention as a rapid BOD measurement method, little attempts have been made to apply the mediated BOD biosensors to the flow injection analysis system. In this work, a mediated BOD sensor system of flow injection mode, constructed by combining an immobilized microbial reactor with an electrochemical flow cell of three electrodes configuration, has been developed to estimate BOD of shochu distillery wastewater (SDW). It was demonstrated consequently that the mediated sensing was realized by employing phosphate buffer containing potassium hexacyanoferrate as the carrier. The output current was found to yield a peak with a sample injection, and to result from reoxidation of reduced mediator at the electrode. By employing the peak area as the sensor response, the effects of flow rate and pH of the carrier on the sensitivity were investigated. The sensor system using a microorganism of high SDW-assimilation capacity showed good performance and proved to be available for estimation of BOD of SDW. Copyright 2010 Elsevier B.V. All rights reserved.

Material-mediated pyrogens in medical devices: Applicability of the in vitro Monocyte Activation Test.

PubMed

Borton, Lindsey K; Coleman, Kelly P

2018-06-14

Pyrogenicity presents a challenge to clinicians, medical device manufactures, and regulators. A febrile response may be caused by endotoxin contamination, microbial components other than endotoxin, or chemical agents that generate a material-mediated pyrogenic response. While test methods for the assessment of endotoxin contamination and some microbial components other than endotoxin are well-established, material-mediated pyrogens remain elusively undefined. This review presents the findings of literature searches conducted to identify material-mediated pyrogens associated with medical devices. The in vivo rabbit pyrogen test (RPT) is considered to be the "gold standard" for medical device pyrogenicity testing, despite the fact that few medical device-derived material-mediated pyrogens are known. In line with global efforts to reduce the use of research animals, an in vitro monocyte activation test (MAT) has the potential to replace the RPT. The MAT is used to detect substances that activate human monocytes to release cytokines. This review will also describe the potential opportunities and challenges associated with MAT adoption for the detection of material-mediated pyrogens in medical device testing.

International Space Station environmental microbiome - microbial inventories of ISS filter debris.

PubMed

Venkateswaran, Kasthuri; Vaishampayan, Parag; Cisneros, Jessica; Pierson, Duane L; Rogers, Scott O; Perry, Jay

2014-01-01

Despite an expanding array of molecular approaches for detecting microorganisms in a given sample, rapid and robust means of assessing the differential viability of the microbial cells, as a function of phylogenetic lineage, remain elusive. A propidium monoazide (PMA) treatment coupled with downstream quantitative polymerase chain reaction (qPCR) and pyrosequencing analyses was carried out to better understand the frequency, diversity, and distribution of viable microorganisms associated with debris collected from the crew quarters of the International Space Station (ISS). The cultured bacterial counts were more in the ISS samples than cultured fungal population. The rapid molecular analyses targeted to estimate viable population exhibited 5-fold increase in bacterial (qPCR-PMA assay) and 25-fold increase in microbial (adenosine triphosphate assay) burden than the cultured bacterial population. The ribosomal nucleic acid-based identification of cultivated strains revealed the presence of only four to eight bacterial species in the ISS samples, however, the viable bacterial diversity detected by the PMA-pyrosequencing method was far more diverse (12 to 23 bacterial taxa) with the majority consisting of members of actinobacterial genera (Propionibacterium, Corynebacterium) and Staphylococcus. Sample fractions not treated with PMA (inclusive of both live and dead cells) yielded a great abundance of highly diverse bacterial (94 to 118 taxa) and fungal lineages (41 taxa). Even though deep sequencing capability of the molecular analysis widened the understanding about the microbial diversity, the cultivation assay also proved to be essential since some of the spore-forming microorganisms were detected only by the culture-based method. Presented here are the findings of the first comprehensive effort to assess the viability of microbial cells associated with ISS surfaces, and correlate differential viability with phylogenetic affiliation.

Exposure to microbial components and allergens in population studies: a comparison of two house dust collection methods applied by participants and fieldworkers.

PubMed

Schram-Bijkerk, D; Doekes, G; Boeve, M; Douwes, J; Riedler, J; Ublagger, E; von Mutius, E; Benz, M; Pershagen, G; Wickman, M; Alfvén, T; Braun-Fahrländer, C; Waser, M; Brunekreef, B

2006-12-01

Dust collection by study participants instead of fieldworkers would be a practical and cost-effective alternative in large-scale population studies estimating exposure to indoor allergens and microbial agents. We aimed to compare dust weights and biological agent levels in house dust samples taken by study participants with nylon socks, with those in samples taken by fieldworkers using the sampling nozzle of the Allergology Laboratory Copenhagen (ALK). In homes of 216 children, parents and fieldworkers collected house dust within the same year. Dust samples were analyzed for levels of allergens, endotoxin, (1-->3)-beta-D-glucans and fungal extracellular polysaccharides (EPS). Socks appeared to yield less dust from mattresses at relatively low dust amounts and more dust at high dust amounts than ALK samples. Correlations between the methods ranged from 0.47-0.64 for microbial agents and 0.64-0.87 for mite and pet allergens. Cat allergen levels were two-fold lower and endotoxin levels three-fold higher in socks than in ALK samples. Levels of allergens and microbial agents in sock samples taken by study participants are moderately to highly correlated to levels in ALK samples taken by fieldworkers. Absolute levels may differ, probably because of differences in the method rather than in the person who performed the sampling. Practical Implications Dust collection by participants is a reliable and practical option for allergen and microbial agent exposure assessment. Absolute levels of biological agents are not (always) comparable between studies using different dust collection methods, even when expressed per gram dust, because of potential differences in particle-size constitution of the collected dust.

Groundwater ecosystem resilience to organic contaminations: microbial and geochemical dynamics throughout the 5-year life cycle of a surrogate ethanol blend fuel plume.

PubMed

Ma, Jie; Nossa, Carlos W; Alvarez, Pedro J J

2015-09-01

The capacity of groundwater ecosystem to recover from contamination by organic chemicals is a vital concern for environmental scientists. A pilot-scale aquifer system was used to investigate the long-term dynamics of contaminants, groundwater geochemistry, and microbial community structure (by 16S rRNA gene pyrosequencing and quantitative real-time PCR) throughout the 5-year life cycle of a surrogate ethanol blend fuel plume (10% ethanol + 50 mg/L benzene + 50 mg/L toluene). Two-year continuous ethanol-blended release significantly changed the groundwater geochemistry (resulted in anaerobic, low pH, and organotrophic conditions) and increased bacterial and archaeal populations by 82- and 314-fold respectively. Various anaerobic heterotrophs (fermenters, acetogens, methanogens, and hydrocarbon degraders) were enriched. Two years after the release was shut off, all contaminants and their degradation byproducts disappeared and groundwater geochemistry completely restored to the pre-release states (aerobic, neutral pH, and oligotrophic). Bacterial and archaeal populations declined by 18- and 45-fold respectively (relative to the time of shut off). Microbial community structure reverted towards the pre-release states and alpha diversity indices rebounded, suggesting the resilience of microbial community to ethanol blend releases. We also found shifts from O2-sensitive methanogens (e.g., Methanobacterium) to methanogens that are not so sensitive to O2 (e.g., Methanosarcina and Methanocella), which is likely to contribute to the persistence of methanogens and methane generation following the source removal. Overall, the rapid disappearance of contaminants and their metabolites, rebound of geochemical footprints, and resilience of microbial community unequivocally document the natural capacity of groundwater ecosystem to attenuate and recover from a large volume of catastrophic spill of ethanol-based biofuel. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Importance of TLR2 and Macrophages in Modulating a Humoral Response after Encountering Streptococcus pneumoniae

DTIC Science & Technology

2008-03-26

Response after Encountering Streptococcus Pneumoniae" Brian Schae:5 ,Ph.D. Department of Microbi ogy & Immunology Committee Chairperson Masters...presenting cells (APCs), such as macrophages (M ) and dendritic cells (DC) recognize microbial surface components via cell surface receptors (i.e...stimulating factor (GM-CSF). TH1 cells are able to secrete IFN- , which is important in activating M to produce mediators important for microbial

AUGMENTATION OF LIMB PERFUSION AND REVERSAL OF TISSUE ISCHEMIA PRODUCED BY ULTRASOUND-MEDIATED MICROBUBBLE CAVITATION

PubMed Central

Belcik, J. Todd; Mott, Brian H.; Xie, Aris; Zhao, Yan; Kim, Sajeevani; Lindner, Nathan J.; Ammi, Azzdine; Linden, Joel M.; Lindner, Jonathan R.

2015-01-01

Background Ultrasound can increase tissue blood flow in part through the intravascular shear produced by oscillatory pressure fluctuations. We hypothesized that ultrasound-mediated increases in perfusion can be augmented by microbubble contrast agents that undergo ultrasound-mediated cavitation, and sought to characterize the biologic mediators. Methods and Results Contrast ultrasound perfusion imaging of hindlimb skeletal muscle and femoral artery diameter measurement were performed in non-ischemic mice after unilateral 10 min exposure to intermittent ultrasound alone (mechanical index [MI] 0.6 or 1.3) or ultrasound with lipid microbubbles (2×108 I.V.). Studies were also performed after inhibiting shear- or pressure-dependent vasodilator pathways, and in mice with hindlimb ischemia. Ultrasound alone produced a 2-fold increase (p<0.05) in muscle perfusion regardless of ultrasound power. Ultrasound-mediated augmentation in flow was greater with microbubbles (3-fold and 10-fold higher than control for MI 0.6 and 1.3, respectively; p<0.05), as was femoral artery dilation. Inhibition of endothelial nitric oxide synthase (eNOS) attenuated flow augmentation produced by ultrasound and microbubbles by 70% (p<0.01), whereas inhibition of adenosine-A2a receptors and epoxyeicosatrienoic acids had minimal effect. Limb nitric oxide (NO) production and muscle phospho-eNOS increased in a stepwise fashion by ultrasound and ultrasound with microbubbles. In mice with unilateral hindlimb ischemia (40–50% reduction in flow), ultrasound (MI 1.3) with microbubbles increased perfusion by 2-fold to a degree that was greater than the control non-ischemic limb. Conclusions Increases in muscle blood flow during high-power ultrasound are markedly amplified by the intravascular presence of microbubbles and can reverse tissue ischemia. These effects are most likely mediated by cavitation-related increases in shear and activation of eNOS. PMID:25834183

Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer

PubMed Central

Rabaey, Korneel; Boon, Nico; Siciliano, Steven D.; Verhaege, Marc; Verstraete, Willy

2004-01-01

Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2 of electrode surface to a maximal level of 4.31 W m−2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1 day−1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components. PMID:15345423

Biogeochemistry of three small Eutrophic Lakes Differentially Influenced by Marine Waters from Bayou Chico Bay, Pensacola, Florida

EPA Science Inventory

Biogeochemical models predict microbial mediated pathways but generally do not account for microorganisms. This study was undertaken to better understand relationships among microbial communities and N, S, Fe and C cycling in three lakes. Jackson Lakes formed from abandoned sand...

Shifts in microbial communities and soil nutrients along a fire chronosequence in Alaskan boreal forest

NASA Astrophysics Data System (ADS)

Treseder, K. K.; Mack, M. C.; Cross, A.

2002-12-01

Fires are important pathways of carbon loss from boreal forests, while microbial communities form equally important mechanisms for carbon accumulation between fires. We used a chronosequence in Alaska to examine shifts in microbial abundance and community composition in the several decades following severe fire, and then related these responses to soil characteristics in the same sites. The sites are located in upland forests near Delta Junction, Alaska, and represent stages at 3-, 15-, 45-, and over 100-yr following fire. Plant communities shift from herbaceous species in the youngest site, to deciduous shrubs and trees (e.g. Populus tremuloides and Salix) in the intermediate sites, to black spruce (Picea mariana) forest in the oldest site. Soil organic matter accumulated 2.8-fold over time. Potential mineralization was highest in the intermediate-aged sites, as was nitrification and standing pools of inorganic nitrogen. In contrast, inorganic phosphorus pools were highest immediately following fire, and then decreased nine-fold with age. As measured with BiologTM plates, bacterial diversity and abundance were greatest in the oldest sites. Plant roots in the intermediate-aged sites displayed higher colonization by ecto- and arbuscular mycorrhizal fungi than those in the youngest and oldest sites. Likewise, glomalin, a glycoprotein produced by arbuscular mycorrhizal fungi, was most abundant in the 14-yr old site. Glomalin is believed to contribute to the formation of water-stable aggregates in the soil. However, water stable aggregates were most abundant in the younger sites and did not follow the pattern of glomalin or arbuscular mycorrhizal abundance. Our results indicate that fire may maintain landscape-level diversity of microbial functional groups, and that carbon sequestration in microbial tissues (e.g. glomalin and fungal biomass) may be greatest in areas that have burned several decades earlier. Changes in soil structure may not be directly attributable to microbial activity.

Geoelectrical Evidence of Microbial Degradation of Diesel Contaminated Sediments

NASA Astrophysics Data System (ADS)

Werkema, D. D.; Atekwana, E. A.; Rossbach, S.; Sauck, W. A.

2003-12-01

The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynamics were determined by the rDNA intergenic spacer analysis (RISA), microbial mineralization of diesel fuel was assessed using dissolved inorganic carbon (DIC), enhanced mineral dissolution was determined by dissolved calcium, and the vertical geoelectrical profile was measured using DC resistivity (converted to conductivity). The columns simulated a saturation profile and contained sanitized, uniform sand with the following experimental treatments: diesel + microbes, diesel, microbes, and no treatment. After 16 months, two important conclusions were drawn. First, the relative increase in magnitude of the parameters measured was highest in the diesel + microbe column (showing at least 110% increase), lower in the diesel column and lowest (actually showing a decrease) in the column with no treatment. Further, the diesel + microbe column showed the greatest increase in oil degrading microbial populations (135%) compared to the column with no treatment, which showed no changes. Secondly, the depth at which the conductivity reached the maximum occurred within and slightly above the diesel layer (which represents a depth that was originally water wet). It was further observed that the relative change in bulk conductivity below the saturated zone is of a lower magnitude than above (<10%). These results suggest the diesel layer, and the zone slightly above, were the most biologically active. Additionally, the diesel + microbe column showed RISA fragments attributed to microbial succession typically observed in organic contaminant plumes. A simple Archie's Law analysis was used to estimate the pore water conductivities necessary to reproduce the bulk conductivity measured. This analysis shows that relative to the column with only microbes (selected as the control to be most representative of field conditions), the diesel column revealed a 2.3 fold increase and the diesel + microbe column showed a 3 fold increase in pore water conductivity. This increase was located within the diesel layer above the water saturated zone. Within the saturated zone, the no treatment column showed a 0.81 fold increase, the diesel column a 1.28, and the diesel + microbe column 1.45. We conclude from this study that microbial activity and the resultant biogeochemical changes played an important role in modifying the geoelectrical properties of aquifers and sediments rich in organic carbon and mineralized by bacteria by increasing the bulk conductivity. This conductive zone occurred within and immediately above the free-phase petroleum layer. In natural environments with high concentrations of organic compounds available as electron donors, geophysical techniques may potentially be used as indicators of microbial activity. Notice: This is an abstract of a proposed presentation and does not necessarily reflect the United States Environmental Protection Agency (EPA) policy. The actual presentation has not been peer reviewed by EPA. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Comparative performances of microbial capacitive deionization cell and microbial fuel cell fed with produced water from the Bakken shale.

PubMed

Shrestha, Namita; Chilkoor, Govinda; Wilder, Joseph; Ren, Zhiyong Jason; Gadhamshetty, Venkataramana

2018-06-01

This study evaluates and compares the performance of microbial fuel cells (MFCs) and microbial capacitive deionization cells (MCDCs) fed with wastewater produced from the Bakken shale. The produced water was characterized by high levels of dissolved solids and chemical oxygen demand (COD). Two-compartment MFCs and three-compartment MCDCs were evaluated under batch-fed mode using mixed microbial consortia in the anode, ferricyanide in the cathode, and produced water as the electrolyte in the anode and capacitive deionization units. COD removal in the MFCs was 88%, while that in the MCDCs was limited to 76%. The lower performance of the MCDCs was due to the large impedance (6600 Ω cm 2 ) compared with the MFCs (870 Ω cm 2 ). However, the MCDCs achieved two-fold higher removal of dissolved solids. Both the MFCs and MCDCs suffered from a higher impedance induced by fouling in the latter stages of the operation. Copyright © 2018 Elsevier B.V. All rights reserved.

Eicosanoid-mediated immunity in insects

USDA-ARS?s Scientific Manuscript database

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

Extracellular enzyme kinetics scale with resource availability

EPA Science Inventory

Microbial community metabolism relies on external digestion, mediated by extracellular enzymes that break down complex organic matter into molecules small enough for cells to assimilate. We analyzed the kinetics of 40 extracellular enzymes that mediate the degradation and assimi...

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

PubMed

Dick, Gregory J; Tebo, Bradley M

2010-05-01

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep-sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)-oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over-represented in the plume. Eight Mn(II)-oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome-level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.

Harnessing biodiesel-producing microbes: from genetic engineering of lipase to metabolic engineering of fatty acid biosynthetic pathway.

PubMed

Yan, Jinyong; Yan, Yunjun; Madzak, Catherine; Han, Bingnan

2017-02-01

Microbial production routes, notably whole-cell lipase-mediated biotransformation and fatty-acids-derived biosynthesis, offer new opportunities for synthesizing biodiesel. They compare favorably to immobilized lipase and chemically catalyzed processes. Genetically modified whole-cell lipase-mediated in vitro route, together with in vivo and ex vivo microbial biosynthesis routes, constitutes emerging and rapidly developing research areas for effective production of biodiesel. This review presents recent advances in customizing microorganisms for producing biodiesel, via genetic engineering of lipases and metabolic engineering (including system regulation) of fatty-acids-derived pathways. Microbial hosts used include Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Aspergillus oryzae. These microbial cells can be genetically modified to produce lipases under different forms: intracellularly expressed, secreted or surface-displayed. They can be metabolically redesigned and systematically regulated to obtain balanced biodiesel-producing cells, as highlighted in this study. Such genetically or metabolically modified microbial cells can support not only in vitro biotransformation of various common oil feedstocks to biodiesel, but also de novo biosynthesis of biodiesel from glucose, glycerol or even cellulosic biomass. We believe that the genetically tractable oleaginous yeast Yarrowia lipolytica could be developed to an effective biodiesel-producing microbial cell factory. For this purpose, we propose several engineered pathways, based on lipase and wax ester synthase, in this promising oleaginous host.

Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing

PubMed Central

Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

2011-01-01

Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species—the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E−9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E−14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356–896 OTUs) was >2-fold higher than in the MI (112–567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that can effectively breakdown a wide variety of complex polysaccharides. PMID:21451584

Solution structure of CXCL5--a novel chemokine and adipokine implicated in inflammation and obesity.

PubMed

Sepuru, Krishna Mohan; Poluri, Krishna Mohan; Rajarathnam, Krishna

2014-01-01

The chemokine CXCL5 is selectively expressed in highly specialized cells such as epithelial type II cells in the lung and white adipose tissue macrophages in muscle, where it mediates diverse functions from combating microbial infections by regulating neutrophil trafficking to promoting obesity by inhibiting insulin signaling. Currently very little is known regarding the structural basis of how CXCL5 mediates its novel functions. Towards this missing knowledge, we have solved the solution structure of the CXCL5 dimer by NMR spectroscopy. CXCL5 is a member of a subset of seven CXCR2-activating chemokines (CAC) that are characterized by the highly conserved ELR motif in the N-terminal tail. The structure shows that CXCL5 adopts the typical chemokine fold, but also reveals several distinct differences in the 30 s loop and N-terminal residues; not surprisingly, crosstalk between N-terminal and 30 s loop residues have been implicated as a major determinant of receptor activity. CAC function also involves binding to highly sulfated glycosaminoglycans (GAG), and the CXCL5 structure reveals a distinct distribution of positively charged residues, suggesting that differences in GAG interactions also influence function. The availability of the structure should now facilitate the design of experiments to better understand the molecular basis of various CXCL5 functions, and also serve as a template for the design of inhibitors for use in a clinical setting.

Microbial mediated retention/transformation of organic and inorganic materials in freshwater and marine ecosystems

EPA Science Inventory

Aquatic ecosystems are globally connected by hydrological and biogeochemical cycles. Microorganisms inhabiting aquatic ecosystems form the basis of food webs, mediate essential element cycles, decompose natural organic matter, transform inorganic nutrients and metals, and degrad...

Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products.

PubMed

Tremblay, Pier-Luc; Höglund, Daniel; Koza, Anna; Bonde, Ida; Zhang, Tian

2015-11-04

Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic, and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components, and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism.

Fungicide dissipation and impact on metolachlor aerobic soil degradation and soil microbial dynamics.

PubMed

White, Paul M; Potter, Thomas L; Culbreath, Albert K

2010-02-15

Pesticides are typically applied as mixtures and or sequentially to soil and plants during crop production. A common scenario is herbicide application at planting followed by sequential fungicide applications post-emergence. Fungicides depending on their spectrum of activity may alter and impact soil microbial communities. Thus there is a potential to impact soil processes responsible for herbicide degradation. This may change herbicide efficacy and environmental fate characteristics. Our study objective was to determine the effects of 4 peanut fungicides, chlorothalonil (2,4,5,6-tetrachloro-1,3-benzenedicarbonitrile), tebuconazole (alpha-[2-(4-chlorophenyl)ethyl]-alpha-(1,1-dimethylethyl)-1H-1,2,4-triazole-1-ethanol), flutriafol (alpha-(2-fluorophenyl)-alpha-(4-fluorophenyl)-1H-1,2,4-triazole-1-ethanol), and cyproconazole (alpha-(4-chlorophenyl)-alpha-(1-cyclopropylethyl)-1H-1,2,4-triazole-1-ethanol) on the dissipation kinetics of the herbicide, metolachlor (2-chloro-N-(6-ethyl-o-tolyl)-N-[(1RS)-2-methoxy-1-methylethyl]acetamide), and on the soil microbial community. This was done through laboratory incubation of field treated soil. Chlorothalonil significantly reduced metolachlor soil dissipation as compared to the non-treated control or soil treated with the other fungicides. Metolachlor DT(50) was 99 days for chlorothalonil-treated soil and 56, 45, 53, and 46 days for control, tebuconazole, flutriafol, and cyproconazole-treated soils, respectively. Significant reductions in predominant metolachlor metabolites, metolachlor ethane sulfonic acid (MESA) and metolachlor oxanilic acid (MOA), produced by oxidation of glutathione-metolachlor conjugates were also observed in chlorothalonil-treated soil. This suggested that the fungicide impacted soil glutathione-S-transferase (GST) activity. Fungicide DT(50) was 27-80 days but impacts on the soil microbial community as indicated by lipid biomarker analysis were minimal. Overall study results indicated that chlorothalonil has the potential to substantially increase soil persistence (2-fold) of metolachlor and alter fate and transport processes. GST mediated metabolism is common pesticide detoxification process in soil; thus there are implications for the fate of many active ingredients.

Effect of Microbial inoculation in combating the aluminium toxicity effect on growth of Zea mays.

PubMed

Arora, P; Singh, G; Tiwari, A

2017-07-31

The present study is aimed at improving the aluminium tolerance in maize crop employing the potential of microbial inoculants in conferring resistance to these toxicities via production of certain chelating compounds like siderophores, exopolysachharides and organic acids. Acid soils have now-a-days become one of the key factors for limiting growth of many agriculturally important crops. Aluminium  is one of the major elements present in acid soils and is mainly responsible for toxicity in the soil. This aluminium is rapidly soluble in soil water and hence absorbed by plant roots under conditions where soil pH is below 5. This toxicity leads to severe root growth inhibition, thereby limiting the production of maize crops. It was observed that use of microbial inoculums can be helpful in elimination of these toxic compounds and prevent the inhibition of root growth . It was found that the soils contaminated with aluminium toxicity decreased the root length of maize plant significantly by 65% but Bacillus and Burkholderia inoculation increased this root length significantly by 1.4- folds and 2- folds respectively thereby combating the effect of aluminium toxicity. Aluminium concentration was found maximum in roots of plants which were grown under aluminium stress condition. But this aluminium accumulation decreased ̴ 2-folds when Burkholderia was used as seed inoculants under aluminium stress conditions. Also, at 60mM aluminium accumulation, phosphorus solubilisation in roots was found to be increased upto 30% on Burkholderia inoculation. However, Bacillus inoculation didn't show any significant difference in either of the case. Thus, the inoculation of seeds with Burkholderia isolates could prove to be a boon in sequestering aluminium toxicity in Zea mays.

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone.

PubMed

Ganesh, Sangita; Bristow, Laura A; Larsen, Morten; Sarode, Neha; Thamdrup, Bo; Stewart, Frank J

2015-12-01

The genetic composition of marine microbial communities varies at the microscale between particle-associated (PA; >1.6 μm) and free-living (FL; 0.2-1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8- to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (>1.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5-9.4nMNd(-1)) fell to zero and N2 production by denitrification (0.5-1.7nMNd(-1)) and anammox (0.3-1.9nMNd(-1)) declined by 53-85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N2O and N2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N2O and N2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs.

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

PubMed Central

Ganesh, Sangita; Bristow, Laura A; Larsen, Morten; Sarode, Neha; Thamdrup, Bo; Stewart, Frank J

2015-01-01

The genetic composition of marine microbial communities varies at the microscale between particle-associated (PA; >1.6 μm) and free-living (FL; 0.2–1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8- to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (>1.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5–9.4nMNd−1) fell to zero and N2 production by denitrification (0.5–1.7nMNd−1) and anammox (0.3–1.9nMNd−1) declined by 53–85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N2O and N2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N2O and N2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs. PMID:25848875

Metabolic Surgery Profoundly Influences Gut Microbial-Host Metabolic Crosstalk

PubMed Central

Li, Jia V.; Ashrafian, Hutan; Bueter, Marco; Kinross, James; Sands, Caroline; le Roux, Carel W; Bloom, Stephen R.; Darzi, Ara; Athanasiou, Thanos; Marchesi, Julian R.; Nicholson, Jeremy K.; Holmes, Elaine

2013-01-01

Background and Aims Bariatric surgery is increasingly performed worldwide to treat morbid obesity and is also known as metabolic surgery to reflect its beneficial metabolic effects especially with respect to improvement in type 2 diabetes. Understanding surgical weight loss mechanisms and metabolic modulation is required to enhance patient benefits and operative outcomes. Methods We apply a parallel and statistically integrated metagenomic and metabonomic approach to characterize Roux-en-Y gastric bypass (RYGB) effects in a rat model. Results We show substantial shifts of the main gut phyla towards higher levels of Proteobacteria (52-fold) specifically Enterobacter hormaechei. We also find low levels of Firmicutes (4.5-fold) and Bacteroidetes (2-fold) in comparison to sham-operated rats. Faecal extraction studies reveal a decrease in faecal bile acids and a shift from protein degradation to putrefaction through decreased faecal tyrosine with concomitant increases in faecal putrescine and diamnoethane. We find decreased urinary amines and cresols and demonstrate indices of modulated energy metabolism post-RYGB including decreased urinary succinate, 2-oxoglutarate, citrate and fumarate. These changes could also indicate renal tubular acidosis, which associates with increased flux of mitochondrial tricarboxylic acid cycle intermediates. A surgically-induced effect on the gut-brain-liver metabolic axis is inferred by increased neurotropic compounds; faecal γ-aminobutyric acid (GABA) and glutamate. Conclusion This profound co-dependence of mammalian and microbial metabolism, which is systematically altered following RYGB surgery, suggests that RYGB exerts local and global metabolic activities. The effect of RYGB surgery on the host metabolic-microbial crosstalk augments our understanding of the metabolic phenotype of bariatric procedures and can facilitate enhanced treatments for obesity-related diseases. PMID:21572120

Impedance Spectroscopy as a Tool for Non-Intrusive Detection of Extracellular Mediators in Microbial Fuel Cells

DTIC Science & Technology

2009-12-01

bioseparation. Hoboken, NJ: John Wiley & Sons, p. 267. HernandezME, Kappler A, Newman DK. 2004. Phenazines and other redox active antibiotics promote...Verstraete W. 2005. Microbial phenazine production enhances electron transfer in biofuel cells. Environ Sci Technol 39:3401. Ramasamy RP, Ren Z, Mench MM

Influence of redox mediators and salinity level on the (bio)transformation of Direct Blue 71: kinetics aspects.

PubMed

Alvarez, Luis H; Meza-Escalante, Edna R; Gortáres-Moroyoqui, Pablo; Morales, Luz; Rosas, Krystal; García-Reyes, Bernardo; García-González, Alicone

2016-12-01

The rate-limiting step of azo dye decolorization was elucidated by exploring the microbial reduction of a model quinone and the chemical decolorization by previously reduced quinone at different salinity conditions (2-8%). Microbial experiments were performed in batch with a marine consortium. The decolorization of Direct Blue 71 (DB71) by the marine consortium at 2% salinity, mediated with anthraquinone-2,6-disulfonate (AQDS), showed the highest rate of decolorization as compared with those obtained with riboflavin, and two samples of humic acids. Moreover, the incubations at different salinity conditions (0-8%) performed with AQDS showed that the highest rate of decolorization of DB71 by the marine consortium occurred at 2% and 4% salinity. In addition, the highest microbial reduction rate of AQDS occurred in incubations at 0%, 2%, and 4% of salinity. The chemical reduction of DB71 by reduced AQDS occurred in two stages and proceeded faster at 4% and 6% salinity. The results indicate that the rate-limiting step during azo decolorization was the microbial reduction of AQDS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Aerobic biological treatment of synthetic municipal wastewater in membrane-coupled bioreactors.

PubMed

Klatt, Christian G; LaPara, Timothy M

2003-05-05

Membrane-coupled bioreactors (MBRs) offer many benefits compared to conventional biological wastewater treatment systems; however, their performance characteristics are poorly understood. Laboratory-scale MBRs were used to study bacterial adaptations in physiology and community structure. MBRs were fed a mixture of starch, gelatin, and polyoxyethylene-sorbitan monooleate to simulate the polysaccharide, protein, and lipid components of municipal wastewater. Physiological adaptations were detected by measuring ectoenzyme activity while structural dynamics were studied by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments. As cell biomass accumulated in the MBRs, pollutant removal efficiency initially improved and then stabilized with respect to effluent concentrations of chemical oxygen demand, protein, and carbohydrate. Comparison of the MBR effluent to filtered reactor fluid indicated that a portion of the observed pollutant removal was due to filtration by the membrane rather than microbial activity. The rates of ectoenzyme-mediated polysaccharide (alpha-glucosidase) and protein (leucine aminopeptidase) hydrolysis became relatively constant once pollutant removal efficiency stabilized. However, the maximum rate of lipid hydrolysis (heptanoate esterase) concomitantly increased more than 10-fold. Similarly, alpha-glucosidase and leucine aminopeptidase ectoenzyme affinities were relatively constant, while the heptanoate esterase affinity increased more than 30-fold. Community analysis revealed that a substantial community shift occurred within the first 7 days of operation. A Flavobacterium-like bacterial population dominated the community (>50% of total band intensity) and continued to do so for the remainder of the experiment. Copyright 2003 Wiley Periodicals, Inc.

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

PubMed Central

Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

2014-01-01

Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling. PMID:24694714

Incorporating the soil environment and microbial community into plant competition theory

PubMed Central

Ke, Po-Ju; Miki, Takeshi

2015-01-01

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

Exploitation of microbes for enhancing bacoside content and reduction of Meloidogyne incognita infestation in Bacopa monnieri L.

PubMed

Gupta, Rupali; Tiwari, Sudeep; Saikia, Shilpi K; Shukla, Virendra; Singh, Rashmi; Singh, S P; Kumar, P V Ajay; Pandey, Rakesh

2015-01-01

Despite the vast exploration of rhizospheric microbial wealth for crop yield enhancement, knowledge about the efficacy of microbial agents as biocontrol weapons against root-knot disease is scarce, especially in medicinal plants, viz., Bacopa monnieri. In the present investigation, rhizospheric microbes, viz., Bacillus megaterium, Glomus intraradices, Trichoderma harzianum ThU, and their combinations were evaluated for the management of Meloidogyne incognita (Kofoid and White) Chitwood and bacoside content enhancement in B. monnieri var CIM-Jagriti. A novel validated method Fourier transform near infrared was used for rapid estimation of total bacoside content. A significant reduction (2.75-fold) in root-knot indices was observed in the combined treatment of B. megaterium and T. harzianum ThU in comparison to untreated control plants. The same treatment also showed significant enhancement (1.40-fold) in total bacoside contents (plant active molecule) content using Fourier transform near-infrared (FT-NIR) method that analyses samples rapidly in an hour without solvent usage and provides ample scope for natural product studies.

Effects of pre-fermentation and pulsed-electric-field treatment of primary sludge in microbial electrochemical cells.

PubMed

Ki, Dongwon; Parameswaran, Prathap; Popat, Sudeep C; Rittmann, Bruce E; Torres, César I

2015-11-01

The aim of this study was to investigate the combination of two technologies - pulsed electric field (PEF) pre-treatment and semi-continuous pre-fermentation of primary sludge (PS) - to produce volatile fatty acids (VFAs) as the electron donor for microbial electrolysis cells (MECs). Pre-fermentation with a 3-day solids retention time (SRT) led to the maximum generation of VFAs, with or without pretreatment of the PS through pulsed-electric-fields (PEF). PEF treatment before fermentation enhanced the accumulation of the preferred VFA, acetate, by 2.6-fold. Correspondingly, MEC anodes fed with centrate from 3-day pre-fermentation of PEF-treated PS had a maximum current density ∼3.1 A/m(2), which was 2.4-fold greater than the control pre-fermented centrate. Over the full duration of batch MEC experiments, using pre-fermented centrate led to successful performance in terms of Coulombic efficiency (95%), Coulombic recovery (80%), and COD-removal efficiency (85%). Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimization of cold-adapted lysozyme production from the psychrophilic yeast Debaryomyces hansenii using statistical experimental methods.

PubMed

Wang, Quanfu; Hou, Yanhua; Yan, Peisheng

2012-06-01

Statistical experimental designs were employed to optimize culture conditions for cold-adapted lysozyme production of a psychrophilic yeast Debaryomyces hansenii. In the first step of optimization using Plackett-Burman design (PBD), peptone, glucose, temperature, and NaCl were identified as significant variables that affected lysozyme production, the formula was further optimized using a four factor central composite design (CCD) to understand their interaction and to determine their optimal levels. A quadratic model was developed and validated. Compared to the initial level (18.8 U/mL), the maximum lysozyme production (65.8 U/mL) observed was approximately increased by 3.5-fold under the optimized conditions. Cold-adapted lysozymes production was first optimized using statistical experimental methods. A 3.5-fold enhancement of microbial lysozyme was gained after optimization. Such an improved production will facilitate the application of microbial lysozyme. Thus, D. hansenii lysozyme may be a good and new resource for the industrial production of cold-adapted lysozymes. © 2012 Institute of Food Technologists®

Microbial mercury methylation in Antarctic sea ice.

PubMed

Gionfriddo, Caitlin M; Tate, Michael T; Wick, Ryan R; Schultz, Mark B; Zemla, Adam; Thelen, Michael P; Schofield, Robyn; Krabbenhoft, David P; Holt, Kathryn E; Moreau, John W

2016-08-01

Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.

Folding and unfolding pathway of chaperonin GroEL monomer and elucidation of thermodynamic parameters.

PubMed

Puri, Sarita; Chaudhuri, Tapan K

2017-03-01

The conformation and thermodynamic stability of monomeric GroEL were studied by CD and fluorescence spectroscopy. GroEL denaturation with urea and dilution in buffer leads to formation of a folded GroEL monomer. The monomeric nature of this protein was verified by size-exclusion chromatography and native PAGE. It has a well-defined secondary and tertiary structure, folding activity (prevention of aggregation) for substrate protein and is resistant to proteolysis. Being a properly folded and reversibly refoldable, monomeric GroEL is amenable for the study of thermodynamic stability by unfolding transition methods. We present the equilibrium unfolding of monomeric GroEL as studied by urea and heat mediated unfolding processes. The urea mediated unfolding shows two transitions and a single transition in the heat mediated unfolding process. In the case of thermal unfolding, some residual structure unfolds at a higher temperature (70-75°C). The process of folding/unfolding is reversible in both cases. Analysis of folding/unfolding data provides a measure of ΔG NU H 2 O , T m , ΔH van and ΔS van of monomeric GroEL. The thermodynamic stability parameter ΔG NU H 2 O is similar with both CD and intrinsic fluorescence i.e. 7.10±1.0kcal/mol. The calculated T m , ΔH van and ΔS van from the thermal unfolding transition is 46±0.5°C, 43.3±0.1kcal/mol and 143.9±0.1cal/mol/k respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial Diversity in Endostromatolites (cf. Fissure Calcretes) and in the Surrounding Permafrost Landscape, Haughton Impact Structure Region, Devon Island, Canada

NASA Astrophysics Data System (ADS)

Pellerin, André; Lacelle, Denis; Fortin, Danielle; Clark, Ian D.; Lauriol, Bernard

2009-11-01

In recent years, endostromatolites, which consist of finely laminated calcite columns that grow orthogonally within millimeter- to centimeter-thick fissures in limestone bedrock outcrops, have been discovered in dolomitic outcrops in the Haughton impact structure region, Devon Island, Canada. The growth mechanism of the endostromatolites is believed to be very slow and possibly intertwined with biotic and abiotic processes. Therefore, to discern how endostromatolites form in this polar desert environment, the composition of the microbial community of endostromatolites was determined by means of molecular phylogenetic analysis and compared to the microbial communities found in the surrounding soils. The microbial community present within endostromatolites can be inferred to be (given the predominant metabolic traits of related organisms) mostly aerobic and chemoheterotrophic, and belongs in large part to the phylum Actinobacteria and the subphylum Alphaproteobacteria. The identification of these bacteria suggests that the conditions within the fissure were mostly oxidizing during the growth of endostromatolite. The DNA sequences also indicate that a number of bacteria that closely resemble Rubrobacter radiotolerans are abundant in the endostromatolites as well as other Actinobacteria and Alphaproteobacteria. Some of these taxa have been associated with calcite precipitation, which suggests that the endostromatolites might in fact be microbially mediated. Bacterial communities from nearby permanently frozen soils were more diverse and harbored all the phyla found in the endostromatolites with additional taxa. This study on the microbial communities preserved in potentially microbially mediated secondary minerals in the Arctic could help in the search for evidence of life-forms near the edge of habitability on other planetary bodies.

Geobacter Dominates the Inner Layers of a Stratified Biofilm on a Fluidized Anode During Brewery Wastewater Treatment

PubMed Central

Tejedor-Sanz, Sara; Fernández-Labrador, Patricia; Hart, Steven; Torres, Cesar I.; Esteve-Núñez, Abraham

2018-01-01

In this study, we designed a microbial electrochemical fluidized bed reactor (ME-FBR), with an electroconductive anodic bed made of activated carbon particles for treating a brewery wastewater. Under a batch operating mode, acetate and propionate consumption rates were 13-fold and 2.4-fold higher, respectively, when the fluidized anode was polarized (0.2 V) with respect to open circuit conditions. Operating in a continuous mode, this system could effectively treat the brewery effluent at organic loading rates (OLR) over 1.7 kg m-3NRV d-1 and with removal efficiencies of 95 ± 1.4% (hydraulic retention time of 1 day and an influent of 1.7 g-COD L-1). The coulombic efficiency values highly depended upon the OLR applied, and varied from a 56 ± 15% to 10 ± 1%. Fluorescence in situ hybridization (FISH) analysis revealed a relative high abundance of Geobacter species (ca. 20%), and clearly showed a natural microbial stratification. Interestingly, the Geobacter cluster was highly enriched in the innermost layers of the biofilm (thickness of 10 μm), which were in contact with the electroconductive particles of bed, whereas the rest of bacteria were located in the outermost layers. To our knowledge, this is the first time that such a clear microbial stratification has been observed on an anode-respiring biofilm. Our results revealed the relevant role of Geobacter in switching between the electrode and other microbial communities performing metabolic reactions in the outermost environment of the biofilm. PMID:29568284

Immune-related genetic enrichment in frontotemporal dementia: An analysis of genome-wide association studies.

PubMed

Broce, Iris; Karch, Celeste M; Wen, Natalie; Fan, Chun C; Wang, Yunpeng; Tan, Chin Hong; Kouri, Naomi; Ross, Owen A; Höglinger, Günter U; Muller, Ulrich; Hardy, John; Momeni, Parastoo; Hess, Christopher P; Dillon, William P; Miller, Zachary A; Bonham, Luke W; Rabinovici, Gil D; Rosen, Howard J; Schellenberg, Gerard D; Franke, Andre; Karlsen, Tom H; Veldink, Jan H; Ferrari, Raffaele; Yokoyama, Jennifer S; Miller, Bruce L; Andreassen, Ole A; Dale, Anders M; Desikan, Rahul S; Sugrue, Leo P

2018-01-01

Converging evidence suggests that immune-mediated dysfunction plays an important role in the pathogenesis of frontotemporal dementia (FTD). Although genetic studies have shown that immune-associated loci are associated with increased FTD risk, a systematic investigation of genetic overlap between immune-mediated diseases and the spectrum of FTD-related disorders has not been performed. Using large genome-wide association studies (GWASs) (total n = 192,886 cases and controls) and recently developed tools to quantify genetic overlap/pleiotropy, we systematically identified single nucleotide polymorphisms (SNPs) jointly associated with FTD-related disorders-namely, FTD, corticobasal degeneration (CBD), progressive supranuclear palsy (PSP), and amyotrophic lateral sclerosis (ALS)-and 1 or more immune-mediated diseases including Crohn disease, ulcerative colitis (UC), rheumatoid arthritis (RA), type 1 diabetes (T1D), celiac disease (CeD), and psoriasis. We found up to 270-fold genetic enrichment between FTD and RA, up to 160-fold genetic enrichment between FTD and UC, up to 180-fold genetic enrichment between FTD and T1D, and up to 175-fold genetic enrichment between FTD and CeD. In contrast, for CBD and PSP, only 1 of the 6 immune-mediated diseases produced genetic enrichment comparable to that seen for FTD, with up to 150-fold genetic enrichment between CBD and CeD and up to 180-fold enrichment between PSP and RA. Further, we found minimal enrichment between ALS and the immune-mediated diseases tested, with the highest levels of enrichment between ALS and RA (up to 20-fold). For FTD, at a conjunction false discovery rate < 0.05 and after excluding SNPs in linkage disequilibrium, we found that 8 of the 15 identified loci mapped to the human leukocyte antigen (HLA) region on Chromosome (Chr) 6. We also found novel candidate FTD susceptibility loci within LRRK2 (leucine rich repeat kinase 2), TBKBP1 (TBK1 binding protein 1), and PGBD5 (piggyBac transposable element derived 5). Functionally, we found that the expression of FTD-immune pleiotropic genes (particularly within the HLA region) is altered in postmortem brain tissue from patients with FTD and is enriched in microglia/macrophages compared to other central nervous system cell types. The main study limitation is that the results represent only clinically diagnosed individuals. Also, given the complex interconnectedness of the HLA region, we were not able to define the specific gene or genes on Chr 6 responsible for our pleiotropic signal. We show immune-mediated genetic enrichment specifically in FTD, particularly within the HLA region. Our genetic results suggest that for a subset of patients, immune dysfunction may contribute to FTD risk. These findings have potential implications for clinical trials targeting immune dysfunction in patients with FTD.

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

PubMed

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

2018-02-09

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

Quorum-Quenching Human Designer Cells for Closed-Loop Control of Pseudomonas aeruginosa Biofilms.

PubMed

Sedlmayer, Ferdinand; Jaeger, Tina; Jenal, Urs; Fussenegger, Martin

2017-08-09

Current antibiotics gradually lose their efficacy against chronic Pseudomonas aeruginosa infections due to development of increased resistance mediated by biofilm formation, as well as the large arsenal of microbial virulence factors that are coordinated by the cell density-dependent phenomenon of quorum sensing. Here, we address this issue by using synthetic biology principles to rationally engineer quorum-quencher cells with closed-loop control to autonomously dampen virulence and interfere with biofilm integrity. Pathogen-derived signals dynamically activate a synthetic mammalian autoinducer sensor driving downstream expression of next-generation anti-infectives. Engineered cells were able to sensitively score autoinducer levels from P. aeruginosa clinical isolates and mount a 2-fold defense consisting of an autoinducer-inactivating enzyme to silence bacterial quorum sensing and a bipartite antibiofilm effector to dissolve the biofilm matrix. The self-guided cellular device fully cleared autoinducers, potentiated bacterial antibiotic susceptibility, substantially reduced biofilms, and alleviated cytotoxicity to lung epithelial cells. We believe this strategy of dividing otherwise coordinated pathogens and breaking up their shielded stronghold represents a blueprint for cellular anti-infectives in the postantibiotic era.

Linking Chaotic Advection with Subsurface Biogeochemical Processes

NASA Astrophysics Data System (ADS)

Mays, D. C.; Freedman, V. L.; White, S. K.; Fang, Y.; Neupauer, R.

2017-12-01

This work investigates the extent to which groundwater flow kinematics drive subsurface biogeochemical processes. In terms of groundwater flow kinematics, we consider chaotic advection, whose essential ingredient is stretching and folding of plumes. Chaotic advection is appealing within the context of groundwater remediation because it has been shown to optimize plume spreading in the laminar flows characteristic of aquifers. In terms of subsurface biogeochemical processes, we consider an existing model for microbially-mediated reduction of relatively mobile uranium(VI) to relatively immobile uranium(IV) following injection of acetate into a floodplain aquifer beneath a former uranium mill in Rifle, Colorado. This model has been implemented in the reactive transport code eSTOMP, the massively parallel version of STOMP (Subsurface Transport Over Multiple Phases). This presentation will report preliminary numerical simulations in which the hydraulic boundary conditions in the eSTOMP model are manipulated to simulate chaotic advection resulting from engineered injection and extraction of water through a manifold of wells surrounding the plume of injected acetate. This approach provides an avenue to simulate the impact of chaotic advection within the existing framework of the eSTOMP code.

Enhancing the electron transfer capacity and subsequent color removal in bioreactors by applying thermophilic anaerobic treatment and redox mediators.

PubMed

dos Santos, A B; Traverse, J; Cervantes, F J; van Lier, J B

2005-01-05

The effect of temperature, hydraulic retention time (HRT) and the redox mediator anthraquinone-2,6-disulfonate (AQDS), on electron transfer and subsequent color removal from textile wastewater was assessed in mesophilic and thermophilic anaerobic bioreactors. The results clearly show that compared with mesophilic anaerobic treatment, thermophilic treatment at 55 degrees C is an effective approach for increasing the electron transfer capacity in bioreactors, and thus improving the decolorization rates. Furthermore, similar color removals were found at 55 degrees C between the AQDS-free and AQDS-supplemented reactors, whereas a significant difference (up to 3.6-fold) on decolorization rates occurred at 30 degrees C. For instance, at an HRT of 2.5 h and in the absence of AQDS, the color removal was 5.3-fold higher at 55 degrees C compared with 30 degrees C. The impact of a mix of mediators with different redox potentials on the decolorization rate was investigated with both industrial textile wastewater and the azo dye Reactive Red 2 (RR2). Color removal of RR2 in the presence of anthraquinone-2-sulfonate (AQS) (standard redox potential E(0)' of -225 mV) was 3.8-fold and 2.3-fold higher at 30 degrees C and 55 degrees C, respectively, than the values found in the absence of AQS. Furthermore, when the mediators 1,4-benzoquinone (BQ) (E(0)' of +280 mV), and AQS were incubated together, there was no improvement on the decolorization rates compared with the bottles solely supplemented with AQS. Results imply that the use of mixed redox mediators with positive and negative E(0)' under anaerobic conditions is not an efficient approach to improve color removal in textile wastewaters. (c) 2004 Wiley Periodicals, Inc.

Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

NASA Astrophysics Data System (ADS)

Kritee, K.; Barkay, Tamar; Blum, Joel D.

2009-03-01

Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg degradation experiments and, based on estimates of the rates of the various steps involved in this mer mediated pathway, suggest which steps in the process could contribute towards the observed extent of fractionation. This framework suggests that at lower cell densities catalysis by MerB was the rate limiting step while at higher cell densities transport into the cell, which does not cause fractionation, became the rate limiting step. In addition to presenting evidence for absence of MIF during mer mediated Hg transformations, based on the nature of Hg compounds and microbe-Hg interactions, we suggest that the nuclear spin dependent MIF (i.e., the magnetic isotope effect) is also unlikely to occur during other non mer mediated 'dark' microbial Hg transformations (e.g., formation of MMHg and oxidative degradation of MMHg). Because of the important implications of the absence of MIF during biological processes on Hg isotope systematics, we discuss theoretical considerations and experimental strategies that could be used to confirm this suggestion.

γ–Butyrobetaine is a pro-atherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO

PubMed Central

Koeth, Robert A.; Levison, Bruce S.; Culley, Miranda K.; Buffa, Jennifer A.; Wang, Zeneng; Gregory, Jill C.; Org, Elin; Wu, Yuping; Li, Lin; Smith, Jonathan D.; Wilson Tang, W. H.; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

2014-01-01

Summary L- Carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ~1000-fold higher than the formation of TMA. Moreover, we show γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, and like dietary L-carnitine, in a gut microbiota-dependent manner is converted into TMA and TMAO, and accelerates atherosclerosis. Gut microbial composition and functional metabolic studies reveal distinct taxa are associated with the production of γBB versus TMA/TMAO from dietary L-carnitine. Moreover, despite their close structural similarity, chronic dietary exposure to L-carnitine versus γBB promotes development of functionally distinct microbial communities optimized for the metabolism of L-carnitine versus γBB, respectively. PMID:25440057

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

Stimulating soil microorganisms for mineralizing the herbicide isoproturon by means of microbial electroremediating cells.

PubMed

Rodrigo Quejigo, Jose; Dörfler, Ulrike; Schroll, Reiner; Esteve-Núñez, Abraham

2016-05-01

The absence of suitable terminal electron acceptors (TEA) in soil might limit the oxidative metabolism of environmental microbial populations. Microbial electroremediating cells (MERCs) consist in a variety of bioelectrochemical devices that aim to overcome electron acceptor limitation and maximize metabolic oxidation with the purpose of enhancing the biodegradation of a pollutant in the environment. The objective of this work was to use MERCs principles for stimulating soil bacteria to achieve the complete biodegradation of the herbicide (14) C-isoproturon (IPU) to (14) CO(2) in soils. Our study concludes that using electrodes at a positive potential [+600 mV (versus Ag/AgCl)] enhanced the mineralization by 20-fold respect the electrode-free control. We also report an overall profile of the (14) C-IPU metabolites and a (14) C mass balance in response to the different treatments. The remarkable impact of electrodes on the microbial activity of natural communities suggests a promising future for this emerging environmental technology that we propose to name bioelectroventing. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

PubMed Central

2015-01-01

The establishment of early life microbiota in the human infant gut is highly variable and plays a crucial role in host nutrient availability/uptake and maturation of immunity. Although high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the acquisition of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. This method dramatically improved the overall depth of infant gut proteome measurement, with an increase in the number of identified low-abundance proteins and a greater than 2-fold improvement in microbial protein identification and quantification. This enhancement of proteome measurement depth enabled a more extensive microbiome comparison between infants by not only increasing the confidence of identified microbial functional categories but also revealing previously undetected categories. PMID:25350865

Relationship between the omega-3 index and specialized pro-resolving lipid mediators in patients with peripheral arterial disease taking fish oil supplements.

PubMed

Schaller, Melinda S; Zahner, Greg J; Gasper, Warren J; Harris, William S; Conte, Michael S; Hills, Nancy K; Grenon, S Marlene

Oral supplementation with n-3 polyunsaturated fatty acids (PUFA) increases the omega-3 index, a biomarker of red blood cell eicosapentaenoic acid and docosahexaenoic acid, and plasma levels of biosynthesis pathway markers and potent lipid mediators involved in the resolution of inflammation among patients with peripheral arterial disease (PAD). We aimed to quantify the association between an upstream change in the omega-3 index and downstream changes in lipid mediator production. We conducted a secondary analysis of the OMEGA-PAD I Trial, a randomized, placebo controlled trial investigating high-dose n-3 PUFA oral supplementation in PAD patients. Eighty subjects were randomized to either 4.4 g of fish oil or placebo for 1 month. Regression analyses using generalized estimating equation techniques were used to investigate the relationship between changes in the omega-3 index and changes in lipid mediators, pre- and post-intervention. In the fish oil group, there was a significant increase in the omega-3 index (5 ± 1% to 9 ± 2%, P < .001) as well as in the plasma levels of several downstream lipid mediator pathway markers of resolution, which are involved with the regulation of leukocyte effector function and host defense. A doubling of the omega-3 index correlated with increases of 2.3-fold in 18-hydroxy-eicosapentaenoic acid (HEPE; P < .0001), 1.7-fold in 15-HEPE (P = .03), 1.9-fold in 5-HEPE (P = .04), and 3.6-fold in 4-hydroxy-docosahexaenoic acid (P < .001). Among subjects with symptomatic PAD who took oral fish oil supplements for 1 month, observed changes in the omega-3 index were strongly associated with increases in downstream mediators in the biochemical pathways of resolution. Copyright © 2017 National Lipid Association. All rights reserved.

Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

NASA Astrophysics Data System (ADS)

Wang, G.; Mayes, M. A.; Gu, L.; Schadt, C. W.

2013-12-01

Experimental observations and modeling efforts have shown that dormancy is likely a common strategy for microorganisms to contend with environmental stress. We review the state-of-the-art in modeling approaches for microbial dormancy and discuss the rationales of these models. We proved that the physiological state index model is not appropriate for describing transformation between active and dormant states. Based on the generally accepted assumptions summarized from ten existing models, we postulated a new synthetic microbial physiology component within the Microbial-ENzyme-mediated Decomposition (MEND) model. Both the steady state active fraction (rss) and substrate saturation level (Øss) positively depend on two physiological indices: α and β. The index α = mR /(μG+ mR), where μG and mR represent the maximum specific growth and maintenance rates, respectively, for active microbes. β denotes the ratio of dormant to active maintenance rate. The rss equals to Øss only under the condition of β→0, and they are identical to α. When substrate availability is the only limiting factor, the maximum rss is ca. 0.5 with α≤0.5 and β ≤0.01. This threshold value (0.5) of rss (not dynamic r) can explain the low active microbial fractions observed in undisturbed soils. The applications of the improved model to a 14C-labeled glucose induced respiration dataset and a batch experimental dataset show satisfactory model performance. We found that the exponential growth respiration rates can only be used to determine μG and initial active microbial biomass (Ba0), thus we suggest using respiration data representing both exponential growth and non-accelerating phases to robustly determine other important parameters such as initial total live microbial biomass (B0), initial active fraction (r0), μG, α, and the half-saturation constant (Ks). Similar improved representations of microbial physiology should be incorporated into existing ecosystem models in order to account for the significance of dormancy in microbially-mediated processes.

The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota

PubMed Central

Cox, Laura M.; Cho, Ilseung; Young, Scott A.; Anderson, W. H. Kerr; Waters, Bartholomew J.; Hung, Shao-Ching; Gao, Zhan; Mahana, Douglas; Bihan, Monika; Alekseyenko, Alexander V.; Methé, Barbara A.; Blaser, Martin J.

2013-01-01

Diet influences host metabolism and intestinal microbiota; however, detailed understanding of this tripartite interaction is limited. To determine whether the nonfermentable fiber hydroxypropyl methylcellulose (HPMC) could alter the intestinal microbiota and whether such changes correlated with metabolic improvements, C57B/L6 mice were normalized to a high-fat diet (HFD), then either maintained on HFD (control), or switched to HFD supplemented with 10% HPMC, or a low-fat diet (LFD). Compared to control treatment, both LFD and HPMC reduced weight gain (11.8 and 5.7 g, respectively), plasma cholesterol (23.1 and 19.6%), and liver triglycerides (73.1 and 44.6%), and, as revealed by 454-pyrosequencing of the microbial 16S rRNA gene, decreased microbial α-diversity and differentially altered intestinal microbiota. Both LFD and HPMC increased intestinal Erysipelotrichaceae (7.3- and 12.4-fold) and decreased Lachnospiraceae (2.0- and 2.7-fold), while only HPMC increased Peptostreptococcaceae (3.4-fold) and decreased Ruminococcaceae (2.7-fold). Specific microorganisms were directly linked with weight change and metabolic parameters in HPMC and HFD mice, but not in LFD mice, indicating that the intestinal microbiota may play differing roles during the two dietary modulations. This work indicates that HPMC is a potential prebiotic fiber that influences intestinal microbiota and improves host metabolism.—Cox, L. M., Cho, I., Young, S. A., Kerr Anderson, W. H., Waters, B. J., Hung, S.-C., Gao, Z., Mahana, D., Bihan, M., Alekseyenko, A. V., Methé, B. A., Blaser, M. J. The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota. PMID:23154883

Microbial imprint on soil-atmosphere H2, COS, and CO2 fluxes

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Commane, R.; Munger, J. W.; Wofsy, S. C.; Prinn, R. G.

2013-12-01

Microorganisms drive large trace gas fluxes between soil and atmosphere, but the signal can be difficult to detect and quantify in the presence of stronger exchange processes in an ecosystem. Partitioning methods are often needed to estimate trace gas budgets and to develop process-based models to explore the sensitivity of microbe-mediated fluxes. In this study, we test the performance of trace gases with predominantly microbe-mediated soil fluxes as a metric of the soil microbial uptake activity of other trace gases. Using simultaneous, collocated measurements at Harvard Forest, we consider three trace gases with microbe-mediated soil fluxes of various importance relative to their other (mainly plant-mediated) ecosystem fluxes: molecular hydrogen (H2), carbonyl sulfide (COS), and carbon dioxide (CO2). These gases probe different aspects of the soil trace-gas microbiology. Soil H2 uptake is a redox reaction driving the energy metabolism of a portion of the microbial community, while soil CO2 respiration is a partial proxy for the overall soil microbial metabolism. In comparison, very little is understood about the microbiological and environmental drivers of soil COS uptake and emissions. In this study, we find that H2, COS, and CO2 soil uptake rates are often correlated, but the relative soil uptake between gases is not constant, and is influenced by seasonality and local environmental conditions. We also consider how differences in the microbial communities and pathways involved in the soil fluxes may explain differences in the observations. Our results are important for informing previous studies using tracer approaches. For example, H2 has been used to estimate COS soil uptake, which must be accounted for to use COS as a carbon cycle tracer. Furthermore, the global distribution of H2 deposition velocity has been inferred from net primary productivity (CO2). Given that insufficient measurement frequency and spatial distribution exists to partition global net ecosystem fluxes of many climate-relevant trace gases, insight into the use of certain trace gases to estimate rates of more general biogeochemical processes is useful.

The Role of Microbial Processes in the Oxidation and Removal of Ammonia from Drinking Water

EPA Science Inventory

The purpose of this study was two-fold: (1) to monitor and evaluate nitrification in a full-scale iron removal filtration plant with biologically active granular media filters located in Ohio, and (2) to determine how to most efficiently regain nitrification following filter rebe...

Role of water mediated interactions in protein-protein recognition landscapes.

PubMed

Papoian, Garegin A; Ulander, Johan; Wolynes, Peter G

2003-07-30

The energy landscape picture of protein folding and binding is employed to optimize a number of pair potentials for direct and water-mediated interactions in protein complex interfaces. We find that water-mediated interactions greatly complement direct interactions in discriminating against various types of trap interactions that model those present in the cell. We highlight the context dependent nature of knowledge-based binding potentials, as contrasted with the situation for autonomous folding. By performing a Principal Component Analysis (PCA) of the corresponding interaction matrixes, we rationalize the strength of the recognition signal for each combination of the contact type and reference trap states using the differential in the idealized "canonical" amino acid compositions of native and trap layers. The comparison of direct and water-mediated contact potential matrixes emphasizes the importance of partial solvation in stabilizing charged groups in the protein interfaces. Specific water-mediated interresidue interactions are expected to influence significantly the kinetics as well as thermodynamics of protein association.

Changes in Microbial Nitrogen Across a 100-Year Chronosequence of Upland Hardwood Forests

Treesearch

Travis W. Idol; Phillip E. Pope; Felix, Jr. Ponder

2002-01-01

Soil microorganisms mediate many of the major processes involved in soil N cycling. Also, they are strong competitors with plants for available soil N. Thus, changes in microbial N because of forest harvesting may have significant impacts on N availability and overall forest N cycling. A chronosequence of upland hardwood forest stands in southern Indiana, USA, ranging...

Inhibitory Effects of Sulfate and Nitrate Reduction on Reductive Dechlorination of PCP in a Flooded Paddy Soil

PubMed Central

Xu, Yan; Xue, Lili; Ye, Qi; Franks, Ashley E.; Zhu, Min; Feng, Xi; Xu, Jianming; He, Yan

2018-01-01

Pentachlorophenol (PCP) is highly toxic and persistent in soils. Bioreduction of PCP often co-occurs with varying concentrations of sulfate and nitrate in flooded paddy soils where each can act as an electron acceptor. Anaerobic soil microcosms were constructed to evaluate the influence of sulfate and nitrate amendments and their redox processes. Microcosms with varying sulfate and nitrate concentrations demonstrated an inhibitory effect on reductive dechlorination of PCP compared to an untreated control. Compared to nitrate, sulfate exhibited a more significant impact on PCP dechlorination, as evidenced by a lower maximum reaction rate and a longer time to reach the maximum reaction rate. Dechlorination of PCP was initiated at the ortho-position, and then at the para- and meta-positions to form 3-CP as the final product in all microcosms. Deep sequencing of microbial communities in the microcosms revealed a strong variation in bacterial taxon among treatments. Specialized microbial groups, such as the genus of Desulfovibrio responding to the addition of sulfate, had a potential to mediate the competitive microbial dechlorination of PCP. Our results provide an insight into the competitive microbial-mediated reductive dechlorination of PCP in natural flooded soil or sediment environments. PMID:29643842

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Concurrent Phosphorus Recovery and Energy Generation in Mediator-Less Dual Chamber Microbial Fuel Cells: Mechanisms and Influencing Factors

PubMed Central

Almatouq, Abdullah; Babatunde, Akintunde O.

2016-01-01

This study investigated the mechanism and key factors influencing concurrent phosphorus (P) recovery and energy generation in microbial fuel cells (MFC) during wastewater treatment. Using a mediator-less dual chamber microbial fuel cell operated for 120 days; P was shown to precipitate as struvite when ammonium and magnesium chloride solutions were added to the cathode chamber. Monitoring data for chemical oxygen demand (COD), pH, oxidation reduction potential (ORP) and aeration flow rate showed that a maximum 38% P recovery was achieved; and this corresponds to 1.5 g/L, pH > 8, −550 ± 10 mV and 50 mL/min respectively, for COD, pHcathode, ORP and cathode aeration flow rate. More importantly, COD and aeration flow rate were shown to be the key influencing factors for the P recovery and energy generation. Results further show that the maximum P recovery corresponds to 72 mW/m2 power density. However, the energy generated at maximum P recovery was not the optimum; this shows that whilst P recovery and energy generation can be concurrently achieved in a microbial fuel cell, neither can be at the optimal value. PMID:27043584

Concurrent Phosphorus Recovery and Energy Generation in Mediator-Less Dual Chamber Microbial Fuel Cells: Mechanisms and Influencing Factors.

PubMed

Almatouq, Abdullah; Babatunde, Akintunde O

2016-03-29

This study investigated the mechanism and key factors influencing concurrent phosphorus (P) recovery and energy generation in microbial fuel cells (MFC) during wastewater treatment. Using a mediator-less dual chamber microbial fuel cell operated for 120 days; P was shown to precipitate as struvite when ammonium and magnesium chloride solutions were added to the cathode chamber. Monitoring data for chemical oxygen demand (COD), pH, oxidation reduction potential (ORP) and aeration flow rate showed that a maximum 38% P recovery was achieved; and this corresponds to 1.5 g/L, pH > 8, -550 ± 10 mV and 50 mL/min respectively, for COD, pH(cathode), ORP and cathode aeration flow rate. More importantly, COD and aeration flow rate were shown to be the key influencing factors for the P recovery and energy generation. Results further show that the maximum P recovery corresponds to 72 mW/m² power density. However, the energy generated at maximum P recovery was not the optimum; this shows that whilst P recovery and energy generation can be concurrently achieved in a microbial fuel cell, neither can be at the optimal value.

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization.

PubMed

Orellana, Luis H; Chee-Sanford, Joanne C; Sanford, Robert A; Löffler, Frank E; Konstantinidis, Konstantinos T

2017-11-03

The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for better understanding nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points across one year from two depths (0-5 and 20-30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty-loam), with similar cropping histories. Although microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural water-based ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies. Importance Even though the impact of agricultural management on the microbial community structure has already been recognized, understanding of the dynamics of individual microbial populations and what functions each population encodes are limited. Yet, this information is important for better understanding nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year-round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic compared to their marine counterparts previously studied. Copyright © 2017 American Society for Microbiology.

Microbial Fe biomineralization in mafic and ultramafic rocks

NASA Astrophysics Data System (ADS)

Templeton, A. S.; Mayhew, L.; McCollom, T.; Trainor, T.

2011-12-01

Fluid-filled microfractures within mafic and ultramafic rocks, such as basalt and peridotite, may be one of the most ubiquitous microbial habitats on the modern and ancient earth. In seafloor and subseafloor systems, one of the dominant energy sources is the oxidation of Fe by numerous potential oxidants under aerobic to anaerobic conditions. In particular, the oxidation of Fe may be directly catalyzed by microbial organisms, or result in the production of molecular hydrogen which can then fuel diverse lithotrophic metabolisms. However, it remains challenging to identify the dominant metabolic activities and unravel the microscale biogeochemical processes occuring within such rock-hosted systems. We are investigating the mechanisms of solid-state Fe-oxidation and biomineralization in basalt, olivine, pyroxenes and basalts, in the presence and absence of microbial organisms that can thrive across the full stability range of water. In this talk we will present synchrotron-based x-ray scattering and spectroscopic analyses of Fe speciation within secondary minerals formed during microbially-mediated vs. abiotic water-rock interactions. Determining the valence state and mineralogy of Fe-bearing phases is critical for determining the water-rock reaction pathways and identifying potential biominerals that may form; therefore, we will highlight new approaches for identifying key Fe transformations within complex geological media. In addition, many of our experimental studies involve the growth of lithotrophic biofilms on well-characterized mineral surfaces in order to determine the chemistry of the microbe-mineral interface during progressive electron-transfer reactions. By coupling x-ray spectroscopy, x-ray diffraction, and electron-microscopy measurements, we will also contrast the evolution of mineral surfaces that undergo microbially-mediated oxidative alteration against minerals surfaces that produce H2 to sustain anaerobic microbial communities.

Stimulation of Microbially Mediated Arsenic Release in Bangladesh Aquifers by Young Carbon Indicated by Radiocarbon Analysis of Sedimentary Bacterial Lipids.

PubMed

Whaley-Martin, K J; Mailloux, B J; van Geen, A; Bostick, B C; Silvern, R F; Kim, C; Ahmed, K M; Choudhury, I; Slater, G F

2016-07-19

The sources of reduced carbon driving the microbially mediated release of arsenic to shallow groundwater in Bangladesh remain poorly understood. Using radiocarbon analysis of phospholipid fatty acids (PLFAs) and potential carbon pools, the abundance and carbon sources of the active, sediment-associated, in situ bacterial communities inhabiting shallow aquifers (<30 m) at two sites in Araihazar, Bangladesh, were investigated. At both sites, sedimentary organic carbon (SOC) Δ(14)C signatures of -631 ± 54‰ (n = 12) were significantly depleted relative to dissolved inorganic carbon (DIC) of +24 ± 30‰ and dissolved organic carbon (DOC) of -230 ± 100‰. Sediment-associated PLFA Δ(14)C signatures (n = 10) at Site F (-167‰ to +20‰) and Site B (-163‰ to +21‰) were highly consistent and indicated utilization of carbon sources younger than the SOC, likely from the DOC pool. Sediment-associated PLFA Δ(14)C signatures were consistent with previously determined Δ(14)C signatures of microbial DNA sampled from groundwater at Site F indicating that the carbon source for these two components of the subsurface microbial community is consistent and is temporally stable over the two years between studies. These results demonstrate that the utilization of relatively young carbon sources by the subsurface microbial community occurs at sites with varying hydrology. Further they indicate that these young carbon sources drive the metabolism of the more abundant sediment-associated microbial communities that are presumably more capable of Fe reduction and associated release of As. This implies that an introduction of younger carbon to as of yet unaffected sediments (such as those comprising the deeper Pleistocene aquifer) could stimulate microbial communities and result in arsenic release.

Abundance and activity of soil microorganisms in Cedrus atlantica forests are more related to land use than to altitude or latitude

NASA Astrophysics Data System (ADS)

Ramírez Rojas, Irene; Perez Fernandez, María; Moreno Gallardo, Laura; Lechuga Ordoñez, Victor; Linares, Juan Carlos

2016-04-01

Several environmental traits might change the abundance and the function of soil microorganisms in forest soils by plant-mediated reactions. Few studies have related the landscape-scale forest structural diversity with the micro-scale distribution of microorganism and their activities. High mountain environments harbor ecosystems that are very sensitive to global change and hence highly vulnerable, as those of Atlantic cedar. Altitudinal gradients in mountains are orrelated with changes in vegetation. We propose that altitudinal gradients drive shifts in microbial communities and are correlated with land uses. Thus, the latitudinal and longitudinal pattern of abundance and activity of soil micro-organisms was studied in an intercontinental comparison. We investigate soil extractable organic carbon (EOC) and nitrogen and carbon, microbial biomass and microbial metabolic activities at eight different sites along the latitudinal range of Cedrus atlantica, covering different altitudes and soils characteristics both in Southern Spain and Northern Morocco. Analyses of the abundances of total bacteria, (16S rRNA gene), was conducted using the Ilumina metagenomics technique. Results show that the stands at the highest altitudes had distinct microbial and biochemical characteristics compared with other areas. Overall, microbial activity, as measured by soil respiration, is higher in forests subjected to lower human pressure than in stands highly degraded, probably reflecting the quality of litter input that results of the influence of local assemblage of different tree, shrub and annual species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Our results suggest that in contrast to the observed pronounced altitudinal changes, the kind of human-mediate land management has a stronger role in defining changes in microbial composition and activities in the investigated forest systems.

Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage

PubMed Central

Hughes, D; Mahony, T; Cysneiros, D; Ijaz, U Z; Smith, C J; O'Flaherty, V

2018-01-01

ABSTRACT The development and activity of a cold-adapting microbial community was monitored during low-temperature anaerobic digestion (LtAD) treatment of wastewater. Two replicate hybrid anaerobic sludge bed-fixed-film reactors treated a synthetic sewage wastewater at 12°C, at organic loading rates of 0.25–1.0 kg chemical oxygen demand (COD) m−3 d−1, over 889 days. The inoculum was obtained from a full-scale anaerobic digestion reactor, which was operated at 37°C. Both LtAD reactors readily degraded the influent with COD removal efficiencies regularly exceeding 78% for both the total and soluble COD fractions. The biomass from both reactors was sampled temporally and tested for activity against hydrolytic and methanogenic substrates at 12°C and 37°C. Data indicated that significantly enhanced low-temperature hydrolytic and methanogenic activity developed in both systems. For example, the hydrolysis rate constant (k) at 12°C had increased 20–30-fold by comparison to the inoculum by day 500. Substrate affinity also increased for hydrolytic substrates at low temperature. Next generation sequencing demonstrated that a shift in a community structure occurred over the trial, involving a 1-log-fold change in 25 SEQS (OTU-free approach) from the inoculum. Microbial community structure changes and process performance were replicable in the LtAD reactors. PMID:29846574

Nonadhesive, silica nanoparticles-based brush-coated contact lens cases--compromising between ease of cleaning and microbial transmission to contact lenses.

PubMed

Qu, Wenwen; Hooymans, Johanna M M; Qiu, Jun; de-Bont, Nik; Gelling, Onko-Jan; van der Mei, Henny C; Busscher, Henk J

2013-05-01

Surface properties of lens cases are determinant for their cleanability and for microbial transmission from lens cases to contact lenses (CLs). PEG-polymer-brush-coatings are known to decrease microbial adhesion more than other surface-coatings. Here, we applied a robust, silica nanoparticles-based brush-coating to polypropylene cases to evaluate their ease of cleaning and probability of bacterial transmission to CLs. Adhesion forces of nine bacterial strains (Pseudomonas, Staphylococci, and Serratia) to rigid CLs, polypropylene, and silica nanoparticles-based brush-coated polypropylene were measured using atomic-force-microscopy and subjected to Weibull analyses to yield bacterial transmission probabilities. Biofilms of each strain were grown in coated and uncoated cases and rinsed with a NaCl or antimicrobial lens care solution. Residual, viable organisms were quantified. Bacterial adhesion forces of all strains were significantly, up to tenfold smaller on brush-coated than on uncoated polypropylene. This yielded, higher transmission probabilities to a CL, but mild-rinsing yielded 10-100 fold higher removal of bacteria from brush-coated than from polypropylene cases. Moreover, due to weak adhesion forces, bacteria on brush-coated cases were two-to-three fold more susceptible to an antimicrobial lens care solution than on polypropylene cases. Therewith, the design of lens case surfaces is a compromise between ease of cleaning and transmission probability to CLs. Copyright © 2013 Wiley Periodicals, Inc.

Comparative bioremediation of soils contaminated with diesel oil by natural attenuation, biostimulation and bioaugmentation.

PubMed

Bento, Fatima M; Camargo, Flávio A O; Okeke, Benedict C; Frankenberger, William T

2005-06-01

Bioremediation of diesel oil in soil can occur by natural attenuation, or treated by biostimulation or bioaugmentation. In this study we evaluated all three technologies on the degradation of total petroleum hydrocarbons (TPH) in soil. In addition, the number of diesel-degrading microorganisms present and microbial activity as indexed by the dehydrogenase assay were monitored. Soils contaminated with diesel oil in the field were collected from Long Beach, California, USA and Hong Kong, China. After 12 weeks of incubation, all three treatments showed differing effects on the degradation of light (C12-C23) and heavy (C23-C40) fractions of TPH in the soil samples. Bioaugmentation of the Long Beach soil showed the greatest degradation in the light (72.7%) and heavy (75.2%) fractions of TPH. Natural attenuation was more effective than biostimulation (addition of nutrients), most notably in the Hong Kong soil. The greatest microbial activity (dehydrogenase activity) was observed with bioaugmentation of the Long Beach soil (3.3-fold) and upon natural attenuation of the Hong Kong sample (4.0-fold). The number of diesel-degrading microorganisms and heterotrophic population was not influenced by the bioremediation treatments. Soil properties and the indigenous soil microbial population affect the degree of biodegradation; hence detailed site specific characterization studies are needed prior to deciding on the proper bioremediation method.

Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products

PubMed Central

Tremblay, Pier-Luc; Höglund, Daniel; Koza, Anna; Bonde, Ida; Zhang, Tian

2015-01-01

Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic, and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components, and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism. PMID:26530351

Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage.

PubMed

Keating, C; Hughes, D; Mahony, T; Cysneiros, D; Ijaz, U Z; Smith, C J; O'Flaherty, V

2018-07-01

The development and activity of a cold-adapting microbial community was monitored during low-temperature anaerobic digestion (LtAD) treatment of wastewater. Two replicate hybrid anaerobic sludge bed-fixed-film reactors treated a synthetic sewage wastewater at 12°C, at organic loading rates of 0.25-1.0 kg chemical oxygen demand (COD) m-3 d-1, over 889 days. The inoculum was obtained from a full-scale anaerobic digestion reactor, which was operated at 37°C. Both LtAD reactors readily degraded the influent with COD removal efficiencies regularly exceeding 78% for both the total and soluble COD fractions. The biomass from both reactors was sampled temporally and tested for activity against hydrolytic and methanogenic substrates at 12°C and 37°C. Data indicated that significantly enhanced low-temperature hydrolytic and methanogenic activity developed in both systems. For example, the hydrolysis rate constant (k) at 12°C had increased 20-30-fold by comparison to the inoculum by day 500. Substrate affinity also increased for hydrolytic substrates at low temperature. Next generation sequencing demonstrated that a shift in a community structure occurred over the trial, involving a 1-log-fold change in 25 SEQS (OTU-free approach) from the inoculum. Microbial community structure changes and process performance were replicable in the LtAD reactors.

Facilitated extracellular electron transfer of Shewanella loihica PV-4 by antimony-doped tin oxide nanoparticles as active microelectrodes.

PubMed

Zhang, Xiaojian; Liu, Huan; Wang, Jinrong; Ren, Guangyuan; Xie, Beizhen; Liu, Hong; Zhu, Ying; Jiang, Lei

2015-11-28

Dissimilatory metal reducing bacteria are capable of extracellular electron transfer (EET) to insoluble metal oxides as external electron acceptors for their anaerobic respiration, which is recognized as an important energy-conversion process in natural and engineered environments, such as in mineral cycling, bioremediation, and microbial fuel/electrolysis cells. However, the low EET efficiency remains one of the major bottlenecks for its practical application. We report firstly that the microbial current generated by Shewanella loihica PV-4 (S. loihica PV-4) could be greatly improved that is up to ca. 115 fold, by adding antimony-doped tin oxide (ATO) nanoparticles in the electrochemical reactor. The results demonstrate that the biocompatible, electrically conductive ATO nanoparticles acted as active microelectrodes could facilitate the formation of a cells/ATO composite biofilm and the reduction of the outer membrane c-type cytochromes (OM c-Cyts) that are beneficial for the electron transfer from cells to electrode. Meanwhile, a synergistic effect between the participation of OM c-Cyts and the accelerated EET mediated by cell-secreted flavins may play an important role for the enhanced current generation in the presence of ATO nanoparticles. Moreover, it is worth noting that the TCA cycle in S. loihica PV-4 cells is activated by adding ATO nanoparticles, even if the potential is poised at +0.2 V, thereby also improving the EET process. The results presented here may provide a simple and effective strategy to boost the EET of S. loihica PV-4 cells, which is conducive to providing potential applications in bioelectrochemical systems.

Cryptic carbon and sulfur cycling between surface ocean plankton.

PubMed

Durham, Bryndan P; Sharma, Shalabh; Luo, Haiwei; Smith, Christa B; Amin, Shady A; Bender, Sara J; Dearth, Stephen P; Van Mooy, Benjamin A S; Campagna, Shawn R; Kujawinski, Elizabeth B; Armbrust, E Virginia; Moran, Mary Ann

2015-01-13

About half the carbon fixed by phytoplankton in the ocean is taken up and metabolized by marine bacteria, a transfer that is mediated through the seawater dissolved organic carbon (DOC) pool. The chemical complexity of marine DOC, along with a poor understanding of which compounds form the basis of trophic interactions between bacteria and phytoplankton, have impeded efforts to identify key currencies of this carbon cycle link. Here, we used transcriptional patterns in a bacterial-diatom model system based on vitamin B12 auxotrophy as a sensitive assay for metabolite exchange between marine plankton. The most highly up-regulated genes (up to 374-fold) by a marine Roseobacter clade bacterium when cocultured with the diatom Thalassiosira pseudonana were those encoding the transport and catabolism of 2,3-dihydroxypropane-1-sulfonate (DHPS). This compound has no currently recognized role in the marine microbial food web. As the genes for DHPS catabolism have limited distribution among bacterial taxa, T. pseudonana may use this sulfonate for targeted feeding of beneficial associates. Indeed, DHPS was both a major component of the T. pseudonana cytosol and an abundant microbial metabolite in a diatom bloom in the eastern North Pacific Ocean. Moreover, transcript analysis of the North Pacific samples provided evidence of DHPS catabolism by Roseobacter populations. Other such biogeochemically important metabolites may be common in the ocean but difficult to discriminate against the complex chemical background of seawater. Bacterial transformation of this diatom-derived sulfonate represents a previously unidentified and likely sizeable link in both the marine carbon and sulfur cycles.

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.

Enhanced sulfide removal and bioelectricity generation in microbial fuel cells with anodes modified by vertically oriented nanosheets.

PubMed

Yang, Meng; Zhong, Yuezhi; Zhang, Baogang; Shi, Jiaxin; Huang, Xueyang; Xing, Yi; Su, Lin; Liu, Huipeng; Borthwick, Alistair G L

2018-01-31

Anode materials and structures are of critical importance for microbial fuel cells (MFCs) recovering energy from toxic substrates. Carbon-fiber-felt anodes modified by layers of vertically oriented TiO 2 and Fe 2 O 3 nanosheets were applied in the present study. Enhanced sulfide removal efficiencies (both over 90%) were obtained after a 48-h operation, with maximum power densities improved by 1.53 and 1.36 folds compared with MFCs with raw carbon-fiber-felt anode. The modified anodes provided more active sites for microbial adhesion with increasing biomass densities. High-throughput 16S rRNA gene sequencing analysis also indicated the increase in microbial diversities. Bacteroidetes responsible for bioelectricity generation with Thiobacillus and Spirochaeta dominating sulfide removal were found in the MFCs with the modified anodes, with less anaerobic fermentative bacteria as Firmicutes appeared. This indicates that the proposed materials are competitive for applications of MFCs generating bioelectricity from toxic sulfide.

The force-dependent mechanism of DnaK-mediated mechanical folding

PubMed Central

Perales-Calvo, Judit; Giganti, David; Stirnemann, Guillaume; Garcia-Manyes, Sergi

2018-01-01

It is well established that chaperones modulate the protein folding free-energy landscape. However, the molecular determinants underlying chaperone-mediated mechanical folding remain largely elusive, primarily because the force-extended unfolded conformation fundamentally differs from that characterized in biochemistry experiments. We use single-molecule force-clamp spectroscopy, combined with molecular dynamics simulations, to study the effect that the Hsp70 system has on the mechanical folding of three mechanically stiff model proteins. Our results demonstrate that, when working independently, DnaJ (Hsp40) and DnaK (Hsp70) work as holdases, blocking refolding by binding to distinct substrate conformations. Whereas DnaK binds to molten globule–like forms, DnaJ recognizes a cryptic sequence in the extended state in an unanticipated force-dependent manner. By contrast, the synergetic coupling of the Hsp70 system exhibits a marked foldase behavior. Our results offer unprecedented molecular and kinetic insights into the mechanisms by which mechanical force finely regulates chaperone binding, directly affecting protein elasticity. PMID:29487911

Electron shuttles in biotechnology.

PubMed

Watanabe, Kazuya; Manefield, Mike; Lee, Matthew; Kouzuma, Atsushi

2009-12-01

Electron-shuttling compounds (electron shuttles [ESs], or redox mediators) are essential components in intracellular electron transfer, while microbes also utilize self-produced and naturally present ESs for extracellular electron transfer. These compounds assist in microbial energy metabolism by facilitating electron transfer between microbes, from electron-donating substances to microbes, and/or from microbes to electron-accepting substances. Artificially supplemented ESs can create new routes of electron flow in the microbial energy metabolism, thereby opening up new possibilities for the application of microbes to biotechnology processes. Typical examples of such processes include halogenated-organics bioremediation, azo-dye decolorization, and microbial fuel cells. Herein we suggest that ESs can be applied widely to create new microbial biotechnology processes.

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

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

Kostka, Joel

The goal of this project was to investigate changes in the structure of dissolved and solid phase organic matter, the production of CO 2 and CH 4, and the composition of decomposer microbial communities in response to the climatic forcing of environmental processes that determine the balance between carbon gas production versus storage and sequestration in peatlands. Cutting-edge analytical chemistry and next generation sequencing of microbial genes were been applied to habitats at the Marcell Experimental Forest (MEF), where the US DOE’s Oak Ridge National Laboratory and the USDA Forest Service are constructing a large-scale ecosystem study entitled, “Spruce andmore » Peatland Responses Under Climatic and Environmental Change”(SPRUCE). Our study represented a comprehensive characterization of the sources, transformation, and decomposition of organic matter in the S1 bog at MEF. Multiple lines of evidence point to distinct, vertical zones of organic matter transformation: 1) the acrotelm consisting of living mosses, root material, and newly formed litter (0-30 cm), 2) the mesotelm, a mid-depth transition zone (30-75 cm) characterized by labile organic C compounds and intense decomposition, and 3) the underlying catotelm (below 75cm) characterized by refractory organic compounds as well as relatively low decomposition rates. These zones are in part defined by physical changes in hydraulic conductivity and water table depth. O-alkyl-C, which represents the carbohydrate fraction in the peat, was shown to be an excellent proxy for soil decomposition rates. The carbon cycle in deep peat was shown to be fueled by modern carbon sources further indicating that hydrology and surface vegetation play a role in belowground carbon cycling. We provide the first metagenomic study of an ombrotrophic peat bog, with novel insights into microbial specialization and functions in this unique terrestrial ecosystem. Vertical structuring of microbial communities closely paralleled the chemical evolution of peat, with large shifts in microbial populations occurring in the biogeochemical hotspot, the mesotelm, where the highest rates of decomposition were detected. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens dominated in the deeper catotelm. Evidence pointed to the availability of phosphorus as well as nitrogen limiting the microbially-mediated turnover of organic carbon at MEF. Prior to initiation of the experimental treatments, our study provided key baseline data for the SPRUCE site on the vertical stratification of peat decomposition, key enzymatic pathways, and microbial taxa containing these pathways. The sensitivity of soil carbon turnover to climate change is strongly linked to recalcitrant carbon stocks and the temperature sensitivity of decomposition is thought to increase with increasing molecular complexity of carbon substrates. This project delivered results on how climate change perturbations impact the microbially-mediated turnover of recalcitrant organic matter in peatland forest soils, both under controlled conditions in the laboratory and at the ecosystem-scale in the field. This project revisited the concept of “recalcitrance” in the regulation of soil carbon turnover using a combination of natural abundance radiocarbon and optical spectroscopic measurements on bulk DOM, and high resolution molecular characterization of DOM. The project elucidated how organic matter reactivity and decomposition will respond to climate change in a both a qualitative (organic matter lability) and quantitiative (increased rates) manner. An Aromaticity Index was developed to represent a more direct and accurate parameter for modeling of DOM reactivity in peatlands. The abundance and community composition of soil microorganisms that mediate C cycling were interrogated with depth in the peat, with season, and in manipulated climate enclosures at unprecedented resolution. Therefore this project delivered strategic new insights on the functioning of peatland ecosystems that collectively store approximately one-third of the world's soil carbon. Furthermore, results from the detailed characterization of DOM lability and microbial community structure/ function will be employed to further develop biogeochemical models to include microbial respiration pathways as well as to track carbon flow with a term that incorporates relative reactivity based on aromaticity index. As it stands now, detailed soil organic matter structure and microbial parameters are not included in Earth system models.« less

High salinity facilitates dolomite precipitation mediated by Haloferax volcanii DS52

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

PubMed Central

Korolev, Nikolay; Allahverdi, Abdollah; Yang, Ye; Fan, Yanping; Lyubartsev, Alexander P.; Nordenskiöld, Lars

2010-01-01

The physical mechanism of the folding and unfolding of chromatin is fundamentally related to transcription but is incompletely characterized and not fully understood. We experimentally and theoretically studied chromatin compaction by investigating the salt-mediated folding of an array made of 12 positioning nucleosomes with 177 bp repeat length. Sedimentation velocity measurements were performed to monitor the folding provoked by addition of cations Na+, K+, Mg2+, Ca2+, spermidine3+, Co(NH3)63+, and spermine4+. We found typical polyelectrolyte behavior, with the critical concentration of cation needed to bring about maximal folding covering a range of almost five orders of magnitude (from 2 μM for spermine4+ to 100 mM for Na+). A coarse-grained model of the nucleosome array based on a continuum dielectric description and including the explicit presence of mobile ions and charged flexible histone tails was used in computer simulations to investigate the cation-mediated compaction. The results of the simulations with explicit ions are in general agreement with the experimental data, whereas simple Debye-Hückel models are intrinsically incapable of describing chromatin array folding by multivalent cations. We conclude that the theoretical description of the salt-induced chromatin folding must incorporate explicit mobile ions that include ion correlation and ion competition effects. PMID:20858435

Steady-state structural fluctuation is a predictor of the necessity of pausing-mediated co-translational folding for small proteins.

PubMed

Huang, Wenxi; Liu, Wanting; Jin, Jingjie; Xiao, Qilan; Lu, Ruibin; Chen, Wei; Xiong, Sheng; Zhang, Gong

2018-03-25

Translational pausing coordinates protein synthesis and co-translational folding. It is a common factor that facilitates the correct folding of large, multi-domain proteins. For small proteins, pausing sites rarely occurs in the gene body, and the 3'-end pausing sites are only essential for the folding of a fraction of proteins. The determinant of the necessity of the pausings remains obscure. In this study, we demonstrated that the steady-state structural fluctuation is a predictor of the necessity of pausing-mediated co-translational folding for small proteins. Validated by experiments with 5 model proteins, we found that the rigid protein structures do not, while the flexible structures do need 3'-end pausings to fold correctly. Therefore, rational optimization of translational pausing can improve soluble expression of small proteins with flexible structures, but not the rigid ones. The rigidity of the structure can be quantitatively estimated in silico using molecular dynamic simulation. Nevertheless, we also found that the translational pausing optimization increases the fitness of the expression host, and thus benefits the recombinant protein production, independent from the soluble expression. These results shed light on the structural basis of the translational pausing and provided a practical tool for industrial protein fermentation. Copyright © 2017. Published by Elsevier Inc.

Mechanistic Insight into the Reactivation of BCAII Enzyme from Denatured and Molten Globule States by Eukaryotic Ribosomes and Domain V rRNAs

PubMed Central

Chakraborty, Biprashekhar; Bhakta, Sayan; Sengupta, Jayati

2016-01-01

In all life forms, decoding of messenger-RNA into polypeptide chain is accomplished by the ribosome. Several protein chaperones are known to bind at the exit of ribosomal tunnel to ensure proper folding of the nascent chain by inhibiting their premature folding in the densely crowded environment of the cell. However, accumulating evidence suggests that ribosome may play a chaperone role in protein folding events in vitro. Ribosome-mediated folding of denatured proteins by prokaryotic ribosomes has been studied extensively. The RNA-assisted chaperone activity of the prokaryotic ribosome has been attributed to the domain V, a span of 23S rRNA at the intersubunit side of the large subunit encompassing the Peptidyl Transferase Centre. Evidently, this functional property of ribosome is unrelated to the nascent chain protein folding at the exit of the ribosomal tunnel. Here, we seek to scrutinize whether this unique function is conserved in a primitive kinetoplastid group of eukaryotic species Leishmania donovani where the ribosome structure possesses distinct additional features and appears markedly different compared to other higher eukaryotic ribosomes. Bovine Carbonic Anhydrase II (BCAII) enzyme was considered as the model protein. Our results manifest that domain V of the large subunit rRNA of Leishmania ribosomes preserves chaperone activity suggesting that ribosome-mediated protein folding is, indeed, a conserved phenomenon. Further, we aimed to investigate the mechanism underpinning the ribosome-assisted protein reactivation process. Interestingly, the surface plasmon resonance binding analyses exhibit that rRNA guides productive folding by directly interacting with molten globule-like states of the protein. In contrast, native protein shows no notable affinity to the rRNA. Thus, our study not only confirms conserved, RNA-mediated chaperoning role of ribosome but also provides crucial insight into the mechanism of the process. PMID:27099964

Short Communication: Inhibition of DC-SIGN-Mediated HIV-1 Infection by Complementary Actions of Dendritic Cell Receptor Antagonists and Env-Targeting Virus Inactivators.

PubMed

Pustylnikov, Sergey; Dave, Rajnish S; Khan, Zafar K; Porkolab, Vanessa; Rashad, Adel A; Hutchinson, Matthew; Fieschi, Frank; Chaiken, Irwin; Jain, Pooja

2016-01-01

The DC-SIGN receptor on human dendritic cells interacts with HIV gp120 to promote both infection of antigen-presenting cells and transinfection of T cells. We hypothesized that in DC-SIGN-expressing cells, both DC-SIGN ligands such as dextrans and gp120 antagonists such as peptide triazoles would inhibit HIV infection with potential complementary antagonist effects. To test this hypothesis, we evaluated the effects of dextran (D66), isomaltooligosaccharides (D06), and several peptide triazoles (HNG156, K13, and UM15) on HIV infection of B-THP-1/DC-SIGN cells. In surface plasmon resonance competition assays, D66 (IC50 = 35.4 μM) and D06 (IC50 = 3.4 mM) prevented binding of soluble DC-SIGN to immobilized mannosylated bovine serum albumin (BSA). An efficacious dose-dependent inhibition of DC-SIGN-mediated HIV infection in both pretreatment and posttreatment settings was observed, as indicated by inhibitory potentials (EC50) [D66 (8 μM), D06 (48 mM), HNG156 (40 μM), UM15 (100 nM), and K13 (25 nM)]. Importantly, both dextrans and peptide triazoles significantly decreased HIV gag RNA levels [D66 (7-fold), D06 (13-fold), HNG156 (7-fold), K-13 (3-fold), and UM15 (6-fold)]. Interestingly, D06 at the highest effective concentration showed a 14-fold decrease of infection, while its combination with 50 μM HNG156 showed a 26-fold decrease. Hence, these compounds can combine to inactivate the viruses and suppress DC-SIGN-mediated virus-cell interaction that as shown earlier leads to dendritic cell HIV infection and transinfection dependent on the DC-SIGN receptor.

Short Communication: Inhibition of DC-SIGN-Mediated HIV-1 Infection by Complementary Actions of Dendritic Cell Receptor Antagonists and Env-Targeting Virus Inactivators

PubMed Central

Pustylnikov, Sergey; Dave, Rajnish S.; Khan, Zafar K.; Porkolab, Vanessa; Rashad, Adel A.; Hutchinson, Matthew; Fieschi, Frank; Chaiken, Irwin

2016-01-01

Abstract The DC-SIGN receptor on human dendritic cells interacts with HIV gp120 to promote both infection of antigen-presenting cells and transinfection of T cells. We hypothesized that in DC-SIGN-expressing cells, both DC-SIGN ligands such as dextrans and gp120 antagonists such as peptide triazoles would inhibit HIV infection with potential complementary antagonist effects. To test this hypothesis, we evaluated the effects of dextran (D66), isomaltooligosaccharides (D06), and several peptide triazoles (HNG156, K13, and UM15) on HIV infection of B-THP-1/DC-SIGN cells. In surface plasmon resonance competition assays, D66 (IC50 = 35.4 μM) and D06 (IC50 = 3.4 mM) prevented binding of soluble DC-SIGN to immobilized mannosylated bovine serum albumin (BSA). An efficacious dose-dependent inhibition of DC-SIGN-mediated HIV infection in both pretreatment and posttreatment settings was observed, as indicated by inhibitory potentials (EC50) [D66 (8 μM), D06 (48 mM), HNG156 (40 μM), UM15 (100 nM), and K13 (25 nM)]. Importantly, both dextrans and peptide triazoles significantly decreased HIV gag RNA levels [D66 (7-fold), D06 (13-fold), HNG156 (7-fold), K-13 (3-fold), and UM15 (6-fold)]. Interestingly, D06 at the highest effective concentration showed a 14-fold decrease of infection, while its combination with 50 μM HNG156 showed a 26-fold decrease. Hence, these compounds can combine to inactivate the viruses and suppress DC-SIGN-mediated virus–cell interaction that as shown earlier leads to dendritic cell HIV infection and transinfection dependent on the DC-SIGN receptor. PMID:26383762

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

PubMed

Schirmer, Melanie; Smeekens, Sanne P; Vlamakis, Hera; Jaeger, Martin; Oosting, Marije; Franzosa, Eric A; Ter Horst, Rob; Jansen, Trees; Jacobs, Liesbeth; Bonder, Marc Jan; Kurilshikov, Alexander; Fu, Jingyuan; Joosten, Leo A B; Zhernakova, Alexandra; Huttenhower, Curtis; Wijmenga, Cisca; Netea, Mihai G; Xavier, Ramnik J

2016-11-03

Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP. Copyright © 2016 Elsevier Inc. All rights reserved.

Phytoremediation using microbially mediated metal accumulation in Sorghum bicolor.

PubMed

Phieler, René; Merten, Dirk; Roth, Martin; Büchel, Georg; Kothe, Erika

2015-12-01

Reclaiming land that has been anthropogenically contaminated with multiple heavy metal elements, e.g., during mining operations, is a growing challenge worldwide. The use of phytoremediation has been discussed with varying success. Here, we show that a careful examination of options of microbial determination of plant performance is a key element in providing a multielement remediation option for such landscapes. We used both (a) mycorrhiza with Rhizophagus irregularis and (b) bacterial amendments with Streptomyces acidiscabies E13 and Streptomyces tendae F4 to mediate plant-promoting and metal-accumulating properties to Sorghum bicolor. In pot experiments, the effects on plant growth and metal uptake were scored, and in a field trial at a former uranium leaching heap site near Ronneburg, Germany, we could show the efficacy under field conditions. Different metals could be extracted at the same time, with varying microbial inoculation and soil amendment scenarios possible when a certain metal is the focus of interest. Especially, manganese was extracted at very high levels which might be useful even for phytomining approaches.

Protective and destructive immunity in the periodontium: Part 1--innate and humoral immunity and the periodontium.

PubMed

Teng, Y-T A

2006-03-01

Based on the results of recent research in the field, the present paper will discuss the protective and destructive aspects of the innate vs. adaptive (humoral and cell-mediated) immunity associated with the bacterial virulent factors or antigenic determinants during periodontal pathogenesis. Attention will be focused on: (i) the Toll-like receptors (TLR), the innate immune repertoire for recognizing the unique molecular patterns of microbial components that trigger innate and adaptive immunity for effective host defenses, in some general non-oral vs. periodontal microbial infections; (ii) T-cell-mediated immunity, Th-cytokines, and osteoclastogenesis in periodontal disease progression; and (iii) some molecular techniques developed and used to identify critical microbial virulence factors or antigens associated with host immunity (using Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis as the model species). Therefore, further understanding of the molecular interactions and mechanisms associated with the host's innate and adaptive immune responses will facilitate the development of new and innovative therapeutics for future periodontal treatments.

Extracellular enzymes facilitate electron uptake in biocorrosion and bioelectrosynthesis.

PubMed

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

2015-04-21

Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. The intriguing trait of some microbial organisms to engage in direct electron transfer is thought to be widespread in nature. Consequently, direct uptake of electrons into microbial cells from solid surfaces is assumed to have a significant impact not only on fundamental microbial and biogeochemical processes but also on applied bioelectrochemical systems, such as microbial electrosynthesis and biocorrosion. This study provides a simple mechanistic explanation for frequently observed fast electron uptake kinetics in microbiological systems without a direct transfer: free, cell-derived enzymes can interact with cathodic surfaces and catalyze the formation of intermediates that are rapidly consumed by microbial cells. This electron transfer mechanism likely plays a significant role in various microbial electron transfer reactions in the environment. Copyright © 2015 Deutzmann et al.

Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System.

PubMed

Schiessl, Konstanze T; Janssen, Elisabeth M-L; Kraemer, Stephan M; McNeill, Kristopher; Ackermann, Martin

2017-01-01

A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.

Extracellular Enzymes Facilitate Electron Uptake in Biocorrosion and Bioelectrosynthesis

PubMed Central

Deutzmann, Jörg S.; Sahin, Merve

2015-01-01

ABSTRACT Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. PMID:25900658

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.

PubMed

Liu, Guohong; Weston, Christopher Q; Pham, Long K; Waltz, Shannon; Barnes, Helen; King, Paula; Sphar, Dan; Yamamoto, Robert T; Forsyth, R Allyn

2016-01-01

We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.

Phytase Production and Development of an Ideal Dephytinization Process for Amelioration of Food Nutrition Using Microbial Phytases.

PubMed

Jain, Jinender; Singh, Bijender

2017-04-01

Development of an ideal process for reduction of food phytates using microbial phytases is a demanding task by all food and feed industries all over the world. Phytase production by Bacillus subtilis subsp. subtilis JJBS250 isolated from soil sample was optimized in submerged fermentation using statistical tools. Among all the culture variables tested, sucrose, sodium phytate and Tween-80 were identified as the most significant variables using the Placket-Burman design. Further optimization of these variables resulted in a 6.79-fold improvement in phytase production (7170 U/L) as compared to unoptimized medium. Supplementation of microbial phytases (fungal and bacterial) resulted in improved bioavailability of nutritional components with the concomitant liberation of inorganic phosphorus, reducing sugar, soluble protein and amino acids, thus mitigating anti-nutritional properties of phytic acid.

Methanogenesis-induced pH–Eh shifts drives aqueous metal(loid) mobility in sulfide mineral systems under CO2 enriched conditions

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

Harvey, Omar R.; Qafoku, Nikolla; Cantrell, Kirk J.

2016-01-15

Accounting for microbially-mediated CO2 transformation is pivotal to assessing geochemical implications for elevated CO2 in subsurface environments. A series of batch-reactor experiments were conducted to decipher links between autotrophic methanogenesis, CO2 dynamics and aqueous Fe, As and Pb concentrations in the presence of sulfide minerals. Microbially-mediated solubility-trapping followed by pseudo-first order reduction of HCO3- to CH4 (k’ = 0.28-0.59 d-1) accounted for 95% of the CO2 loss from methanogenic experiments. Bicarbonate-to-methane reduction was pivotal in the mitigation of CO2-induced acidity (~1 pH unit) and enhancement of reducing conditions (Eh change from -0.215 to -0.332V ). Methanogenesis-associated shifts in pH-Eh valuesmore » showed no significant effect on aqueous Pb but favored, 1) increased aqueous As as a result of microbially-mediated dissolution of arsenopyrite and 2) decreased aqueous Fe due to mineral-trapping of CO2-mobilized Fe as Fe-carbonate. Its order of occurrence (and magnitude), relative to solubility- and mineral-trapping, highlighted the potential for autotrophic methanogenesis to modulate both carbon sequestration and contaminant mobility in CO2-impacted subsurface environments.« less

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Electrochemically Active Soluble Mediators from Shewanella oneidensis: Relevance to Microbial Fuel Cells and Extracellular Electron Transfer

DTIC Science & Technology

2008-05-01

A second approach is the use of soluble mediators such as, quinones, phenazines , and riboflavin, which are able to shuttle electrons from the cell...done using the equivalent graphite felt or graphite felt coated with platinum nanoparticles . Fuel cell chambers were separated using a gas-permeable

Microbially Mediated Glass Alteration in the Geological Record: Textural clues for Microbial Functions.

NASA Astrophysics Data System (ADS)

Staudigel, H.; Furnes, H.; McLoughlin, N.; Banerjee, N.

2007-12-01

Fe and Mn oxidizing microbes interact with their environment through the microbially mediated formation of Fe/Mn oxides and through the corrosion textures they may leave behind in the solids they colonize and from which they extract nutrients. Understanding the geo-biology of Fe and Mn oxidation may focus on the study of the microbes themselves, the mineral products, its biocorrosion features and the relationships between these types of observations. We have reviewed our own data on glass bio-corrosion and in particular the wider literature on microbial mineral tunneling to develop a two stage biocorrosion model for volcanic glass that offers feedback for our understanding of the mechanisms and the dynamics of microbial dissolution. Traces of microbially mediated dissolution of volcanic glass are commonly observed in volcanic glass found in submarine volcanoes on the seafloor, and in uplifted submarine volcanoes of almost any geological age back to the origin of life. Two main bioalteration textures care observed, granular and tubular. Based on a comparison of these features in particular with tunneling by ectomycorrhizal fungi, we propose two distinct types of biocorrosion that affects glass: (1) Granular alteration textures, made up of colonies of microbe-sized, near spherical mineral - filled cavities that form irregular clusters ranging to a tens of micron thick bands at the glas surfaces. These granular textures are interpreted as the result of microbial colonization. accompanied by dissolution of the glass in their contact surface, deposition of authigenic minerals and the formation of a biofilm, that eventually seals the glass from easy access by seawater for hydration, or from microbes accessing Fe (II) in the glass. (2) The most spectacular bioalteration feature, repesented by the formation of tubes cannot be easily formed by the former mechanism because near spherical, individual microbes are likely not to produce the directionality that is required to produce the near linear or sometimes coiled tubes. Instead, we envision the activity of hyphae-like organelles or filaments, that may radiate out from a host body located in direct contact with circulating water, possibly penetrating a biofilm and entering/drilling into the fresh glass. Such microdrilling is well described in soils, where hyphae can slowly drill into silicates, in a process that takes about 1000 years to become visible as tunnels.

A novel photo-biological engineering method for Salvia miltiorrhiza-mediated fabrication of silver nanoparticles using LED lights sources and its effectiveness against Aedes aegypti mosquito larvae and microbial pathogens

USDA-ARS?s Scientific Manuscript database

In this study, Salvia miltiorrhiza-synthesized Ag nanoparticles (AgNPs) fabricated using sunlight or various LED lights were studied for their biophysical features and evaluated as larvicides against Aedes aegypti mosquitoes and growth inhibitors on different species of microbial pathogens. AgNPs pr...

Microbial communities mediating algal detritus turnover under anaerobic conditions

PubMed Central

Morrison, Jessica M.; Murphy, Chelsea L.; Baker, Kristina; Zamor, Richard M.; Nikolai, Steve J.; Wilder, Shawn; Elshahed, Mostafa S.

2017-01-01

Background Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. Results Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O’ the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13–16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genus Spirochaeta and the uncultured group SHA-4 within Spirochaetes, Ruminococcaceae, Lachnospiraceae, Yongiibacter, Geosporobacter, and Acidaminobacter within the Firmicutes, and genera Kluyvera, Pantoea, Edwardsiella and Aeromonas, and Buttiauxella within the Gamma-Proteobaceteria order Enterobacteriales. Conclusions Our results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process. PMID:28097050

Unlocking Ft: Modeling thermodynamic controls and isotope fractionation factors in nutrient limited environments

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Giannetta, M.; Sanford, R. A.

2017-12-01

In recent years, reactive transport principles have expanded from early applications, largely based in contaminant hydrology, to a wide range of biologically mediated redox environments including marine sedimentary diagenesis, terrestrial metal ore deposits, soils, and critical zone weathering profiles. A common observation across this diversity of systems is that they often function under energetically limited conditions in comparison to those typical of contaminated aquifers subject to engineered remediation techniques. As a result, the kinetic rate expressions traditionally employed within reactive transport frameworks to simulate microbially mediated redox transformations have required modification. This was recognized in a series of seminal papers by Jin and Bethke (2005, 2007) in which the authors expanded upon a Monod rate law to include a thermodynamic potential factor `Ft' which exerts a limitation on the overall rate based on the thermodynamic driving force of the electron transfer reaction. This new rate expression is now commonly implemented within many of the major reactive transport software packages, though appropriate application has yet to be thoroughly demonstrated. Notably, the characteristically large partitioning of stable isotopes during microbially mediated reactions, which is extensively utilized to identify and quantify these redox transformations, has yet to be simulated under conditions in which the Ft term may be expected to exert a significant mass dependent influence. Here, we develop a series of simplified simulations for the microbially mediated reduction of sulfate based on the datasets reported by Jin and Bethke, and apply appropriate mass-bias within the Ft term to consider the extent to which the resulting isotopic fractionation is consistent with that observed in energetically limited systems. We show that the Ft term can exert a significant influence on the observed fractionation factor under common environmental conditions, resulting in model behavior which is, in effect, a microbial redox analog to the variable observed fractionation factor resulting from a transition state theory rate law as derived by DePaolo (2011).

Effects of Bioreactor Retention Time on Aerobic Microbial Decomposition of CELSS Crop Residues

NASA Technical Reports Server (NTRS)

Strayer, R. F.; Finger, B. W.; Alazraki, M. P.

1997-01-01

The focus of resource recovery research at the KSC-CELSS Breadboard Project has been the evaluation of microbiologically mediated biodegradation of crop residues by manipulation of bioreactor process and environmental variables. We will present results from over 3 years of studies that used laboratory- and breadboard-scale (8 and 120 L working volumes, respectively) aerobic, fed-batch, continuous stirred tank reactors (CSTR) for recovery of carbon and minerals from breadboard grown wheat and white potato residues. The paper will focus on the effects of a key process variable, bioreactor retention time, on response variables indicative of bioreactor performance. The goal is to determine the shortest retention time that is feasible for processing CELSS crop residues, thereby reducing bioreactor volume and weight requirements. Pushing the lower limits of bioreactor retention times will provide useful data for engineers who need to compare biological and physicochemical components. Bioreactor retention times were manipulated to range between 0.25 and 48 days. Results indicate that increases in retention time lead to a 4-fold increase in crop residue biodegradation, as measured by both dry weight losses and CO2 production. A similar overall trend was also observed for crop residue fiber (cellulose and hemicellulose), with a noticeable jump in cellulose degradation between the 5.3 day and 10.7 day retention times. Water-soluble organic compounds (measured as soluble TOC) were appreciably reduced by more than 4-fold at all retention times tested. Results from a study of even shorter retention times (down to 0.25 days), in progress, will also be presented.

Dietary microbial phytase exerts mixed effects on the gut health of tilapia: a possible reason for the null effect on growth promotion.

PubMed

Hu, Jun; Ran, Chao; He, Suxu; Cao, Yanan; Yao, Bin; Ye, Yuantu; Zhang, Xuezhen; Zhou, Zhigang

2016-06-01

The present study evaluated the effects of dietary microbial phytase on the growth and gut health of hybrid tilapia (Oreochromis niloticus ♀×Oreochromis aureus ♂), focusing on the effect on intestinal histology, adhesive microbiota and expression of immune-related cytokine genes. Tilapia were fed either control diet or diet supplemented with microbial phytase (1000 U/kg). Each diet was randomly assigned to four groups of fish reared in cages (3×3×2 m). After 12 weeks of feeding, weight gain and feed conversion ratio of tilapia were not significantly improved by dietary microbial phytase supplementation. However, significantly higher level of P content in the scales, tighter and more regular intestinal mucosa folds were observed in the microbial phytase group and the microvilli density was significantly increased. The adhesive gut bacterial communities were strikingly altered by microbial phytase supplementation (0·41

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

Enhanced succinic acid production from corncob hydrolysate by microbial electrolysis cells.

PubMed

Zhao, Yan; Cao, Weijia; Wang, Zhen; Zhang, Bowen; Chen, Kequan; Ouyang, Pingkai

2016-02-01

In this study, Actinobacillus succinogenes NJ113 microbial electrolysis cells (MECs) were used to enhance the reducing power responsible for succinic acid production from corncob hydrolysate. During corncob hydrolysate fermentation, electric MECs resulted in a 1.31-fold increase in succinic acid production and a 1.33-fold increase in the reducing power compared with those in non-electric MECs. When the hydrolysate was detoxified by combining Ca(OH)2, NaOH, and activated carbon, succinic acid production increased from 3.47 to 6.95 g/l. Using a constant potential of -1.8 V further increased succinic acid production to 7.18 g/l. A total of 18.09 g/l of succinic acid and a yield of 0.60 g/g total sugar were obtained after a 60-h fermentation when NaOH was used as a pH regulator. The improved succinic acid yield from corncob hydrolysate fermentation using A. succinogenes NJ113 in electric MECs demonstrates the great potential of using biomass as a feedstock to cost-effectively produce succinate. Copyright © 2015 Elsevier Ltd. All rights reserved.

Short-chain fatty acids production and microbial community in sludge alkaline fermentation: Long-term effect of temperature.

PubMed

Yuan, Yue; Liu, Ye; Li, Baikun; Wang, Bo; Wang, Shuying; Peng, Yongzhen

2016-07-01

Sludge alkaline fermentation has been reported to achieve efficient short-chain fatty acids (SCFAs) production. Temperature played important role in further improved SCFAs production. Long-term SCFAs production from sludge alkaline fermentation was compared between mesotherm (30±2°C) and microtherm (15±2°C). The study of 90days showed that mesotherm led to 2.2-folds production of SCFAs as microtherm and enhanced the production of acetic acid as major component of SCFAs. Soluble protein and carbohydrate at mesotherm was 2.63-folds as that at microtherm due to higher activities of protease and α-glucosidase, guaranteeing efficient substrates to produce SCFAs. Illumina MiSeq sequencing revealed that microtherm increased the abundance of Corynebacterium, Alkaliflexus, Pseudomonas and Guggenheimella, capable of enhancing hydrolysis. Hydrolytic bacteria, i.e. Alcaligenes, Anaerolinea and Ottowia, were enriched at mesotherm. Meanwhile, acidogenic bacteria showed higher abundance at mesotherm than microtherm. Therefore, enrichment of functional bacteria and higher microbial activities resulted in the improved SCFAs at mesotherm. Copyright © 2016 Elsevier Ltd. All rights reserved.

Seasonality in ocean microbial communities.

PubMed

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

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

Microbial interactions in building of communities

PubMed Central

Wright, Christopher J.; Burns, Logan H.; Jack, Alison A.; Back, Catherine R.; Dutton, Lindsay C.; Nobbs, Angela H.; Lamont, Richard J.; Jenkinson, Howard F.

2012-01-01

SUMMARY Establishment of a community is considered to be essential for microbial growth and survival in the human oral cavity. Biofilm communities have increased resilience to physical forces, antimicrobial agents, and nutritional variations. Specific cell-to-cell adherence processes, mediated by adhesin-receptor pairings on respective microbial surfaces, are able to direct community development. These interactions co-localize species in mutually beneficial relationships, such as streptococci, veillonellae, Porphyromonas gingivalis and Candida albicans. In transition from the planktonic mode of growth to a biofilm community, microorganisms undergo major transcriptional and proteomic changes. These occur in response to sensing of diffusible signals, such as autoinducer molecules, and to contact with host tissues or other microbial cells. Underpinning many of these processes are intracellular phosphorylation events that regulate a large number of microbial interactions relevant to community formation and development. PMID:23253299

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

Zhen Li; Rishika Haynes; Eugene Sato

Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopymore » results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.« less

Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding

PubMed Central

Ozdilek, Bagdeser A.; Thompson, Valery F.; Ahmed, Nasiha S.; White, Connor I.

2017-01-01

Abstract RGG/RG domains are the second most common RNA binding domain in the human genome, yet their RNA-binding properties remain poorly understood. Here, we report a detailed analysis of the RNA binding characteristics of intrinsically disordered RGG/RG domains from Fused in Sarcoma (FUS), FMRP and hnRNPU. For FUS, previous studies defined RNA binding as mediated by its well-folded domains; however, we show that RGG/RG domains are the primary mediators of binding. RGG/RG domains coupled to adjacent folded domains can achieve affinities approaching that of full-length FUS. Analysis of RGG/RG domains from FUS, FMRP and hnRNPU against a spectrum of contrasting RNAs reveals that each display degenerate binding specificity, while still displaying different degrees of preference for RNA. PMID:28575444

Heat-stabilised rice bran consumption by colorectal cancer survivors modulates stool metabolite profiles and metabolic networks: a randomised controlled trial

PubMed Central

Brown, Dustin G.; Borresen, Erica C.; Brown, Regina J.; Ryan, Elizabeth P.

2017-01-01

Rice bran (RB) consumption has been shown to reduce colorectal cancer (CRC) growth in mice and modify the human stool microbiome. Changes in host and microbial metabolism induced by RB consumption was hypothesised to modulate the stool metabolite profile in favour of promoting gut health and inhibiting CRC growth. The objective was to integrate gut microbial metabolite profiles and identify metabolic pathway networks for CRC chemoprevention using non-targeted metabolomics. In all, nineteen CRC survivors participated in a parallel randomised controlled dietary intervention trial that included daily consumption of study-provided foods with heat-stabilised RB (30 g/d) or no additional ingredient (control). Stool samples were collected at baseline and 4 weeks and analysed using GC-MS and ultra-performance liquid chromatography-MS. Stool metabolomics revealed 93 significantly different metabolites in individuals consuming RB. A 264-fold increase in β-hydroxyisovaleroylcarnitine and 18-fold increase in β-hydroxyisovalerate exemplified changes in leucine, isoleucine and valine metabolism in the RB group. A total of thirty-nine stool metabolites were significantly different between RB and control groups, including increased hesperidin (28-fold) and narirutin (14-fold). Metabolic pathways impacted in the RB group over time included advanced glycation end products, steroids and bile acids. Fatty acid, leucine/valine and vitamin B6 metabolic pathways were increased in RB compared with control. There were 453 metabolites identified in the RB food metabolome, thirty-nine of which were identified in stool from RB consumers. RB consumption favourably modulated the stool metabolome of CRC survivors and these findings suggest the need for continued dietary CRC chemoprevention efforts. PMID:28643618

Heat-stabilised rice bran consumption by colorectal cancer survivors modulates stool metabolite profiles and metabolic networks: a randomised controlled trial.

PubMed

Brown, Dustin G; Borresen, Erica C; Brown, Regina J; Ryan, Elizabeth P

2017-05-01

Rice bran (RB) consumption has been shown to reduce colorectal cancer (CRC) growth in mice and modify the human stool microbiome. Changes in host and microbial metabolism induced by RB consumption was hypothesised to modulate the stool metabolite profile in favour of promoting gut health and inhibiting CRC growth. The objective was to integrate gut microbial metabolite profiles and identify metabolic pathway networks for CRC chemoprevention using non-targeted metabolomics. In all, nineteen CRC survivors participated in a parallel randomised controlled dietary intervention trial that included daily consumption of study-provided foods with heat-stabilised RB (30 g/d) or no additional ingredient (control). Stool samples were collected at baseline and 4 weeks and analysed using GC-MS and ultra-performance liquid chromatography-MS. Stool metabolomics revealed 93 significantly different metabolites in individuals consuming RB. A 264-fold increase in β-hydroxyisovaleroylcarnitine and 18-fold increase in β-hydroxyisovalerate exemplified changes in leucine, isoleucine and valine metabolism in the RB group. A total of thirty-nine stool metabolites were significantly different between RB and control groups, including increased hesperidin (28-fold) and narirutin (14-fold). Metabolic pathways impacted in the RB group over time included advanced glycation end products, steroids and bile acids. Fatty acid, leucine/valine and vitamin B6 metabolic pathways were increased in RB compared with control. There were 453 metabolites identified in the RB food metabolome, thirty-nine of which were identified in stool from RB consumers. RB consumption favourably modulated the stool metabolome of CRC survivors and these findings suggest the need for continued dietary CRC chemoprevention efforts.

GroEL actively stimulates folding of the endogenous substrate protein PepQ.

PubMed

Weaver, Jeremy; Jiang, Mengqiu; Roth, Andrew; Puchalla, Jason; Zhang, Junjie; Rye, Hays S

2017-06-30

Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution. Using cryo-electron microscopy, we show that the GroEL C-termini make physical contact with the PepQ folding intermediate and help retain it deep within the GroEL cavity, resulting in reduced compactness of the PepQ monomer. Our findings strongly support an active model of chaperonin-mediated protein folding, where partial unfolding of misfolded intermediates plays a key role.

Lack of mutational hot spots during decitabine-mediated HIV-1 mutagenesis.

PubMed

Rawson, Jonathan M O; Landman, Sean R; Reilly, Cavan S; Bonnac, Laurent; Patterson, Steven E; Mansky, Louis M

2015-11-01

Decitabine has previously been shown to induce lethal mutagenesis of human immunodeficiency virus type 1 (HIV-1). However, the factors that determine the susceptibilities of individual sequence positions in HIV-1 to decitabine have not yet been defined. To investigate this, we performed Illumina high-throughput sequencing of multiple amplicons prepared from proviral DNA that was recovered from decitabine-treated cells infected with HIV-1. We found that decitabine induced an ≈4.1-fold increase in the total mutation frequency of HIV-1, primarily due to a striking ≈155-fold increase in the G-to-C transversion frequency. Intriguingly, decitabine also led to an ≈29-fold increase in the C-to-G transversion frequency. G-to-C frequencies varied substantially (up to ≈80-fold) depending upon sequence position, but surprisingly, mutational hot spots (defined as upper outliers within the mutation frequency distribution) were not observed. We further found that every single guanine position examined was significantly susceptible to the mutagenic effects of decitabine. Taken together, these observations demonstrate for the first time that decitabine-mediated HIV-1 mutagenesis is promiscuous and occurs in the absence of a clear bias for mutational hot spots. These data imply that decitabine-mediated G-to-C mutagenesis is a highly effective antiviral mechanism for extinguishing HIV-1 infectivity. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Alteration of Electrostatic Surface Potential Enhances Affinity and Tumor Killing Properties of Anti-ganglioside GD2 Monoclonal Antibody hu3F8.

PubMed

Zhao, Qi; Ahmed, Mahiuddin; Guo, Hong-fen; Cheung, Irene Y; Cheung, Nai-Kong V

2015-05-22

Ganglioside GD2 is highly expressed on neuroectodermal tumors and an attractive therapeutic target for antibodies that have already shown some clinical efficacy. To further improve the current antibodies, which have modest affinity, we sought to improve affinity by using a combined method of random mutagenesis and in silico assisted design to affinity-mature the anti-GD2 monoclonal antibody hu3F8. Using yeast display, mutants in the Fv with enhanced binding over the parental clone were FACS-sorted and cloned. In silico modeling identified the minimal key interacting residues involved in the important charged interactions with the sialic acid groups of GD2. Two mutations, D32H (L-CDR1) and E1K (L-FR1) altered the electrostatic surface potential of the antigen binding site, allowing for an increase in positive charge to enhance the interaction with the negatively charged GD2-pentasaccharide headgroup. Purified scFv and IgG mutant forms were then tested for antigen specificity by ELISA, for tissue specificity by immunohistochemistry, for affinity by BIACORE, for antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-mediated cytotoxicity in vitro, and for anti-tumor efficacy in xenografted humanized mice. The nearly 7-fold improvement in affinity of hu3F8 with a single D32H (L-CDR1) mutation translated into a ∼12-fold improvement in NK92MI-transfected CD16-mediated ADCC, a 6-fold improvement in CD32-mediated ADCC, and a 2.5-fold improvement in complement-mediated cytotoxicity while maintaining restricted normal tissue cross-reactivity and achieving substantial improvement in tumor ablation in vivo. Despite increasing GD2 affinity, the double mutation D32H (L-CDR1) and E1K (L-FR1) did not further improve anti-tumor efficacy. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Influence of coral and algal exudates on microbially mediated reef metabolism.

PubMed

Haas, Andreas F; Nelson, Craig E; Rohwer, Forest; Wegley-Kelly, Linda; Quistad, Steven D; Carlson, Craig A; Leichter, James J; Hatay, Mark; Smith, Jennifer E

2013-01-01

Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo'orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.

Ultrasound enhances retrovirus-mediated gene transfer.

PubMed

Naka, Toshio; Sakoda, Tsuyoshi; Doi, Takashi; Tsujino, Takeshi; Masuyama, Tohru; Kawashima, Seinosuke; Iwasaki, Tadaaki; Ohyanagi, Mitsumasa

2007-01-01

Viral vector systems are efficient for transfection of foreign genes into many tissues. Especially, retrovirus based vectors integrate the transgene into the genome of the target cells, which can sustain long term expression. However, it has been demonstrated that the transduction efficiency using retrovirus is relatively lower than those of other viruses. Ultrasound was recently reported to increase gene expression using plasmid DNA, with or without, a delivery vehicle. However, there are no reports, which show an ultrasound effect to retrovirus-mediated gene transfer efficiency. Retrovirus-mediated gene transfer systems were used for transfection of 293T cells, bovine aortic endothelial cells (BAECs), rat aortic smooth muscle cells (RASMCs), and rat skeletal muscle myoblasts (L6 cells) with beta-galactosidase (beta-Gal) genes. Transduction efficiency and cell viability assay were performed on 293T cells that were exposed to varying durations (5 to 30 seconds) and power levels (1.0 watts/cm(2) to 4.0 watts/cm(2)) of ultrasound after being transduced by a retrovirus. Effects of ultrasound to the retrovirus itself was evaluated by transduction efficiency of 293T cells. After exposure to varying power levels of ultrasound to a retrovirus for 5 seconds, 293T cells were transduced by a retrovirus, and transduction efficiency was evaluated. Below 1.0 watts/cm(2) and 5 seconds exposure, ultrasound showed increased transduction efficiency and no cytotoxicity to 293T cells transduced by a retrovirus. Also, ultrasound showed no toxicity to the virus itself at the same condition. Exposure of 5 seconds at the power of 1.0 watts/cm(2) of an ultrasound resulted in significant increases in retrovirus-mediated gene expression in all four cell types tested in this experiment. Transduction efficiencies by ultrasound were enhanced 6.6-fold, 4.8-fold, 2.3-fold, and 3.2-fold in 293T cells, BAECs, RASMCs, and L6 cells, respectively. Furthermore, beta-Gal activities were also increased by the retrovirus with ultrasound exposure in these cells. Adjunctive ultrasound exposure was associated with enhanced retrovirus-mediated transgene expression in vitro. Ultrasound associated local gene therapy has potential for not only plasmid-DNA-, but also retrovirus-mediated gene transfer.

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

PubMed

Patin, Nastassia V; Schorn, Michelle; Aguinaldo, Kristen; Lincecum, Tommie; Moore, Bradley S; Jensen, Paul R

2017-02-15

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments. Copyright © 2017 American Society for Microbiology.

The double life of antibiotics.

PubMed

Yap, Mee-Ngan F

2013-01-01

Antibiotic resistance is a persistent health care problem worldwide. Evidence for the negative consequences of subtherapeutic feeding in livestock production has been mounting while the antibiotic pipeline is drying up. In recent years, there has been a paradigm shift in our perception of antibiotics. Apart from its roles in self-defense, antibiotics also serve as inter-microbial signaling molecules, regulators of gene expression, microbial food sources, and as mediators of host immune response.

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease

PubMed Central

Bacci, Giovanni; Fiscarelli, Ersilia; Taccetti, Giovanni; Dolce, Daniela; Paganin, Patrizia; Morelli, Patrizia; Tuccio, Vanessa; De Alessandri, Alessandra; Lucidi, Vincenzina

2017-01-01

In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease. PMID:28758937

Volatile Compounds Emitted by Pseudomonas aeruginosa Stimulate Growth of the Fungal Pathogen Aspergillus fumigatus.

PubMed

Briard, Benoit; Heddergott, Christoph; Latgé, Jean-Paul

2016-03-15

Chronic lung infections with opportunistic bacterial and fungal pathogens are a major cause of morbidity and mortality especially in patients with cystic fibrosis. Pseudomonas aeruginosa is the most frequently colonizing bacterium in these patients, and it is often found in association with the filamentous fungus Aspergillus fumigatus. P. aeruginosa is known to inhibit the growth of A. fumigatus in situations of direct contact, suggesting the existence of interspecies communication that may influence disease outcome. Our study shows that the lung pathogens P. aeruginosa and A. fumigatus can interact at a distance via volatile-mediated communication and expands our understanding of interspecific signaling in microbial communities. Microbiota studies have shown that pathogens cannot be studied individually anymore and that the establishment and progression of a specific disease are due not to a single microbial species but are the result of the activity of many species living together. To date, the interaction between members of the human microbiota has been analyzed in situations of direct contact or liquid-mediated contact between organisms. This study showed unexpectedly that human opportunistic pathogens can interact at a distance after sensing volatiles emitted by another microbial species. This finding will open a new research avenue for the understanding of microbial communities. Copyright © 2016 Briard et al.

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

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

Li, Minjing; Gao, Yuqian; Qian, Wei-Jun

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

Microbial reduction of iodate

USGS Publications Warehouse

Councell, T.B.; Landa, E.R.; Lovley, D.R.

1997-01-01

The different oxidation species of iodine have markedly different sorption properties. Hence, changes in iodine redox states can greatly affect the mobility of iodine in the environment. Although a major microbial role has been suggested in the past to account for these redox changes, little has been done to elucidate the responsible microorganisms or the mechanisms involved. In the work presented here, direct microbial reduction of iodate was demonstrated with anaerobic cell suspensions of the sulfate reducing bacterium Desulfovibrio desulfuricans which reduced 96% of an initial 100 ??M iodate to iodide at pH 7 in 30 mM NaHCO3 buffer, whereas anaerobic cell suspensions of the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens were unable to reduce iodate in 30 mM NaHCO3 buffer (pH 7). Both D. desulfuricans and S. putrefaciens were able to reduce iodate at pH 7 in 10 mM HEPES buffer. Both soluble ferrous iron and sulfide, as well as iron monosulfide (FeS) were shown to abiologically reduce iodate to iodide. These results indicate that ferric iron and/or sulfate reducing bacteria are capable of mediating both direct, enzymatic, as well as abiotic reduction of iodate in natural anaerobic environments. These microbially mediated reactions may be important factors in the fate and transport of 129I in natural systems.

Modeling of drug-mediated CYP3A4 induction by using human iPS cell-derived enterocyte-like cells

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

Negoro, Ryosuke; Takayama, Kazuo; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research

Many drugs have potential to induce the expression of drug-metabolizing enzymes, particularly cytochrome P450 3A4 (CYP3A4), in small intestinal enterocytes. Therefore, a model that can accurately evaluate drug-mediated CYP3A4 induction is urgently needed. In this study, we overlaid Matrigel on the human induced pluripotent stem cells-derived enterocyte-like cells (hiPS-ELCs) to generate the mature hiPS-ELCs that could be applied to drug-mediated CYP3A4 induction test. By overlaying Matrigel in the maturation process of enterocyte-like cells, the gene expression levels of intestinal markers (VILLIN, sucrase-isomaltase, intestine-specific homeobox, caudal type homeobox 2, and intestinal fatty acid-binding protein) were enhanced suggesting that the enterocyte-like cellsmore » were maturated by Matrigel overlay. The percentage of VILLIN-positive cells in the hiPS-ELCs found to be approximately 55.6%. To examine the CYP3A4 induction potential, the hiPS-ELCs were treated with various drugs. Treatment with dexamethasone, phenobarbital, rifampicin, or 1α,25-dihydroxyvitamin D3 resulted in 5.8-fold, 13.4-fold, 9.8-fold, or 95.0-fold induction of CYP3A4 expression relative to that in the untreated controls, respectively. These results suggest that our hiPS-ELCs would be a useful model for CYP3A4 induction test. - Highlights: • The hiPS-ELCs were matured by Matrigel overlay. • The hiPS-ELCs expressed intestinal nuclear receptors, such as PXR, GR and VDR. • The hiPS-ELC is a useful model for the drug-mediated CYP3A4 induction test.« less

Biofilm Filtrates of Pseudomonas aeruginosa Strains Isolated from Cystic Fibrosis Patients Inhibit Preformed Aspergillus fumigatus Biofilms via Apoptosis

PubMed Central

Shirazi, Fazal; Ferreira, Jose A. G.; Stevens, David A.; Clemons, Karl V.; Kontoyiannis, Dimitrios P.

2016-01-01

Pseudomonas aeruginosa (Pa) and Aspergillus fumigatus (Af) colonize cystic fibrosis (CF) patient airways. Pa culture filtrates inhibit Af biofilms, and Pa non-CF, mucoid (Muc-CF) and nonmucoid CF (NMuc-CF) isolates form an ascending inhibitory hierarchy. We hypothesized this activity is mediated through apoptosis induction. One Af and three Pa (non-CF, Muc-CF, NMuc-CF) reference isolates were studied. Af biofilm was formed in 96 well plates for 16 h ± Pa biofilm filtrates. After 24 h, apoptosis was characterized by viability dye DiBAc, reactive oxygen species (ROS) generation, mitochondrial membrane depolarization, DNA fragmentation and metacaspase activity. Muc-CF and NMuc-CF filtrates inhibited and damaged Af biofilm (p<0.0001). Intracellular ROS levels were elevated (p<0.001) in NMuc-CF-treated Af biofilms (3.7- fold) compared to treatment with filtrates from Muc-CF- (2.5- fold) or non-CF Pa (1.7- fold). Depolarization of mitochondrial potential was greater upon exposure to NMuc-CF (2.4-fold) compared to Muc-CF (1.8-fold) or non-CF (1.25-fold) (p<0.0001) filtrates. Exposure to filtrates resulted in more DNA fragmentation in Af biofilm, compared to control, mediated by metacaspase activation. In conclusion, filtrates from CF-Pa isolates were more inhibitory against Af biofilms than from non-CF. The apoptotic effect involves mitochondrial membrane damage associated with metacaspase activation. PMID:26930399

Biofilm Filtrates of Pseudomonas aeruginosa Strains Isolated from Cystic Fibrosis Patients Inhibit Preformed Aspergillus fumigatus Biofilms via Apoptosis.

PubMed

Shirazi, Fazal; Ferreira, Jose A G; Stevens, David A; Clemons, Karl V; Kontoyiannis, Dimitrios P

2016-01-01

Pseudomonas aeruginosa (Pa) and Aspergillus fumigatus (Af) colonize cystic fibrosis (CF) patient airways. Pa culture filtrates inhibit Af biofilms, and Pa non-CF, mucoid (Muc-CF) and nonmucoid CF (NMuc-CF) isolates form an ascending inhibitory hierarchy. We hypothesized this activity is mediated through apoptosis induction. One Af and three Pa (non-CF, Muc-CF, NMuc-CF) reference isolates were studied. Af biofilm was formed in 96 well plates for 16 h ± Pa biofilm filtrates. After 24 h, apoptosis was characterized by viability dye DiBAc, reactive oxygen species (ROS) generation, mitochondrial membrane depolarization, DNA fragmentation and metacaspase activity. Muc-CF and NMuc-CF filtrates inhibited and damaged Af biofilm (p<0.0001). Intracellular ROS levels were elevated (p<0.001) in NMuc-CF-treated Af biofilms (3.7- fold) compared to treatment with filtrates from Muc-CF- (2.5- fold) or non-CF Pa (1.7- fold). Depolarization of mitochondrial potential was greater upon exposure to NMuc-CF (2.4-fold) compared to Muc-CF (1.8-fold) or non-CF (1.25-fold) (p<0.0001) filtrates. Exposure to filtrates resulted in more DNA fragmentation in Af biofilm, compared to control, mediated by metacaspase activation. In conclusion, filtrates from CF-Pa isolates were more inhibitory against Af biofilms than from non-CF. The apoptotic effect involves mitochondrial membrane damage associated with metacaspase activation.

Augmentation of limb perfusion and reversal of tissue ischemia produced by ultrasound-mediated microbubble cavitation.

PubMed

Belcik, J Todd; Mott, Brian H; Xie, Aris; Zhao, Yan; Kim, Sajeevani; Lindner, Nathan J; Ammi, Azzdine; Linden, Joel M; Lindner, Jonathan R

2015-04-01

Ultrasound can increase tissue blood flow, in part, through the intravascular shear produced by oscillatory pressure fluctuations. We hypothesized that ultrasound-mediated increases in perfusion can be augmented by microbubble contrast agents that undergo ultrasound-mediated cavitation and sought to characterize the biological mediators. Contrast ultrasound perfusion imaging of hindlimb skeletal muscle and femoral artery diameter measurement were performed in nonischemic mice after unilateral 10-minute exposure to intermittent ultrasound alone (mechanical index, 0.6 or 1.3) or ultrasound with lipid microbubbles (2×10(8) IV). Studies were also performed after inhibiting shear- or pressure-dependent vasodilator pathways, and in mice with hindlimb ischemia. Ultrasound alone produced a 2-fold increase (P<0.05) in muscle perfusion regardless of ultrasound power. Ultrasound-mediated augmentation in flow was greater with microbubbles (3- and 10-fold higher than control for mechanical index 0.6 and 1.3, respectively; P<0.05), as was femoral artery dilation. Inhibition of endothelial nitric oxide synthase attenuated flow augmentation produced by ultrasound and microbubbles by 70% (P<0.01), whereas inhibition of adenosine-A2a receptors and epoxyeicosatrienoic acids had minimal effect. Limb nitric oxide production and muscle phospho-endothelial nitric oxide synthase increased in a stepwise fashion by ultrasound and ultrasound with microbubbles. In mice with unilateral hindlimb ischemia (40%-50% reduction in flow), ultrasound (mechanical index, 1.3) with microbubbles increased perfusion by 2-fold to a degree that was greater than the control nonischemic limb. Increases in muscle blood flow during high-power ultrasound are markedly amplified by the intravascular presence of microbubbles and can reverse tissue ischemia. These effects are most likely mediated by cavitation-related increases in shear and activation of endothelial nitric oxide synthase. © 2015 American Heart Association, Inc.

Designing pH induced fold switch in proteins

NASA Astrophysics Data System (ADS)

Baruah, Anupaul; Biswas, Parbati

2015-05-01

This work investigates the computational design of a pH induced protein fold switch based on a self-consistent mean-field approach by identifying the ensemble averaged characteristics of sequences that encode a fold switch. The primary challenge to balance the alternative sets of interactions present in both target structures is overcome by simultaneously optimizing two foldability criteria corresponding to two target structures. The change in pH is modeled by altering the residual charge on the amino acids. The energy landscape of the fold switch protein is found to be double funneled. The fold switch sequences stabilize the interactions of the sites with similar relative surface accessibility in both target structures. Fold switch sequences have low sequence complexity and hence lower sequence entropy. The pH induced fold switch is mediated by attractive electrostatic interactions rather than hydrophobic-hydrophobic contacts. This study may provide valuable insights to the design of fold switch proteins.

Biochar in co-contaminated soil manipulates arsenic solubility and microbiological community structure, and promotes organochlorine degradation.

PubMed

Gregory, Samuel J; Anderson, Christopher W N; Camps-Arbestain, Marta; Biggs, Patrick J; Ganley, Austen R D; O'Sullivan, Justin M; McManus, Michael T

2015-01-01

We examined the effect of biochar on the water-soluble arsenic (As) concentration and the extent of organochlorine degradation in a co-contaminated historic sheep-dip soil during a 180-d glasshouse incubation experiment. Soil microbial activity, bacterial community and structure diversity were also investigated. Biochar made from willow feedstock (Salix sp) was pyrolysed at 350 or 550°C and added to soil at rates of 10 g kg-1 and 20 g kg-1 (representing 30 t ha-1 and 60 t ha-1). The isomers of hexachlorocyclohexane (HCH) alpha-HCH and gamma-HCH (lindane), underwent 10-fold and 4-fold reductions in concentration as a function of biochar treatment. Biochar also resulted in a significant reduction in soil DDT levels (P < 0.01), and increased the DDE:DDT ratio. Soil microbial activity was significantly increased (P < 0.01) under all biochar treatments after 60 days of treatment compared to the control. 16S amplicon sequencing revealed that biochar-amended soil contained more members of the Chryseobacterium, Flavobacterium, Dyadobacter and Pseudomonadaceae which are known bioremediators of hydrocarbons. We hypothesise that a recorded short-term reduction in the soluble As concentration due to biochar amendment allowed native soil microbial communities to overcome As-related stress. We propose that increased microbiological activity (dehydrogenase activity) due to biochar amendment was responsible for enhanced degradation of organochlorines in the soil. Biochar therefore partially overcame the co-contaminant effect of As, allowing for enhanced natural attenuation of organochlorines in soil.

Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™.

PubMed

Luck, Ashley N; Slatko, Barton E; Foster, Jeremy M

2017-01-01

Efficient transcriptomic sequencing of microbial mRNA derived from host-microbe associations is often compromised by the much lower relative abundance of microbial RNA in the mixed total RNA sample. One solution to this problem is to perform extensive sequencing until an acceptable level of transcriptome coverage is obtained. More cost-effective methods include use of prokaryotic and/or eukaryotic rRNA depletion strategies, sometimes in conjunction with depletion of polyadenylated eukaryotic mRNA. Here, we report use of Cappable-seq™ to specifically enrich, in a single step, Wolbachia endobacterial mRNA transcripts from total RNA prepared from the parasitic filarial nematode, Brugia malayi. The obligate Wolbachia endosymbiont is a proven drug target for many human filarial infections, yet the precise nature of its symbiosis with the nematode host is poorly understood. Insightful analysis of the expression levels of Wolbachia genes predicted to underpin the mutualistic association and of known drug target genes at different life cycle stages or in response to drug treatments is typically challenged by low transcriptomic coverage. Cappable-seq resulted in up to ~ 5-fold increase in the number of reads mapping to Wolbachia. On average, coverage of Wolbachia transcripts from B. malayi microfilariae was enriched ~40-fold by Cappable-seq. Additionally, this method has an additional benefit of selectively removing abundant prokaryotic ribosomal RNAs.The deeper microbial transcriptome sequencing afforded by Cappable-seq facilitates more detailed characterization of gene expression levels of pathogens and symbionts present in animal tissues.

Leaching of vanadium from waste V2O5-WO3/TiO2 catalyst catalyzed by functional microorganisms.

PubMed

Wang, Shuhua; Xie, Yaling; Yan, Weifu; Wu, Xuee; Wang, Chin-Tsan; Zhao, Feng

2018-05-22

Solid wastes are currently produced in large amounts. Although bioleaching of metals from solid wastes is an economical and sustainable technology, it has seldom been used to recycle metals from abandoned catalyst. In this study, the bioleaching of vanadium from V 2 O 5 -WO 3 /TiO 2 catalyst were comprehensively investigated through five methods: Oligotrophic way, Eutrophic way, S-mediated way, Fe-mediated way and Mixed way of S-mediated and Fe-mediated. The observed vanadium bioleaching effectiveness of the assayed methods was follows: S-mediated > Mixed > Oligotrophic > Eutrophic > Fe-mediated, which yielded the maximum bioleaching efficiencies of approximately 90%, 35%, 33%, 20% and 7%, respectively. The microbial community analysis suggested that the predominant genera Acidithiobacillus and Sulfobacillus from the S-mediated bioleaching way effectively catalyzed the vanadium leaching, which could have occurred through the indirect mechanism from the microbial oxidation of S 0 . In addition, the direct mechanism, involving direct electron transfer between the catalyst and the microorganisms that attached to the catalyst surface, should also help the vanadium to be leached more effectively. Therefore, this work provides guidance for future research and practical application on the treatment of waste V 2 O 5 -WO 3 /TiO 2 catalyst. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial recycling of glycerol to biodiesel.

PubMed

Yang, Liu; Zhu, Zhi; Wang, Weihua; Lu, Xuefeng

2013-12-01

The sustainable supply of lipids is the bottleneck for current biodiesel production. Here microbial recycling of glycerol, byproduct of biodiesel production to biodiesel in engineered Escherichia coli strains was reported. The KC3 strain with capability of producing fatty acid ethyl esters (FAEEs) from glucose was used as a starting strain to optimize fermentation conditions when using glycerol as sole carbon source. The YL15 strain overexpressing double copies of atfA gene displayed 1.7-fold increase of FAEE productivity compared to the KC3 strain. The titer of FAEE in YL15 strain reached to 813 mg L(-1) in minimum medium using glycerol as sole carbon source under optimized fermentation conditions. The titer of glycerol-based FAEE production can be significantly increased by both genetic modifications and fermentation optimization. Microbial recycling of glycerol to biodiesel expands carbon sources for biodiesel production. Copyright © 2013 Elsevier Ltd. All rights reserved.

Rate dependent fractionation of sulfur isotopes in through-flowing systems

NASA Astrophysics Data System (ADS)

Giannetta, M.; Sanford, R. A.; Druhan, J. L.

2017-12-01

The fidelity of reactive transport models in quantifying microbial activity in the subsurface is often improved through the use stable isotopes. However, the accuracy of current predictions for microbially mediated isotope fractionations within open through-flowing systems typically depends on nutrient availability. This disparity arises from the common application of a single `effective' fractionation factor assigned to a given system, despite extensive evidence for variability in the fractionation factor between eutrophic environments and many naturally occurring, nutrient-limited environments. Here, we demonstrate a reactive transport model with the capacity to simulate a variable fractionation factor over a range of microbially mediated reduction rates and constrain the model with experimental data for nutrient limited conditions. Two coupled isotope-specific Monod rate laws for 32S and 34S, constructed to quantify microbial sulfate reduction and predict associated S isotope partitioning, were parameterized using a series of batch reactor experiments designed to minimize microbial growth. In the current study, we implement these parameterized isotope-specific rate laws within an open, through-flowing system to predict variable fractionation with distance as a function of sulfate reduction rate. These predictions are tested through a supporting laboratory experiment consisting of a flow-through column packed with homogenous porous media inoculated with the same species of sulfate reducing bacteria used in the previous batch reactors, Desulfovibrio vulgaris. The collective results of batch reactor and flow-through column experiments support a significant improvement for S isotope predictions in isotope-sensitive multi-component reactive transport models through treatment of rate-dependent fractionation. Such an update to the model will better equip reactive transport software for isotope informed characterization of microbial activity within energy and nutrient limited environments.

Application of a weak magnetic field to improve microbial fuel cell performance.

PubMed

Tong, Zhong-Hua; Yu, Han-Qing; Li, Wen-Wei; Wang, Yun-Kun; Sun, Min; Liu, Xian-Wei; Sheng, Guo-Ping

2015-12-01

Microbial fuel cells (MFCs) have emerged as a promising technology for wastewater treatment with concomitant energy production but the performance is usually limited by low microbial activities. This has spurred intensive research interest for microbial enhancement. This study demonstrated an interesting stimulation effect of a static magnetic field (MF) on sludge-inoculated MFCs and explored into the mechanisms. The implementation of a 100-mT MF accelerated the reactor startup and led to increased electricity generation. Under the MF exposure, the activation loss of the MFC was decreased, but there was no increased secretion of redox mediators. Thus, the MF effect was mainly due to enhanced bioelectrochemical activities of anodic microorganisms, which are likely attributed to the oxidative stress and magnetohydrodynamic effects under an MF exposure. This work implies that weak MF may be applied as a simple and effective approach to stimulate microbial activities for various bioelectrochemical energy production and decontamination applications.

Mediation of the effect of malaria in pregnancy on stillbirth and neonatal death in an area of low transmission: observational data analysis.

PubMed

Moore, Kerryn A; Fowkes, Freya J I; Wiladphaingern, Jacher; Wai, Nan San; Paw, Moo Kho; Pimanpanarak, Mupawjay; Carrara, Verena I; Raksuansak, Jathee; Simpson, Julie A; White, Nicholas J; Nosten, François; McGready, Rose

2017-05-10

Malaria in pregnancy is preventable and contributes significantly to the estimated 5.5 million stillbirths and neonatal deaths that occur annually. The contribution of malaria in pregnancy in areas of low transmission has not been quantified, and the roles of maternal anaemia, small-for-gestational-age status, and preterm birth in mediating the effect of malaria in pregnancy on stillbirth and neonatal death are poorly elucidated. We analysed observational data routinely collected at antenatal clinics on the Thai-Myanmar border (1986-2015). We used Cox regression and sequential mediation analysis to determine the effect of falciparum and vivax malaria in pregnancy on antepartum (death in utero) and intrapartum (death during labour) stillbirth and neonatal mortality as well as mediation through maternal anaemia, preterm birth, and small-for-gestational-age status. Of 61,836 women, 9350 (15%) had malaria in pregnancy, and 526 (0.8%) had stillbirths. In a sub-set of 9090 live born singletons followed from birth there were 153 (1.7%) neonatal deaths. The hazard of antepartum stillbirth increased 2.24-fold [95% confidence interval: 1.47, 3.41] following falciparum malaria (42% mediated through small-for-gestational-age status and anaemia), driven by symptomatic falciparum malaria (hazard ratio, HR: 2.99 [1.83, 4.89]) rather than asymptomatic falciparum malaria (HR: 1.35 [0.61, 2.96]). The hazard of antepartum stillbirth increased 2.21-fold [1.12, 4.33] following symptomatic vivax malaria (24% mediated through small-for-gestational-age status and anaemia) but not asymptomatic vivax malaria (HR: 0.54 [0.20, 1.45]). There was no association between falciparum or vivax malaria in pregnancy and intrapartum stillbirth (falciparum HR: 1.03 [0.58, 1.83]; vivax HR: 1.18 [0.66, 2.11]). Falciparum and vivax malaria in pregnancy increased the hazard of neonatal death 2.55-fold [1.54, 4.22] and 1.98-fold [1.10, 3.57], respectively (40% and 50%, respectively, mediated through small-for-gestational-age status and preterm birth). Prevention of malaria in pregnancy, new and existing interventions to prevent small-for-gestational-age status and maternal anaemia, and improved capacity for managing preterm and small-for-gestational-age newborns will reduce the number of malaria-associated stillbirths and neonatal deaths in malaria-endemic areas.

Arsenic release from shallow aquifers of the Hetao basin, Inner Mongolia: evidence from bacterial community in aquifer sediments and groundwater.

PubMed

Li, Yuan; Guo, Huaming; Hao, Chunbo

2014-12-01

Indigenous microbes play crucial roles in arsenic mobilization in high arsenic groundwater systems. Databases concerning the presence and the activity of microbial communities are very useful in evaluating the potential of microbe-mediated arsenic mobilization in shallow aquifers hosting high arsenic groundwater. This study characterized microbial communities in groundwaters at different depths with different arsenic concentrations by DGGE and one sediment by 16S rRNA gene clone library, and evaluated arsenic mobilization in microcosm batches with the presence of indigenous bacteria. DGGE fingerprints revealed that the community structure changed substantially with depth at the same location. It indicated that a relatively higher bacterial diversity was present in the groundwater sample with lower arsenic concentration. Sequence analysis of 16S rRNA gene demonstrated that the sediment bacteria mainly belonged to Pseudomonas, Dietzia and Rhodococcus, which have been widely found in aquifer systems. Additionally, NO3(-)-reducing bacteria Pseudomonas sp. was the largest group, followed by Fe(III)-reducing, SO4(2-)-reducing and As(V)-reducing bacteria in the sediment sample. These anaerobic bacteria used the specific oxyanions as electron acceptor and played a significant role in reductive dissolution of Fe oxide minerals, reduction of As(V), and release of arsenic from sediments into groundwater. Microcosm experiments, using intact aquifer sediments, showed that arsenic release and Fe(III) reduction were microbially mediated in the presence of indigenous bacteria. High arsenic concentration was also observed in the batch without amendment of organic carbon, demonstrating that the natural organic matter in sediments was the potential electron donor for microbially mediated arsenic release from these aquifer sediments.

Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota

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

Warren, Melissa J.; Lin, Xueju; Gaby, John C.

We present that Microbial N 2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO 2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O 2, CO 2, and CH 4) on potential rates of diazotrophy measured by acetylene (C 2H 2) reduction and 15N 2incorporation. A molecularmore » analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (15N 2 was suppressed 90% by O 2 and 55% by C 2H 2 and was unaffected by CH 4 and CO 2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C 2H 2-sensitive and C 2H 2-insensitive microbes that are more active at low concentrations of O 2 and show similar activity at high and low concentrations of CH 4. Importance: Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. In conclusion, our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.« less

Electron transfer capacity dependence of quinone-mediated Fe(III) reduction and current generation by Klebsiella pneumoniae L17.

PubMed

Li, Xiaomin; Liu, Liang; Liu, Tongxu; Yuan, Tian; Zhang, Wei; Li, Fangbai; Zhou, Shungui; Li, Yongtao

2013-06-01

Quinone groups in exogenous electron shuttles can accelerate extracellular electron transfer (EET) from bacteria to insoluble terminal electron acceptors, such as Fe(III) oxides and electrodes, which are important in biogeochemical redox processes and microbial electricity generation. However, the relationship between quinone-mediated EET performance and electron-shuttling properties of the quinones remains incompletely characterized. This study investigates the effects of a series of synthetic quinones (SQs) on goethite reduction and current generation by a fermenting bacterium Klebsiella pneumoniae L17. In addition, the voltammetric behavior and electron transfer capacities (ETCs) of SQ, including electron accepting (EAC) and donating (EDC) capacities, is also examined using electrochemical methods. The results showed that SQ can significantly increase both the Fe(III) reduction rates and current outputs of L17. Each tested SQ reversibly accepted and donated electrons as indicated by the cyclic voltammograms. The EAC and EDC results showed that Carmine and Alizarin had low relative capacities of electron transfer, whereas 9,10-anthraquinone-2,6-disulfonic acid (AQDS), 2-hydroxy-1,4-naphthoquinone (2-HNQ), and 5-hydroxy-1,4-naphthoquinone (5-HNQ) showed stronger relative ETC, and 9,10-anthraquinone-2-carboxylic acid (AQC) and 9,10-anthraquinone-2-sulfonic acid (AQS) had high relative ETC. Enhancement of microbial goethite reduction kinetics and current outputs by SQ had a good linear relationship with their ETC, indicating that the effectiveness of quinone-mediated EET may be strongly dependent on the ETC of the quinones. Therefore, the presence of quinone compounds and fermenting microorganisms may increase the diversity of microbial populations that contribute to element transformation in natural environments. Moreover, ETC determination of different SQ would help to evaluate their performance for microbial EET under anoxic conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota

DOE PAGES

Warren, Melissa J.; Lin, Xueju; Gaby, John C.; ...

2017-06-30

We present that Microbial N 2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO 2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O 2, CO 2, and CH 4) on potential rates of diazotrophy measured by acetylene (C 2H 2) reduction and 15N 2incorporation. A molecularmore » analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (15N 2 was suppressed 90% by O 2 and 55% by C 2H 2 and was unaffected by CH 4 and CO 2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C 2H 2-sensitive and C 2H 2-insensitive microbes that are more active at low concentrations of O 2 and show similar activity at high and low concentrations of CH 4. Importance: Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. In conclusion, our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.« less

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Modulation of opioid analgesia by agmatine.

PubMed

Kolesnikov, Y; Jain, S; Pasternak, G W

1996-01-18

Administered alone, agmatine at doses of 0.1 or 10 mg/kg is without effect in the mouse tailflick assay. However, agmatine enhances morphine analgesia in a dose-dependent manner, shifting morphine's ED50 over 5-fold. A far greater effect is observed when morphine is given intrathecally (9-fold shift) than after intracerebroventricular administration (2-fold). In contrast to the potentiation of morphine analgesia, agmatine (10 mg/kg) has no effect on morphine's inhibition of gastrointestinal transit. delta-Opioid receptor-mediated analgesia also is potentiated by agmatine, but kappa1-receptor-mediated (U50,488H; trans-3,4-dichloro-N-methyl-N-[2-(1-pyrrolidinyl)cyclohexyl] benzeneacetemide) and kappa3-opioid receptor-mediated (naloxone benzoylhydrazone) analgesia is not significantly enhanced by any dose of agmatine tested in this acute model. In chronic studies, agmatine at a low dose (0.1 mg/kg) which does not affect morphine analgesia acutely prevents tolerance following chronic morphine dosing for 10 days. A higher agmatine dose (10 mg/kg) has a similar effect. Agmatine also blocks tolerance to the delta-opioid receptor ligand [D-Pen2,D-Pen5]enkephalin given intrathecally, but not to the kappa3-opioid receptor agonist naloxone benzoylhydrazone. Despite its inactivity on kappa1-opioid analgesia in the acute model, agmatine prevents kappa1-opioid receptor-mediated tolerance. These studies demonstrate the dramatic interactions between agmatine and opioid analgesia and tolerance.

Neurotoxicity of fungal volatile organic compounds in Drosophila melanogaster.

PubMed

Inamdar, Arati A; Masurekar, Prakash; Bennett, Joan Wennstrom

2010-10-01

Many volatile organic compounds (VOCs) are found in indoor environment as products of microbial metabolism. In damp indoor environments, fungi are associated with poor air quality. Some epidemiological studies have suggested that microbial VOCs have a negative impact on human health. Our study was designed to provide a reductionist approach toward studying fungal VOC-mediated toxicity using the inexpensive model organism, Drosophila melanogaster, and pure chemical standards of several important fungal VOCs. Low concentrations of the following known fungal VOCs, 0.1% of 1-octen-3-ol and 0.5% of 2-octanone; 2,5 dimethylfuran; 3-octanol; and trans-2-octenal, caused locomotory defects and changes in green fluorescent protein (GFP)- and antigen-labeled dopaminergic neurons in adult D. melanogaster. Locomotory defects could be partially rescued with L-DOPA. Ingestion of the antioxidant, vitamin E, improved the survival span and delayed the VOC-mediated changes in dopaminergic neurons, indicating that the VOC-mediated toxicity was due, in part, to generation of reactive oxygen species.

Phosphate-Mediated Remediation of Metals and Radionuclides

DOE PAGES

Martinez, Robert J.; Beazley, Melanie J.; Sobecky, Patricia A.

2014-01-01

Worldwide industrialization activities create vast amounts of organic and inorganic waste streams that frequently result in significant soil and groundwater contamination. Metals and radionuclides are of particular concern due to their mobility and long-term persistence in aquatic and terrestrial environments. As the global population increases, the demand for safe, contaminant-free soil and groundwater will increase as will the need for effective and inexpensive remediation strategies. Remediation strategies that include physical and chemical methods (i.e., abiotic) or biological activities have been shown to impede the migration of radionuclide and metal contaminants within soil and groundwater. However, abiotic remediation methods are oftenmore » too costly owing to the quantities and volumes of soils and/or groundwater requiring treatment. The in situ sequestration of metals and radionuclides mediated by biological activities associated with microbial phosphorus metabolism is a promising and less costly addition to our existing remediation methods. This review highlights the current strategies for abiotic and microbial phosphate-mediated techniques for uranium and metal remediation.« less

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

PubMed

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A light-induced shortcut in the planktonic microbial loop

NASA Astrophysics Data System (ADS)

Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A.; Calbet, Albert; Nejstgaard, Jens C.; Gasol, Josep M.; Isari, Stamatina; Moorthi, Stefanie D.; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F.; Tsagaraki, Tatiana M.; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D.; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A.; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi

2016-07-01

Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light.

A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.

PubMed

Beloglazova, Natalia; Brown, Greg; Zimmerman, Matthew D; Proudfoot, Michael; Makarova, Kira S; Kudritska, Marina; Kochinyan, Samvel; Wang, Shuren; Chruszcz, Maksymilian; Minor, Wladek; Koonin, Eugene V; Edwards, Aled M; Savchenko, Alexei; Yakunin, Alexander F

2008-07-18

Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure of SSO1404 was solved at 1.6A resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.

Amplification of the groESL operon in Pseudomonas putida increases siderophore gene promoter activity.

PubMed

Venturi, V; Wolfs, K; Leong, J; Weisbeek, P J

1994-10-17

Pseudobactin 358 is the yellow-green fluorescent siderophore [microbial iron(III) transport agent] produced by Pseudomonas putida WCS358 under iron-limiting conditions. The genes encoding pseudobactin 358 biosynthesis are iron-regulated at the level of transcription. In this study, the molecular characterization is reported of a cosmid clone of WCS358 DNA that can stimulate, in an iron-dependent manner, the activity of a WCS358 siderophore gene promoter in the heterologous Pseudomonas strain A225. The functional region in the clone was identified by subcloning, transposon mutagenesis and DNA sequencing as the groESL operon of strain WCS358. This increase in promoter activity was not observed when the groESL genes of strain WCS358 were integrated via a transposon vector into the genome of Pseudomonas A225, indicating that multiple copies of the operon are necessary for the increase in siderophore gene promoter activity. Amplification of the Escherichia coli and WCS358 groESL genes also increased iron-regulated promoter activity in the parent strain WCS358. The groESL operon codes for the chaperone proteins GroES and GroEL, which are responsible for mediating the folding and assembly of many proteins.

Increased Butyrate Production During Long-Term Fermentation of In Vitro-Digested High Amylose Cornstarch Residues with Human Feces.

PubMed

Li, Li; Jiang, Hongxin; Kim, Hyun-Jung; Yum, Man-Yu; Campbell, Mark R; Jane, Jay-Lin; White, Pamela J; Hendrich, Suzanne

2015-09-01

An in vitro semi-continuous long-term (3 wk) anaerobic incubation system simulating lower gut fermentation was used to determine variability in gut microbial metabolism between 4 predigested high amylose-resistant starch residues (SR): SRV, SRVI, SRVII, and SRGEMS in human fecal samples. Subjects participated twice, 5 mo apart: 30 in Phase I (15 lean, 9 overweight and 6 obese), 29 in Phase II (15 lean, 9 overweight, 5 obese); 13 of 15 lean subjects participated in both phases. Of the 4 SRs, SRV displayed the highest gelatinization temperature, peak temperature, enthalpy changes, and the least digestibility compared with the other SRs. In both phases, compared with blank controls, all SRs increased butyrate ∼2-fold which stabilized at week 2 and only SRV caused greater propionate concentration (∼30%) after 3 wk which might have been partly mediated by its lesser digestibility. Fecal samples from lean and overweight/obese subjects incubated with SRs showed similar short-chain fatty acid production across both time points, which suggests that resistant starch may benefit individuals across BMIs. © 2015 Institute of Food Technologists®

Functional genomics to discover antibiotic resistance genes: The paradigm of resistance to colistin mediated by ethanolamine phosphotransferase in Shewanella algae MARS 14.

PubMed

Telke, Amar A; Rolain, Jean-Marc

2015-12-01

Shewanella algae MARS 14 is a colistin-resistant clinical isolate retrieved from bronchoalveolar lavage of a hospitalised patient. A functional genomics strategy was employed to discover the molecular support for colistin resistance in S. algae MARS 14. A pZE21 MCS-1 plasmid-based genomic expression library was constructed in Escherichia coli TOP10. The estimated library size was 1.30×10(8) bp. Functional screening of colistin-resistant clones was carried out on Luria-Bertani agar containing 8 mg/L colistin. Five colistin-resistant clones were obtained after complete screening of the genomic expression library. Analysis of DNA sequencing results found a unique gene in all selected clones. Amino acid sequence analysis of this unique gene using the Integrated Microbial Genomes (IMG) and KEGG databases revealed that this gene encodes ethanolamine phosphotransferase (EptA, or so-called PmrC). Reverse transcription PCR analysis indicated that resistance to colistin in S. algae MARS 14 was associated with overexpression of EptA (27-fold increase), which plays a crucial role in the arrangement of outer membrane lipopolysaccharide. Copyright © 2015 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Lipidomic profiling of bioactive lipids by mass spectrometry during microbial infections.

PubMed

Tam, Vincent C

2013-10-31

Bioactive lipid mediators play crucial roles in promoting the induction and resolution of inflammation. Eicosanoids and other related unsaturated fatty acids have long been known to induce inflammation. These signaling molecules can modulate the circulatory system and stimulate immune cell infiltration into the site of infection. Recently, DHA- and EPA-derived metabolites have been discovered to promote the resolution of inflammation, an active process. Not only do these molecules stop the further infiltration of immune cells, they prompt non-phlogistic phagocytosis of apoptotic neutrophils, stimulating the tissue to return to homeostasis. After the rapid release of lipid precursors from the plasma membrane upon stimulation, families of enzymes in a complex network metabolize them to produce a large array of lipid metabolites. With current advances in mass spectrometry, the entire lipidome can be accurately quantified to assess the immune response upon microbial infection. In this review, we discuss the various lipid metabolism pathways in the context of the immune response to microbial pathogens, as well as their complex network interactions. With the advancement of mass spectrometry, these approaches have also been used to characterize the lipid mediator response of macrophages and neutrophils upon immune stimulation in vitro. Lastly, we describe the recent efforts to apply systems biology approaches to dissect the role of lipid mediators during bacterial and viral infections in vivo. Copyright © 2013 Elsevier Ltd. All rights reserved.

Responses of microbial tolerance to heavy metals along a century-old metal ore pollution gradient in a subarctic birch forest.

PubMed

Rousk, Johannes; Rousk, Kathrin

2018-05-07

Heavy metals are some of the most persistent and potent anthropogenic environmental contaminants. Although heavy metals may compromise microbial communities and soil fertility, it is challenging to causally link microbial responses to heavy metals due to various confounding factors, including correlated soil physicochemistry or nutrient availability. A solution is to investigate whether tolerance to the pollutant has been induced, called Pollution Induced Community Tolerance (PICT). In this study, we investigated soil microbial responses to a century-old gradient of metal ore pollution in an otherwise pristine subarctic birch forest generated by a railway source of iron ore transportation. To do this, we determined microbial biomass, growth, and respiration rates, and bacterial tolerance to Zn and Cu in replicated distance transects (1 m-4 km) perpendicular to the railway. Microbial biomass, growth and respiration rates were stable across the pollution gradient. The microbial community structure could be distinguished between sampled distances, but most of the variation was explained by soil pH differences, and it did not align with distance from the railroad pollution source. Bacterial tolerance to Zn and Cu started from background levels at 4 km distance from the pollution source, and remained at background levels for Cu throughout the gradient. Yet, bacterial tolerance to Zn increased 10-fold 100 m from the railway source. Our results show that the microbial community structure, size and performance remained unaffected by the metal ore exposure, suggesting no impact on ecosystem functioning. Copyright © 2018 Elsevier Ltd. All rights reserved.

Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

NASA Astrophysics Data System (ADS)

Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

2016-09-01

Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

PubMed

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

Microbial community assembly and metabolic function during mammalian corpse decomposition

USGS Publications Warehouse

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

2016-01-01

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

An overview of field-specific designs of microbial EOR

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

Robertson, E.P.; Bala, G.A.; Fox, S.L.

1995-12-31

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

Microbial community assembly and metabolic function during mammalian corpse decomposition

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

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.

2015-12-10

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

Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid K-252a.

PubMed

Schiering, Nikolaus; Knapp, Stefan; Marconi, Marina; Flocco, Maria M; Cui, Jean; Perego, Rita; Rusconi, Luisa; Cristiani, Cinzia

2003-10-28

The protooncogene c-met codes for the hepatocyte growth factor receptor tyrosine kinase. Binding of its ligand, hepatocyte growth factor/scatter factor, stimulates receptor autophosphorylation, which leads to pleiotropic downstream signaling events in epithelial cells, including cell growth, motility, and invasion. These events are mediated by interaction of cytoplasmic effectors, generally through Src homology 2 (SH2) domains, with two phosphotyrosine-containing sequence motifs in the unique C-terminal tail of c-Met (supersite). There is a strong link between aberrant c-Met activity and oncogenesis, which makes this kinase an important cancer drug target. The furanosylated indolocarbazole K-252a belongs to a family of microbial alkaloids that also includes staurosporine. It was recently shown to be a potent inhibitor of c-Met. Here we report the crystal structures of an unphosphorylated c-Met kinase domain harboring a human cancer mutation and its complex with K-252a at 1.8-A resolution. The structure follows the well established architecture of protein kinases. It adopts a unique, inhibitory conformation of the activation loop, a catalytically noncompetent orientation of helix alphaC, and reveals the complete C-terminal docking site. The first SH2-binding motif (1349YVHV) adopts an extended conformation, whereas the second motif (1356YVNV), a binding site for Grb2-SH2, folds as a type II Beta-turn. The intermediate portion of the supersite (1353NATY) assumes a type I Beta-turn conformation as in an Shc-phosphotyrosine binding domain peptide complex. K-252a is bound in the adenosine pocket with an analogous binding mode to those observed in previously reported structures of protein kinases in complex with staurosporine.

The clinical and cellular basis of contact lens-related corneal infections

PubMed Central

Robertson, Danielle M; Cavanagh, H Dwight

2008-01-01

Microbial keratitis (MK) is the most visually devastating complication associated with contact lens wear. Pseudomonas aeruginosa (PA) is highly invasive in the corneal epithelium and is responsible for more than half of the reported cases of contact lens-related MK. To protect against Pseudomonas-mediated MK, the corneal epithelium has evolved overlapping defense mechanisms that function to protect the ocular surface from microbial invasion. Research has shown that contact lens wear disrupts these protective mechanisms through breakdown of normal homeostatic surface renewal as well as damaging the corneal surface, exposing underlying cell membrane receptors that bind and internalize PA through the formation of lipid rafts. Human clinical trials have shown that initial adherence of PA with resulting increased risk for microbial infection is mediated in part by contact lens oxygen transmissibility. Recently, chemical preserved multipurpose solutions (MPS) have been implicated in increasing PA adherence to corneal epithelial cells, in addition to inducing significant levels of toxic staining when used in conjunction with specific silicone hydrogel lenses. This review summarizes what is currently known about the relationship between contact lenses, the corneal epithelium, MPS, and infection. PMID:19277209

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease

NASA Astrophysics Data System (ADS)

Baldassano, Steven N.; Bassett, Danielle S.

2016-05-01

The gut microbiome plays a key role in human health, and alterations of the normal gut flora are associated with a variety of distinct disease states. Yet, the natural dependencies between microbes in healthy and diseased individuals remain far from understood. Here we use a network-based approach to characterize microbial co-occurrence in individuals with inflammatory bowel disease (IBD) and healthy (non-IBD control) individuals. We find that microbial networks in patients with IBD differ in both global structure and local connectivity patterns. While a “core” microbiome is preserved, network topology of other densely interconnected microbe modules is distorted, with potent inflammation-mediating organisms assuming roles as integrative and highly connected inter-modular hubs. We show that while both networks display a rich-club organization, in which a small set of microbes commonly co-occur, the healthy network is more easily disrupted by elimination of a small number of key species. Further investigation of network alterations in disease might offer mechanistic insights into the specific pathogens responsible for microbiome-mediated inflammation in IBD.

Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

PubMed Central

Bian, Yunqiang; Zhang, Jian; Wang, Jun; Wang, Jihua; Wang, Wei

2015-01-01

How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA. PMID:26030098

Interdomain communication revealed in the diabetes drug target mitoNEET

PubMed Central

Jennings, Patricia A.

2011-01-01

MitoNEET is a recently identified drug target for a commonly prescribed diabetes drug, Pioglitazone. It belongs to a previously uncharacterized ancient family of proteins for which the hallmark is the presence of a unique 39 amino acid CDGSH domain. In order to characterize the folding landscape of this novel fold, we performed thermodynamic simulations on MitoNEET using a structure-based model. Additionally, we implement a method of contact map clustering to partition out alternate pathways in folding. This cluster analysis reveals a detour late in folding and enables us to carefully examine the folding mechanism of each pathway rather than the macroscopic average. We observe that tightness in a region distal to the iron–sulfur cluster creates a constraint in folding and additionally appears to mediate communication in folding between the two domains of the protein. We demonstrate that by making changes at this site we are able to tweak the order of folding events in the cluster binding domain as well as decrease the barrier to folding. PMID:21402934

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses.

PubMed

Ge, Zhongming; Sheh, Alexander; Feng, Yan; Muthupalani, Sureshkumar; Ge, Lili; Wang, Chuanwu; Kurnick, Susanna; Mannion, Anthony; Whary, Mark T; Fox, James G

2018-05-22

C57BL/6 (B6) mice from Taconic Sciences (Tac) and the Jackson Laboratory (Jax) were infected with H. pylori PMSS1 (Hp) for 16 week; there was no significant difference in the gastric histologic activity index between Hp infected Tac and Jax B6. However, the degree of gastric mucous metaplasia and Th1-associated IgG2c levels in response to Hp infection were increased in Tac mice over Jax mice, whereas the colonization levels of gastric Hp were higher by 8-fold in Jax B6 compared with Tac B6. Additionally, mRNA expression of gastric Il-1β, Il-17A and RegIIIγ were significantly lower in the infected Tac compared to the infected Jax mice. There were significant differences in the microbial community structures in stomach, colon, and feces between Jax and Tac B6 females. Differences in gastric microbial communities between Jax and Tac B6 females are predicted to affect the metagenome. Moreover, Hp infection perturbed the microbial community structures in the stomach, colon and feces of Jax mice, but only altered the colonic microbial composition of Tac mice. Our data indicate that the GI microbiome of Tac B6 mice is compositionally distinct from Jax B6 mice, which likely resulted in different pathological, immunological, and microbial responses to Hp infection.

Modeling biogechemical reactive transport in a fracture zone

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

Molinero, Jorge; Samper, Javier; Yang, Chan Bing, and Zhang, Guoxiang

2005-01-14

A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes inmore » biochemical parameters.« less

Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review.

PubMed

Zhu, Xiaomin; Chen, Baoliang; Zhu, Lizhong; Xing, Baoshan

2017-08-01

Biochars have attracted tremendous attention due to their effects on soil improvement; they enhance carbon storage, soil fertility and quality, and contaminant (organic and heavy metal) immobilization and transformation. These effects could be achieved by modifying soil microbial habitats and (or) directly influencing microbial metabolisms, which together induce changes in microbial activity and microbial community structures. This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars. In particular, we summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation. Special attention has been paid to biochar effects on the formation and protection of soil aggregates, biochar adsorption of contaminants, biochar-mediated transformation of soil contaminants by microorganisms, and biochar-facilitated electron transfer between microbial cells and contaminants and soil organic matter. Certain reactive organic compounds and heavy metals in biochar may induce toxicity to soil microorganisms. Adsorption and hydrolysis of signaling molecules by biochar interrupts microbial interspecific communications, potentially altering soil microbial community structures. Further research is urged to verify the proposed mechanisms involved in biochar-microbiota interactions for soil remediation and improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial-mediated method for metal oxide nanoparticle formation

DOEpatents

Rondinone, Adam J.; Moon, Ji Won; Love, Lonnie J.; Yeary, Lucas W.; Phelps, Tommy J.

2015-09-08

The invention is directed to a method for producing metal oxide nanoparticles, the method comprising: (i) subjecting a combination of reaction components to conditions conducive to microbial-mediated formation of metal oxide nanoparticles, wherein said combination of reaction components comprise: metal-reducing microbes, a culture medium suitable for sustaining said metal-reducing microbes, an effective concentration of one or more surfactants, a reducible metal oxide component containing one or more reducible metal species, and one or more electron donors that provide donatable electrons to said metal-reducing microbes during consumption of the electron donor by said metal-reducing microbes; and (ii) isolating said metal oxide nanoparticles, which contain a reduced form of said reducible metal oxide component. The invention is also directed to metal oxide nanoparticle compositions produced by the inventive method.

PCBs Alter Dopamine Mediated Function in Aging Workers

DTIC Science & Technology

2010-01-01

sympathomimetic agents, beta-adrenergic blocking agents, angiotensin-converting enzyme inhibitors, COX-2 inhibitors, other non - steroidal anti - inflammatory ...other non - steroidal anti - inflammatory agents, opiate agonists, miscellaneous analgesics and antipyretics, thyroid agents and antithyroid agents. ⁎ p...fold from peak values during occupational PCB use but remain elevated (two-fold) compared to a similar-aged non -occupationally exposed population

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

Electrochemical performance and microbial community profiles in microbial fuel cells in relation to electron transfer mechanisms.

PubMed

Uria, Naroa; Ferrera, Isabel; Mas, Jordi

2017-10-18

Microbial fuel cells (MFCs) operating with complex microbial communities have been extensively reported in the past, and are commonly used in applications such as wastewater treatment, bioremediation or in-situ powering of environmental sensors. However, our knowledge on how the composition of the microbial community and the different types of electron transfer to the anode affect the performance of these bioelectrochemical systems is far from complete. To fill this gap of knowledge, we designed a set of three MFCs with different constrains limiting direct and mediated electron transfer to the anode. The results obtained indicate that MFCs with a naked anode on which a biofilm was allowed unrestricted development (MFC-A) had the most diverse archaeal and bacterial community, and offered the best performance. In this MFC both, direct and mediated electron transfer, occurred simultaneously, but direct electron transfer was the predominant mechanism. Microbial fuel cells in which the anode was enclosed in a dialysis membrane and biofilm was not allowed to develop (MFC-D), had a much lower power output (about 60% lower), and a prevalence of dissolved redox species that acted as putative electron shuttles. In the anolyte of this MFC, Arcobacter and Methanosaeta were the prevalent bacteria and archaea respectively. In the third MFC, in which the anode had been covered by a cation selective nafion membrane (MFC-N), power output decreased a further 5% (95% less than MFC-A). In this MFC, conventional organic electron shuttles could not operate and the low power output obtained was presumably attributed to fermentation end-products produced by some of the organisms present in the anolyte, probably Pseudomonas or Methanosaeta. Electron transfer mechanisms have an impact on the development of different microbial communities and in turn on MFC performance. Although a stable current was achieved in all cases, direct electron transfer MFC showed the best performance concluding that biofilms are the major contributors to current production in MFCs. Characterization of the complex microbial assemblages in these systems may help us to unveil new electrogenic microorganisms and improve our understanding on their role to the functioning of MFCs.

Large-scale controls on potential respiration and denitrification in riverine floodplains

PubMed Central

Welti, Nina; Bondar-Kunze, Elisabeth; Singer, Gabriel; Tritthart, Michael; Zechmeister-Boltenstern, Sophie; Hein, Thomas; Pinay, Gilles

2012-01-01

Restoration measures of deteriorated river ecosystems generally aim at increasing the spatial heterogeneity and connectivity of these systems in order to increase biodiversity and ecosystem stability. While this is believed to benefit overall ecological integrity, consequences of such restoration projects on biogeochemical processes per se (i.e. ecosystem functioning) in fluvial systems are rarely considered. We address these issues by evaluating the characteristics of surface water connection between side arms and the main river channel in a former braided river section and the role and degree of connectivity (i.e. duration of surface water connection) on the sediment biogeochemistry. We hypothesized that potential respiration and denitrification would be controlled by the degree of hydrological connectivity, which was increased after floodplain restoration. We measured potential microbial respiration (SIR) and denitrification (DEA) and compared a degraded floodplain section of the Danube River with a reconnected and restored floodplain in the same river section. Re-establishing surface water connection altered the controls on sediment microbial respiration and denitrification ultimately impacting potential microbial activities. Meta-variables were created to characterize the effects of hydrology, morphology, and the available carbon and nutrient pools on potential microbial processing. Mantel statistics and path analysis were performed and demonstrate a hierarchy where the effects of hydrology on the available substrates and microbial processing are mediated by the morphology of the floodplain. In addition, these processes are highest in the least connected sites. Surface water connection, mediated by morphology regulates the potential denitrification rate and the ratio of N2O to N2 emissions, demonstrating the effects of restoration in floodplain systems. PMID:23565037

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

PubMed

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

2016-07-01

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

Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions.

PubMed

Azizi, Aqil; Kim, Wonduck; Lee, Jung Hyun

2016-10-01

Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.

Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling

DOE PAGES

Zhang, Feng; Yao, Jian; Ke, Jiyuan; ...

2015-08-10

The plant hormone jasmonate plays crucial roles in regulating plant responses to herbivorous insects and microbial pathogens and is an important regulator of plant growth and development. Key mediators of jasmonate signalling include MYC transcription factors, which are repressed by jasmonate ZIM-domain (JAZ) transcriptional repressors in the resting state. In the presence of active jasmonate, JAZ proteins function as jasmonate co-receptors by forming a hormone-dependent complex with COI1, the F-box subunit of an SCF-type ubiquitin E3 ligase. The hormone-dependent formation of the COI1–JAZ co-receptor complex leads to ubiquitination and proteasome-dependent degradation of JAZ repressors and release of MYC proteins frommore » transcriptional repression. The mechanism by which JAZ proteins repress MYC transcription factors and how JAZ proteins switch between the repressor function in the absence of hormone and the co-receptor function in the presence of hormone remain enigmatic. In this paper, we show that Arabidopsis MYC3 undergoes pronounced conformational changes when bound to the conserved Jas motif of the JAZ9 repressor. The Jas motif, previously shown to bind to hormone as a partly unwound helix, forms a complete α-helix that displaces the amino (N)-terminal helix of MYC3 and becomes an integral part of the MYC N-terminal fold. In this position, the Jas helix competitively inhibits MYC3 interaction with the MED25 subunit of the transcriptional Mediator complex. Finally, our structural and functional studies elucidate a dynamic molecular switch mechanism that governs the repression and activation of a major plant hormone pathway.« less

Effects of applied potential on phosphine formation in synthetic wastewater treatment by Microbial Electrolysis Cell (MEC).

PubMed

Liu, Wei; Niu, Xiaojun; Chen, Weiyi; An, Shaorong; Sheng, Hong

2017-04-01

Phosphine (PH 3 ) emission from conventional biological wastewater treatment is very inefficient (ng-μg m -3 ). In this work, we investigated the feasibility of promoting PH 3 formation from inorganic phosphorus (IP) or organic phosphorus (OP) containing synthetic wastewater treatment by Microbial Electrolysis Cell (MEC) for the first time. Positive effect of applied potential on PH 3 production was observed after methanogens was inhibited. The highest production of PH 3 (1103.10 ± 72.02 ng m -3 ) was obtained in IP-fed MEC operated at -0.6 V, which was about 5-fold and 2-fold compared to that in open circuit experiment and OP-fed MEC, respectively. Meanwhile, PH 3 formation corresponded positively with current density and alkaline phosphatase activity. This result showed that suitable potential could enhance the activity of relevant enzymes and boost the biosynthesis of PH 3 . Bacterial communities analysis based on high-throughput sequencing revealed that applied potential was conductive to the enrichment of phosphate-reducing organisms in contrast to the control test. These results provide a new idea for resource utilization of phosphorus in wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adaptive laboratory evolution of Klebsiella pneumoniae for improving 2,3-butanediol production

PubMed Central

Li, Hongbiao; Zhang, Genlin; Dang, Yanyan

2016-01-01

ABSTRACT Microbial production of 2,3-butanediol is limited by the toxic components in the lignocellulose hydrolysate. To improve the 2,3-butanediol production via Klebsiella pneumoniae from cotton stalk hydrolysate, a method coupling a high tolerance of strain and detoxification of the hydrolysate was thus investigated in this study. The strain tolerance of K. pneumoniae to the cotton stalk hydrolysate was improved via an adaptive laboratory evolution, which involved a stepwise increase in the hydrolysate concentration in the medium. Compared with the initial strain, the resulting strain increased the biomass 3.2-fold in a medium of 20 g/L hydrolysate and produced 10.45 g/L of 2,3-butanediol at an optimal concentration of 60 g/L hydrolysate. After detoxification of cotton stalk hydrolysate, the cell metabolism of K. pneumoniae was further promoted, and the 2,3-butanediol production increased by 1.2 folds. Using fed-batch fermentation, the concentration of 2,3-butanediol reached 35.5 g/L with a yield of 0.43 g/g. The results demonstrated that the bioconversion of low-cost cotton stalk hydrolysate into 2,3-butanediol improves the economics of microbial 2,3-butanediol production. PMID:27442598

Respiratory interactions of soil bacteria with (semi)conductive iron-oxide minerals.

PubMed

Kato, Souichiro; Nakamura, Ryuhei; Kai, Fumiyoshi; Watanabe, Kazuya; Hashimoto, Kazuhito

2010-12-01

Pure-culture studies have shown that dissimilatory metal-reducing bacteria are able to utilize iron-oxide nanoparticles as electron conduits for reducing distant terminal acceptors; however, the ecological relevance of such energy metabolism is poorly understood. Here, soil microbial communities were grown in electrochemical cells with acetate as the electron donor and electrodes (poised at 0.2 V versus Ag/AgCl) as the electron acceptors in the presence and absence of iron-oxide nanoparticles, and respiratory current generation and community structures were analysed. Irrespective of the iron-oxide species (hematite, magnetite or ferrihydrite), the supplementation with iron-oxide minerals resulted in large increases (over 30-fold) in current, while only a moderate increase (∼10-fold) was observed in the presence of soluble ferric/ferrous irons. During the current generation, insulative ferrihydrite was transformed into semiconductive goethite. Clone-library analyses of 16S rRNA gene fragments PCR-amplified from the soil microbial communities revealed that iron-oxide supplementation facilitated the occurrence of Geobacter species affiliated with subsurface clades 1 and 2. We suggest that subsurface-clade Geobacter species preferentially thrive in soil by utilizing (semi)conductive iron oxides for their respiration. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

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

PubMed

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

2018-06-01

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

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Transiently disordered tails accelerate folding of globular proteins.

PubMed

Mallik, Saurav; Ray, Tanaya; Kundu, Sudip

2017-07-01

Numerous biological proteins exhibit intrinsic disorder at their termini, which are associated with multifarious functional roles. Here, we show the surprising result that an increased percentage of terminal short transiently disordered regions with enhanced flexibility (TstDREF) is associated with accelerated folding rates of globular proteins. Evolutionary conservation of predicted disorder at TstDREFs and drastic alteration of folding rates upon point-mutations suggest critical regulatory role(s) of TstDREFs in shaping the folding kinetics. TstDREFs are associated with long-range intramolecular interactions and the percentage of native secondary structural elements physically contacted by TstDREFs exhibit another surprising positive correlation with folding kinetics. These results allow us to infer probable molecular mechanisms behind the TstDREF-mediated regulation of folding kinetics that challenge protein biochemists to assess by direct experimental testing. © 2017 Federation of European Biochemical Societies.

Structural Basis of a Thiol-Disulfide Oxidoreductase in the Hedgehog-Forming Actinobacterium Corynebacterium matruchotii.

PubMed

Luong, Truc Thanh; Tirgar, Reyhaneh; Reardon-Robinson, Melissa E; Joachimiak, Andrzej; Osipiuk, Jerzy; Ton-That, Hung

2018-05-01

The actinobacterium Corynebacterium matruchotii has been implicated in nucleation of oral microbial consortia leading to biofilm formation. Due to the lack of genetic tools, little is known about basic cellular processes, including protein secretion and folding, in this organism. We report here a survey of the C. matruchotii genome, which encodes a large number of exported proteins containing paired cysteine residues, and identified an oxidoreductase that is highly homologous to the Corynebacterium diphtheriae thiol-disulfide oxidoreductase MdbA (MdbA Cd ). Crystallization studies uncovered that the 1.2-Å resolution structure of C. matruchotii MdbA (MdbA Cm ) possesses two conserved features found in actinobacterial MdbA enzymes, a thioredoxin-like fold and an extended α-helical domain. By reconstituting the disulfide bond-forming machine in vitro , we demonstrated that MdbA Cm catalyzes disulfide bond formation within the actinobacterial pilin FimA. A new gene deletion method supported that mdbA is essential in C. matruchotii Remarkably, heterologous expression of MdbA Cm in the C. diphtheriae Δ mdbA mutant rescued its known defects in cell growth and morphology, toxin production, and pilus assembly, and this thiol-disulfide oxidoreductase activity required the catalytic motif CXXC. Altogether, the results suggest that MdbA Cm is a major thiol-disulfide oxidoreductase, which likely mediates posttranslocational protein folding in C. matruchotii by a mechanism that is conserved in Actinobacteria IMPORTANCE The actinobacterium Corynebacterium matruchotii has been implicated in the development of oral biofilms or dental plaque; however, little is known about the basic cellular processes in this organism. We report here a high-resolution structure of a C. matruchotii oxidoreductase that is highly homologous to the Corynebacterium diphtheriae thiol-disulfide oxidoreductase MdbA. By biochemical analysis, we demonstrated that C. matruchotii MdbA catalyzes disulfide bond formation in vitro Furthermore, a new gene deletion method revealed that deletion of mdbA is lethal in C. matruchotii Remarkably, C. matruchotii MdbA can replace C. diphtheriae MdbA to maintain normal cell growth and morphology, toxin production, and pilus assembly. Overall, our studies support the hypothesis that C. matruchotii utilizes MdbA as a major oxidoreductase to catalyze oxidative protein folding. Copyright © 2018 American Society for Microbiology.

Biological Low-pH Mn(II) Oxidation in a Manganese Deposit Influenced by Metal-Rich Groundwater

PubMed Central

Bohu, Tsing; Akob, Denise M.; Abratis, Michael; Lazar, Cassandre S.

2016-01-01

ABSTRACT The mechanisms, key organisms, and geochemical significance of biological low-pH Mn(II) oxidation are largely unexplored. Here, we investigated the structure of indigenous Mn(II)-oxidizing microbial communities in a secondary subsurface Mn oxide deposit influenced by acidic (pH 4.8) metal-rich groundwater in a former uranium mining area. Microbial diversity was highest in the Mn deposit compared to the adjacent soil layers and included the majority of known Mn(II)-oxidizing bacteria (MOB) and two genera of known Mn(II)-oxidizing fungi (MOF). Electron X-ray microanalysis showed that romanechite [(Ba,H2O)2(Mn4+,Mn3+)5O10] was conspicuously enriched in the deposit. Canonical correspondence analysis revealed that certain fungal, bacterial, and archaeal groups were firmly associated with the autochthonous Mn oxides. Eight MOB within the Proteobacteria, Actinobacteria, and Bacteroidetes and one MOF strain belonging to Ascomycota were isolated at pH 5.5 or 7.2 from the acidic Mn deposit. Soil-groundwater microcosms demonstrated 2.5-fold-faster Mn(II) depletion in the Mn deposit than adjacent soil layers. No depletion was observed in the abiotic controls, suggesting that biological contribution is the main driver for Mn(II) oxidation at low pH. The composition and species specificity of the native low-pH Mn(II) oxidizers were highly adapted to in situ conditions, and these organisms may play a central role in the fundamental biogeochemical processes (e.g., metal natural attenuation) occurring in the acidic, oligotrophic, and metalliferous subsoil ecosystems. IMPORTANCE This study provides multiple lines of evidence to show that microbes are the main drivers of Mn(II) oxidation even at acidic pH, offering new insights into Mn biogeochemical cycling. A distinct, highly adapted microbial community inhabits acidic, oligotrophic Mn deposits and mediates biological Mn oxidation. These data highlight the importance of biological processes for Mn biogeochemical cycling and show the potential for new bioremediation strategies aimed at enhancing biological Mn oxidation in low-pH environments for contaminant mitigation. PMID:26969702

Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques (Macaca mulatta).

PubMed

Balasubramaniam, Krishna; Beisner, Brianne; Guan, Jiahui; Vandeleest, Jessica; Fushing, Hsieh; Atwill, Edward; McCowan, Brenda

2018-01-01

In group-living animals, heterogeneity in individuals' social connections may mediate the sharing of microbial infectious agents. In this regard, the genetic relatedness of individuals' commensal gut bacterium Escherichia coli may be ideal to assess the potential for pathogen transmission through animal social networks. Here we use microbial phylogenetics and population genetics approaches, as well as host social network reconstruction, to assess evidence for the contact-mediated sharing of E. coli among three groups of captively housed rhesus macaques ( Macaca mulatta ), at multiple organizational scales. For each group, behavioral data on grooming, huddling, and aggressive interactions collected for a six-week period were used to reconstruct social network communities via the Data Cloud Geometry (DCG) clustering algorithm. Further, an E. coli isolate was biochemically confirmed and genotypically fingerprinted from fecal swabs collected from each macaque. Population genetics approaches revealed that Group Membership, in comparison to intrinsic attributes like age, sex, and/or matriline membership of individuals, accounted for the highest proportion of variance in E. coli genotypic similarity. Social network approaches revealed that such sharing was evident at the community-level rather than the dyadic level. Specifically, although we found no links between dyadic E. coli similarity and social contact frequencies, similarity was significantly greater among macaques within the same social network communities compared to those across different communities. Moreover, tests for one of our study-groups confirmed that E. coli isolated from macaque rectal swabs were more genotypically similar to each other than they were to isolates from environmentally deposited feces. In summary, our results suggest that among frequently interacting, spatially constrained macaques with complex social relationships, microbial sharing via fecal-oral, social contact-mediated routes may depend on both individuals' direct connections and on secondary network pathways that define community structure. They lend support to the hypothesis that social network communities may act as bottlenecks to contain the spread of infectious agents, thereby encouraging disease control strategies to focus on multiple organizational scales. Future directions includeincreasing microbial sampling effort per individual to better-detect dyadic transmission events, and assessments of the co-evolutionary links between sociality, infectious agent risk, and host immune function.

NF-kappaB Activity in Macrophages Determines Metastatic Potential of Breast Tumor Cells

DTIC Science & Technology

2011-08-01

Cheng DS, Chodosh LA, Blackwell TS, Yull FE: Activation of nuclear factor kappa B in mammary epithelium promotes milk loss during mammary... microbial products (15, 16). To date, the potential role of macrophages in the fetal lung innate immune response has not been closely examined. Studies...In this model, microbial products initially activate NF-kB in lung macrophages. The release of inflammatory mediators, particularly IL-1b and/or TNF-a

Fruit extracts of Momordica charantia potentiate glucose uptake and up-regulate Glut-4, PPAR gamma and PI3K.

PubMed

Kumar, Ramadhar; Balaji, S; Uma, T S; Sehgal, P K

2009-12-10

Momordica charantia fruit is a widely used traditional medicinal herb as, anti-diabetic, anti-HIV, anti-ulcer, anti-inflammatory, anti-leukemic, anti-microbial, and anti-tumor. The present study is undertaken to investigate the possible mode of action of fruit extracts derived from Momordica charantia (MC) and study its pharmacological effects for controlling diabetic mellitus. Effects of aqueous and chloroform extracts of Momordica charantia fruit on glucose uptake and up-regulation of glucose transporter (Glut-4), peroxisome proliferator activator receptor gamma (PPAR gamma) and phosphatidylinositol-3 kinase (PI3K), were investigated to show its efficacy as a hypoglycaemic agent. Dose dependent glucose uptake assay was performed on L6 myotubes using 2-deoxy-D-[1-(3)H] glucose. Up-regulatory effects of the extracts on the mRNA expression level of Glut-4, PPAR gamma and PI3K have been studied. The association of Momordica charantia with the aqueous and chloroform extracts of Momordica charantia fruit at 6 microg/ml has shown significant up-regulatory effect, respectively, by 3.6-, 2.8- and 3.8-fold on the battery of targets Glut-4, PPAR gamma and PI3K involved in glucose transport. The up-regulation of glucose uptake was comparable with insulin and rosiglitazone which was approximately 2-fold over the control. Moreover, the inhibitory effect of the cyclohexamide on Momordica charantia fruit extract mediated glucose uptake suggested the requirement of new protein synthesis for the enhanced glucose uptake. This study demonstrated the significance of Glut-4, PPAR gamma and PI3K up-regulation by Momordica charantia in augmenting the glucose uptake and homeostasis.

Activation of persulfates by natural magnetic pyrrhotite for water disinfection: Efficiency, mechanisms, and stability.

PubMed

Xia, Dehua; Li, Yan; Huang, Guocheng; Yin, Ran; An, Taicheng; Li, Guiying; Zhao, Huijun; Lu, Anhuai; Wong, Po Keung

2017-04-01

This study introduces natural occurring magnetic pyrrhotite (NP) as an environmentally friendly, easy available, and cost-effective alternative catalyst to activate persulfate (PS) of controlling microbial water contaminants. The E. coli K-12 inactivation kinetics observed in batch experiments was well described with first-order reaction. The optimum inactivation rate (k = 0.47 log/min) attained at a NP dose of 1 g/L and a PS dose of 1 mM, corresponding to total inactivation of 7 log 10  cfu/mL cells within 15 min. Measured k increased > 2-fold when temperature increased from 20 to 50 °C; and > 4-fold when pH decreased from 9 to 3. Aerobic conditions were more beneficial to cell inactivation than anaerobic conditions due to more reactive oxygen species (ROS) generated. ROS responsible for the inactivation were identified to be SO 4 -  > OH > H 2 O 2 based on a positive scavenging test and in situ ROS determination. In situ characterization suggested that PS effectively bind to NP surface was likely to form charge transfer complex (≡Fe(II)⋯O 3 SOOSO 3 - ), which mediated ROS generation and E. coli K-12 oxidation. The increased cell-envelope lesions consequently aggravated intracellular protein depletion and genome damage to cause definite bacterial death. The NP still maintained good physiochemical structure and stable activity even after 4 cycle. Moreover, NP/PS system also exhibited good E. coli K-12 inactivation efficiency in authentic water matrices like surface water and effluents of secondary wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Regulation of Hydrolytic Enzyme Activity in Aquatic Microbial Communities Hosted by Carnivorous Pitcher Plants.

PubMed

Young, Erica B; Sielicki, Jessica; Grothjan, Jacob J

2018-04-20

Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities. Chitinase, protease, and phosphatase activities were measured using fluorometric assays. Enzyme activity in field pitchers was positively correlated with bacterial abundance, and activity was suppressed by antibiotics suggesting predominantly bacterial sources of chitinase and protease activity. Fungi, algae, and rotifers observed could also contribute enzyme activity, but fresh insect prey released minimal chitinase activity. Activity of chitinase and proteases was upregulated in response to insect additions, and phosphatase activity was suppressed by phosphate additions. Particulate organic P in prey was broken down, appearing as increasing dissolved organic and inorganic P pools within 14 days. Chitinase and protease were not significantly suppressed by availability of dissolved organic substrates, though organic C and N stimulated bacterial growth, resulting in elevated enzyme activity. This comprehensive field and experimental study show that pitcher plant microbial communities dynamically regulate hydrolytic enzyme activity, to digest prey nutrients to simpler forms, mediating biogeochemical nutrient transformations and release of nutrients for microbial and host plant uptake.

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

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

Jeremy Semrau; Sung-Woo Lee; Jeongdae Im

2010-09-30

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

Novel approaches to microbial enhancement of oil recovery.

PubMed

Kryachko, Yuriy

2018-01-20

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

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

Wang, Mengmeng; Liu, Shanshan; Wang, Feng; ...

2015-10-26

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Microbial diversity in restored wetlands of San Francisco Bay

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

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

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

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

Microbial ecology of hot desert edaphic systems.

PubMed

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

2015-03-01

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

Microbial community assembly and metabolic function during mammalian corpse decomposition.

PubMed

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

2016-01-08

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations. Copyright © 2016, American Association for the Advancement of Science.

Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study

PubMed Central

Callender, Katrina L.; Roy, Sébastien; Khasa, Damase P.; Whyte, Lyle G.; Greer, Charles W.

2016-01-01

Phytotechnologies are rapidly replacing conventional ex-situ remediation techniques as they have the added benefit of restoring aesthetic value, important in the reclamation of mine sites. Alders are pioneer species that can tolerate and proliferate in nutrient-poor, contaminated environments, largely due to symbiotic root associations with the N2-fixing bacteria, Frankia and ectomycorrhizal (ECM) fungi. In this study, we investigated the growth of two Frankia-inoculated (actinorhizal) alder species, A. crispa and A. glutinosa, in gold mine waste rock from northern Quebec. Alder species had similar survival rates and positively impacted soil quality and physico-chemical properties in similar ways, restoring soil pH to neutrality and reducing extractable metals up to two-fold, while not hyperaccumulating them into above-ground plant biomass. A. glutinosa outperformed A. crispa in terms of growth, as estimated by the seedling volume index (SVI), and root length. Pyrosequencing of the bacterial 16S rRNA gene for bacteria and the ribosomal internal transcribed spacer (ITS) region for fungi provided a comprehensive, direct characterization of microbial communities in gold mine waste rock and fine tailings. Plant- and treatment-specific shifts in soil microbial community compositions were observed in planted mine residues. Shannon diversity and the abundance of microbes involved in key ecosystem processes such as contaminant degradation (Sphingomonas, Sphingobium and Pseudomonas), metal sequestration (Brevundimonas and Caulobacter) and N2-fixation (Azotobacter, Mesorhizobium, Rhizobium and Pseudomonas) increased over time, i.e., as plants established in mine waste rock. Acetate mineralization and most probable number (MPN) assays showed that revegetation positively stimulated both bulk and rhizosphere communities, increasing microbial density (biomass increase of 2 orders of magnitude) and mineralization (five-fold). Genomic techniques proved useful in investigating tripartite (plant-bacteria-fungi) interactions during phytostabilization, contributing to our knowledge in this field of study. PMID:26928913

Environmental Stress-mediated EPS Production Shape Microbial Activity on Various Hydrated Rough Surfaces

NASA Astrophysics Data System (ADS)

Wang, G.; Liu, L.; Chen, G.

2016-12-01

The complex environmental physical and chemical processes and interplay with the associating biological responses are keys to understanding the environmental microbiology ensconced in environmental remediation, water quality control, food safety, nutrient cycling, and etc., yet remain poorly understood. Using experimental micromodels, we study how environmental conditions (e.g., hydration fluctuation, nutrient limitation, pH variation, etc.) affect microbial extracellular polymeric substances (EPS) production and their configuration within various hydrated surfaces, and impacts on microbial motility, surface attachment, aggregation, and other bioremediation activities. To elucidate the potential mechanisms underlying the complex bio-physicochemical processes, we developed an individual-based and spatio-temporally resolved modeling platform that explicitly considers microscale aqueous-phase configuration and nutrient transport/diffusion and associated biophysical processes affecting individual microbial cell life history. We quantitatively explore the effects of the above microscale environmental processes on bio-physicochemical interactions affecting microbial growth, motility, surface attachment and aggregation, and shaping population interactions and functions. Simulation scenarios of microbial induced pollutant (e.g., roxarsone) biotransformation on various hydrated rough surfaces will also be present.

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

Wang, Mengmeng; Liu, Shanshan; Wang, Feng

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Metabolic interactions and dynamics in microbial communities

NASA Astrophysics Data System (ADS)

Segre', Daniel

Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

Folding and trimerization of clathrin subunits at the triskelion hub.

PubMed

Näthke, I S; Heuser, J; Lupas, A; Stock, J; Turck, C W; Brodsky, F M

1992-03-06

The triskelion shape of the clathrin molecule enables it to form the polyhedral protein network that covers clathrin-coated pits and vesicles. Domains within the clathrin heavy chain that are responsible for maintaining triskelion shape and function were identified and localized. Sequences that mediate trimerization are distal to the carboxyl terminus and are adjacent to a domain that mediates both light chain binding and clathrin assembly. Structural modeling predicts that within this domain, the region of heavy chain-light chain interaction is a bundle of three or four alpha helices. These studies establish a low resolution model of clathrin subunit folding in the central portion (hub) of the triskelion, thus providing a basis for future mutagenesis experiments.

Circulating Inflammatory Mediators in Patients with Fever: Predicting Bloodstream Infection

PubMed Central

Groeneveld, A. B. Johan; Bossink, Ailko W. J.; van Mierlo, Gerard J.; Hack, C. Erik

2001-01-01

The systemic host response to microbial infection involves clinical signs and symptoms of infection, including fever and elevated white blood cell (WBC) counts. In addition, inflammatory mediators are released, including activated complement product C3a, interleukin 6 (IL-6), and the acute-phase reactant secretory phospholipase A2 (sPLA2). To compare the value of the latter with the former in predicting (the degree of) microbial infection at the bedside, we determined clinical variables and took blood samples daily for 3 consecutive days in 300 patients with a new fever (>38.0°C rectally or >38.3°C axillary). Microbiological culture results for 7 days after inclusion were collected. Patients were divided into clinical and microbial categories: those without and with a clinical focus of infection and those with negative cultures, with positive local cultures or specific stains for fungal (n = 13) or tuberculous infections (n = 1), and with positive blood cultures, including one patient with malaria parasitemia. The area under the curve (AUC) of the receiver operating characteristic (ROC) for prediction of positive cultures was 0.60 (P < 0.005) for peak temperature and 0.59 (P < 0.01) for peak WBC count, 0.60 (P < 0.005) for peak C3a, 0.63 (P < 0.001) for peak IL-6, and 0.61 (P < 0.001) for peak sPLA2. The AUC under the ROC curve for prediction of positive blood cultures was 0.68 (P < 0.001) for peak temperature and 0.56 for peak WBC count (P < 0.05). The AUC for peak C3a was 0.69, that for peak IL-6 was 0.70, and that for sPLA2 was 0.67 (for all, P < 0.001). The degree of microbial invasion is thus a major determinant of the clinical and inflammatory host response in patients with fever. Moreover, circulating inflammatory mediators such as C3a and IL-6 may help to predict positive blood cultures, together with clinical signs and symptoms of the host response to microbial infection, even before culture results are available. This may help in the designing of entry criteria for therapeutic intervention studies. PMID:11687462

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation

PubMed Central

Gregory, Samuel J.; Anderson, Christopher W. N.; Camps-Arbestain, Marta; Biggs, Patrick J.; Ganley, Austen R. D.; O’Sullivan, Justin M.; McManus, Michael T.

2015-01-01

We examined the effect of biochar on the water-soluble arsenic (As) concentration and the extent of organochlorine degradation in a co-contaminated historic sheep-dip soil during a 180-d glasshouse incubation experiment. Soil microbial activity, bacterial community and structure diversity were also investigated. Biochar made from willow feedstock (Salix sp) was pyrolysed at 350 or 550°C and added to soil at rates of 10 g kg-1 and 20 g kg-1 (representing 30 t ha-1 and 60 t ha-1). The isomers of hexachlorocyclohexane (HCH) alpha-HCH and gamma-HCH (lindane), underwent 10-fold and 4-fold reductions in concentration as a function of biochar treatment. Biochar also resulted in a significant reduction in soil DDT levels (P < 0.01), and increased the DDE:DDT ratio. Soil microbial activity was significantly increased (P < 0.01) under all biochar treatments after 60 days of treatment compared to the control. 16S amplicon sequencing revealed that biochar-amended soil contained more members of the Chryseobacterium, Flavobacterium, Dyadobacter and Pseudomonadaceae which are known bioremediators of hydrocarbons. We hypothesise that a recorded short-term reduction in the soluble As concentration due to biochar amendment allowed native soil microbial communities to overcome As-related stress. We propose that increased microbiological activity (dehydrogenase activity) due to biochar amendment was responsible for enhanced degradation of organochlorines in the soil. Biochar therefore partially overcame the co-contaminant effect of As, allowing for enhanced natural attenuation of organochlorines in soil. PMID:25923541

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci

PubMed Central

Sandberg, Scott; Reyes, Iris; Fritsche, Thomas R.

2017-01-01

Allergic and autoimmune diseases had been attributed to lack of exposure to biodiversity, an important factor in regulating immune homeostasis in a healthy host. We posit that the microbiome of healthy dairy farmers (DF) will be richer than non-farmers (NF) living in urban settings due to exposure to a greater biodiversity in the dairy environment. However, no studies have investigated the relationships between microbiota of dairy farmers (DF) compared with urban non-farmers (NF). We compared the nasal and oral microbiota of dairy farmers (N_DF, O_DF, respectively) with nasal and oral microbiota of NF in the same geographical area. The N_DF showed high microbial diversity with hundreds of unique genera that reflected environmental/occupational exposures. The nasal and oral microbiomes clustered separately from each other using Principal Coordinate Analysis, and with DF harboring two-fold and 1.5-fold greater exclusive genera in their nose and mouth respectively, than did non-farmers. Additionally, the N_DF group had a lower burden of Staphylococcus spp. suggesting a correlation between higher microbial diversity and competition for colonization by staphylococci. The N_DF samples were negative for the mecA gene, a marker of methicillin-resistance in staphylococci. The lower burden of staphylococci was found to be independent of the abundance of Corynebacterium spp. Exposure to greater biodiversity could enhance microbial competition, thereby reducing colonization with opportunistic pathogens. Future studies will analyze whether exposure to livestock microbiomes offers protection from acute and chronic diseases. PMID:28850578

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci.

PubMed

Shukla, Sanjay K; Ye, Zhan; Sandberg, Scott; Reyes, Iris; Fritsche, Thomas R; Keifer, Matthew

2017-01-01

Allergic and autoimmune diseases had been attributed to lack of exposure to biodiversity, an important factor in regulating immune homeostasis in a healthy host. We posit that the microbiome of healthy dairy farmers (DF) will be richer than non-farmers (NF) living in urban settings due to exposure to a greater biodiversity in the dairy environment. However, no studies have investigated the relationships between microbiota of dairy farmers (DF) compared with urban non-farmers (NF). We compared the nasal and oral microbiota of dairy farmers (N_DF, O_DF, respectively) with nasal and oral microbiota of NF in the same geographical area. The N_DF showed high microbial diversity with hundreds of unique genera that reflected environmental/occupational exposures. The nasal and oral microbiomes clustered separately from each other using Principal Coordinate Analysis, and with DF harboring two-fold and 1.5-fold greater exclusive genera in their nose and mouth respectively, than did non-farmers. Additionally, the N_DF group had a lower burden of Staphylococcus spp. suggesting a correlation between higher microbial diversity and competition for colonization by staphylococci. The N_DF samples were negative for the mecA gene, a marker of methicillin-resistance in staphylococci. The lower burden of staphylococci was found to be independent of the abundance of Corynebacterium spp. Exposure to greater biodiversity could enhance microbial competition, thereby reducing colonization with opportunistic pathogens. Future studies will analyze whether exposure to livestock microbiomes offers protection from acute and chronic diseases.

Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses

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

Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.

Litter decomposition is an enzymatically-complex process that is mediated by a diverse assemblage of saprophytic microorganisms. It is a globally important biogeochemical process that can be suppressed by anthropogenic N deposition. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. Here, we paired extracellular enzyme assays with shotgun metagenomics to assess if anthropogenic N deposition has altered the functional potential of microbial communities inhabiting decaying forest floor. Experimental N deposition significantly reduced the activity of extracellular enzymes mediating plant cell wallmore » decay, which occurred concurrently with changes in the relative abundance of metagenomic functional gene pathways mediating the metabolism of carbohydrates, aromatic compounds, as well as microbial respiration. Moreover, experimental N deposition increased the relative abundance of 50 of the 60 gene pathways, the majority of which were associated with saprotrophic bacteria. Conversely, the relative abundance and composition of fungal genes mediating the metabolism of plant litter was not affected by experimental N deposition. Future rates of atmospheric N deposition have favored saprotrophic soil bacteria, whereas the metabolic potential of saprotrophic fungi appears resilient to this agent of environmental change. Results presented here provide evidence that changes in the functional capacity of saprotrophic soil microorganisms mediate how anthropogenic N deposition increases C storage in soil.« less

Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses

DOE PAGES

Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.; ...

2016-03-02

Litter decomposition is an enzymatically-complex process that is mediated by a diverse assemblage of saprophytic microorganisms. It is a globally important biogeochemical process that can be suppressed by anthropogenic N deposition. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. Here, we paired extracellular enzyme assays with shotgun metagenomics to assess if anthropogenic N deposition has altered the functional potential of microbial communities inhabiting decaying forest floor. Experimental N deposition significantly reduced the activity of extracellular enzymes mediating plant cell wallmore » decay, which occurred concurrently with changes in the relative abundance of metagenomic functional gene pathways mediating the metabolism of carbohydrates, aromatic compounds, as well as microbial respiration. Moreover, experimental N deposition increased the relative abundance of 50 of the 60 gene pathways, the majority of which were associated with saprotrophic bacteria. Conversely, the relative abundance and composition of fungal genes mediating the metabolism of plant litter was not affected by experimental N deposition. Future rates of atmospheric N deposition have favored saprotrophic soil bacteria, whereas the metabolic potential of saprotrophic fungi appears resilient to this agent of environmental change. Results presented here provide evidence that changes in the functional capacity of saprotrophic soil microorganisms mediate how anthropogenic N deposition increases C storage in soil.« less

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

PubMed

Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

2015-06-15

Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial respiration and kinetics of extracellular enzymes activities through rhizosphere and detritusphere at agricultural site

NASA Astrophysics Data System (ADS)

Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2014-05-01

Rhizosphere and detritusphere are soil microsites with very high resource availability for microorganisms affecting their biomass, composition and functions. In the rhizosphere low molecular compounds occur with root exudates and low available polymeric compounds, as belowground plant senescence. In detritusphere the substrate for decomposition is mainly a polymeric material of low availability. We hypothesized that microorganisms adapted to contrasting quality and availability of substrates in the rhizosphere and detritusphere are strongly different in affinity of hydrolytic enzymes responsible for decomposition of organic compounds. According to common ecological principles easily available substrates are quickly consumed by microorganisms with enzymes of low substrate affinity (i.e. r-strategists). The slow-growing K-strategists with enzymes of high substrate affinity are better adapted for growth on substrates of low availability. Estimation of affinity of enzyme systems to the substrate is based on Michaelis-Menten kinetics, reflecting the dependency of decomposition rates on substrate amount. As enzymes-mediated reactions are substrate-dependent, we further hypothesized that the largest differences in hydrolytic activity between the rhizosphere and detritusphere occur at substrate saturation and that these differences are smoothed with increasing limitation of substrate. Affected by substrate limitation, microbial species follow a certain adaptation strategy. To achieve different depth gradients of substrate availability 12 plots on an agricultural field were established in the north-west of Göttingen, Germany: 1) 4 plots planted with maize, reflecting lower substrate availability with depth; 2) 4 unplanted plots with maize litter input (0.8 kg m-2 dry maize residues), corresponding to detritusphere; 3) 4 bare fallow plots as control. Maize litter was grubbed homogenously into the soil at the first 5 cm to ensure comparable conditions for the herbivore and detritivore communities in the soil. The kinetics (Km and Vmax) of four extracellular hydrolytic enzymes responsible for C- and phosphorous-cycle (β-glucosidase, β-xylosidase, β-cellobiohydrolase and acid phosphatase), microbial biomass, basal respiration (BR) and substrate-induced respiration (SIR) were measured in rhizosphere, detritusphere and control from 0 - 10 and 10 - 20 cm. The metabolic quotient (qCO2) was calculated as specific indicator for efficiency of microbial substrate utilization. We observed clear differences in enzymes activities at low and high concentrations of substrate. At substrate saturation enzyme activity rates of were significantly higher in rooted plots compared to litter amended plots, whereas at lower concentration no treatment effect could be found. The BR, SIR and qCO2 values were significantly higher at 0 - 10 cm of the planted treatment compared to litter and control plots, revealing a significantly higher respiration at lower efficiency of microbial substrate utilization in the rhizosphere. The Michaelis-Menten constant (Km) decreased with depth, especially for β-glucosidase, acid phosphatase and β-xylosidase, indicating higher substrate affinity of microorganisms in deeper soil and therefore different enzyme systems functioning. The substrate affinity factor (Vmax/Km) increased 2-fold with depth for various enzymes, reflecting a switch of predominantly occurring microbial strategies. Vmax/Km ratio indicated relative domination of zymogenous microbial communities (r-strategists) in 0 - 10 cm depth as compared with 10 - 20 cm depth where the K-strategists dominated.

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

PubMed Central

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J.; Waghorn, Garry C.; Janssen, Peter H.

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided. PMID:24040342

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

PubMed

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J; Waghorn, Garry C; Janssen, Peter H

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.

Yeast surface display of dehydrogenases in microbial fuel-cells.

PubMed

Gal, Idan; Schlesinger, Orr; Amir, Liron; Alfonta, Lital

2016-12-01

Two dehydrogenases, cellobiose dehydrogenase from Corynascus thermophilus and pyranose dehydrogenase from Agaricus meleagris, were displayed for the first time on the surface of Saccharomyces cerevisiae using the yeast surface display system. Surface displayed dehydrogenases were used in a microbial fuel cell and generated high power outputs. Surface displayed cellobiose dehydrogenase has demonstrated a midpoint potential of -28mV (vs. Ag/AgCl) at pH=6.5 and was used in a mediator-less anode compartment of a microbial fuel cell producing a power output of 3.3μWcm(-2) using lactose as fuel. Surface-displayed pyranose dehydrogenase was used in a microbial fuel cell and generated high power outputs using different substrates, the highest power output that was achieved was 3.9μWcm(-2) using d-xylose. These results demonstrate that surface displayed cellobiose dehydrogenase and pyranose dehydrogenase may successfully be used in microbial bioelectrochemical systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers

PubMed Central

Bauer, Matthias; Knebel, Johannes; Lechner, Matthias; Pickl, Peter; Frey, Erwin

2017-01-01

Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via ‘quorum sensing’. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not. However, the mechanism underlying this phenotypic heterogeneity in quorum-sensing microbial populations has remained elusive. In our theoretical model, cells synthesize and secrete autoinducers into the environment, up-regulate their production in this self-shaped environment, and non-producers replicate faster than producers. We show that the coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits. DOI: http://dx.doi.org/10.7554/eLife.25773.001 PMID:28741470

Using dispersants after oil spills: impacts on the composition and activity of microbial communities.

PubMed

Kleindienst, Sara; Paul, John H; Joye, Samantha B

2015-06-01

Dispersants are globally and routinely applied as an emergency response to oil spills in marine ecosystems with the goal of chemically enhancing the dissolution of oil into water, which is assumed to stimulate microbially mediated oil biodegradation. However, little is known about how dispersants affect the composition of microbial communities or their biodegradation activities. The published findings are controversial, probably owing to variations in laboratory methods, the selected model organisms and the chemistry of different dispersant-oil mixtures. Here, we argue that an in-depth assessment of the impacts of dispersants on microorganisms is needed to evaluate the planning and use of dispersants during future responses to oil spills.

Astrocyte Mediated Protection of Fetal Cerebral Cortical Neurons from Rotenone and Paraquat

PubMed Central

Rathinam, Mary Latha; Watts, Lora Talley; Narasimhan, Madhusudhanan; Riar, Amanjot Kaur; Mahimainathan, Lenin; Henderson, George.I.

2012-01-01

Primary cultures of fetal rat cortical neurons and astrocytes were used to test the hypothesis that astrocyte-mediated control of neuronal glutathione (GSH) is a potent factor in neuroprotection against rotenone and paraquat. In neurons, rotenone (0.025 to 1μM) for 4 and 24 h decreased viability as did paraquat (2 to 100μM). Rotenone (30nM) decreased neuronal viability and GSH by 24% and 30%, while ROS were increased by 56%. Paraquat (30μM) decreased neuronal viability and GSH by 36% and 70%, while ROS were increased by 23%. When neurons were co-cultured with astrocytes, their GSH increased 1.5 fold and 5 fold at 12 and 24 h. Co-culturing with astrocytes blocked neuronal death and damage by rotenone and paraquat. Astrocyte-mediated neuroprotection was dependent on the activity of components of the γ-glutamyl cycle. These studies illustrate the importance of astrocyte-mediated glutathione homeostasis for protection of neurons from rotenone and paraquat and the role of the γ-glutamyl cycle in this neuroprotection PMID:22301167

Reactive Transport Modeling of Microbe-mediated Fe (II) Oxidation for Enhanced Oil Recovery

NASA Astrophysics Data System (ADS)

Surasani, V.; Li, L.

2011-12-01

Microbially Enhanced Oil Recovery (MEOR) aims to improve the recovery of entrapped heavy oil in depleted reservoirs using microbe-based technology. Reservoir ecosystems often contain diverse microbial communities those can interact with subsurface fluids and minerals through a network of nutrients and energy fluxes. Microbe-mediated reactions products include gases, biosurfactants, biopolymers those can alter the properties of oil and interfacial interactions between oil, brine, and rocks. In addition, the produced biomass and mineral precipitates can change the reservoir permeability profile and increase sweeping efficiency. Under subsurface conditions, the injection of nitrate and Fe (II) as the electron acceptor and donor allows bacteria to grow. The reaction products include minerals such as Fe(OH)3 and nitrogen containing gases. These reaction products can have large impact on oil and reservoir properties and can enhance the recovery of trapped oil. This work aims to understand the Fe(II) oxidation by nitrate under conditions relevant to MEOR. Reactive transport modeling is used to simulate the fluid flow, transport, and reactions involved in this process. Here we developed a complex reactive network for microbial mediated nitrate-dependent Fe (II) oxidation that involves both thermodynamic controlled aqueous reactions and kinetic controlled Fe (II) mineral reaction. Reactive transport modeling is used to understand and quantify the coupling between flow, transport, and reaction processes. Our results identify key parameter controls those are important for the alteration of permeability profile under field conditions.

Potential for Mercury Reduction by Microbes in the High Arctic▿

PubMed Central

Poulain, Alexandre J.; Ní Chadhain, Sinéad M.; Ariya, Parisa A.; Amyot, Marc; Garcia, Edenise; Campbell, Peter G. C.; Zylstra, Gerben J.; Barkay, Tamar

2007-01-01

The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse merA genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as mer-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that mer-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and merA-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions. PMID:17293515

Boosting mediated electron transfer in bioelectrochemical systems with tailored defined microbial cocultures.

PubMed

Schmitz, Simone; Rosenbaum, Miriam A

2018-05-19

Bioelectrochemical systems (BES) hold great promise for sustainable energy generation via a microbial catalyst from organic matter, for example, from wastewater. To improve current generation in BES, understanding the underlying microbiology of the electrode community is essential. Electron mediator producing microorganism like Pseudomonas aeruginosa play an essential role in efficient electricity generation in BES. These microbes enable even nonelectroactive microorganism like Enterobacter aerogenes to contribute to current production. Together they form a synergistic coculture, where both contribute to community welfare. To use microbial co-operation in BES, the physical and chemical environments provided in the natural habitats of the coculture play a crucial role. Here, we show that synergistic effects in defined cocultures of P. aeruginosa and E. aerogenes can be strongly enhanced toward high current production by adapting process parameters, like pH, temperature, oxygen demand, and substrate requirements. Especially, oxygen was identified as a major factor influencing coculture behavior and optimization of its supply could enhance electric current production over 400%. Furthermore, operating the coculture in fed-batch mode enabled us to obtain very high current densities and to harvest electrical energy for 1 month. In this optimized condition, the coulombic efficiency of the process was boosted to 20%, which is outstanding for mediator-based electron transfer. This study lays the foundation for a rationally designed utilization of cocultures in BES for bioenergy generation from specific wastewaters or for bioprocess sensing and for benefiting from their synergistic effects under controlled bioprocess condition. © 2018 Wiley Periodicals, Inc.

Essential oil-mediated glycerosomes increase transdermal paeoniflorin delivery: optimization, characterization, and evaluation in vitro and in vivo.

PubMed

Zhang, Kai; Zhang, Yongtai; Li, Zhe; Li, Nana; Feng, Nianping

2017-01-01

In this study, a novel glycerosome carrier containing essential oils was prepared for topical administration of paeoniflorin (PF) to enhance its transdermal drug delivery and improve drug absorption in the synovium. The formulation of glycerosomes was optimized by a uniform design, and the final vehicle was composed of 5% (w/v) phospholipid, 0.6% (w/v) cholesterol, and 10% (v/v) glycerol, with 2% (v/v) Speranskia tuberculata essential oil (STO) as the transdermal enhancer. The in vitro transdermal flux of PF loaded in the STO-glycerosomes was 1.4-fold, 1.6-fold, and 1.7-fold higher than those of glycerosomes, liposomes, and tinctures, respectively. In vivo studies showed that the use of STO-glycerosomes was associated with a 3.1-fold greater accumulation of PF in the synovium than that of common glycerosomes. This finding was confirmed by in vivo imaging studies, which found that the fluorescence intensity of Cy5.5-loaded STO-glycerosomes in mice knee joints was 1.8-fold higher than that of the common glycerosomes 5 h after administration. The glycerosomes mediated by STO exhibited considerable skin permeability as well as improved drug absorption in the synovium, indicating that STO-glycerosomes may be a potential PF transdermal delivery vehicle for the treatment of rheumatoid arthritis caused by synovium lesions.

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

PubMed Central

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central “hubs”. Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates. PMID:26394388

Essential oil-mediated glycerosomes increase transdermal paeoniflorin delivery: optimization, characterization, and evaluation in vitro and in vivo

PubMed Central

Zhang, Kai; Zhang, Yongtai; Li, Zhe; Li, Nana; Feng, Nianping

2017-01-01

In this study, a novel glycerosome carrier containing essential oils was prepared for topical administration of paeoniflorin (PF) to enhance its transdermal drug delivery and improve drug absorption in the synovium. The formulation of glycerosomes was optimized by a uniform design, and the final vehicle was composed of 5% (w/v) phospholipid, 0.6% (w/v) cholesterol, and 10% (v/v) glycerol, with 2% (v/v) Speranskia tuberculata essential oil (STO) as the transdermal enhancer. The in vitro transdermal flux of PF loaded in the STO-glycerosomes was 1.4-fold, 1.6-fold, and 1.7-fold higher than those of glycerosomes, liposomes, and tinctures, respectively. In vivo studies showed that the use of STO-glycerosomes was associated with a 3.1-fold greater accumulation of PF in the synovium than that of common glycerosomes. This finding was confirmed by in vivo imaging studies, which found that the fluorescence intensity of Cy5.5-loaded STO-glycerosomes in mice knee joints was 1.8-fold higher than that of the common glycerosomes 5 h after administration. The glycerosomes mediated by STO exhibited considerable skin permeability as well as improved drug absorption in the synovium, indicating that STO-glycerosomes may be a potential PF transdermal delivery vehicle for the treatment of rheumatoid arthritis caused by synovium lesions. PMID:28503066

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

PubMed Central

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

2012-01-01

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

Activation of G proteins mediates flow-induced prostaglandin E2 production in osteoblasts

NASA Technical Reports Server (NTRS)

Reich, K. M.; McAllister, T. N.; Gudi, S.; Frangos, J. A.

1997-01-01

Interstitial fluid flow may play a role in load-induced bone remodeling. Previously, we have shown that fluid flow stimulates osteoblast production of cAMP inositol trisphosphate (IP3), and PGE2. Flow-induced increases in cAMP and IP3 were shown to be a result of PG production. Thus, PGE2 production appears to be an important component in fluid flow induced signal transduction. In the present study, we investigated the mechanism of flow-induced PGE2 synthesis. Flow-induced a 20-fold increase in PGE2 production in osteoblasts. Increases were also observed with ALF4-(10mM) (98-fold), an activator of guanidine nucleotide-binding proteins (G proteins), and calcium ionophore A23187 (2 microM) (100-fold) in stationary cells. We then investigated whether flow stimulation is mediated by G proteins and increases in intracellular calcium. Flow-induced PGE2 production was inhibited by the G protein inhibitors GDP beta S (100 microM) and pertussis toxin (1 microgram/ml) by 83% and 72%, respectively. Chelation of extracellular calcium by EGTA (2 mM) and intracellular calcium by quin-2/AM (30 microM) blocked flow stimulation by 87% and 67%, respectively. These results suggest that G proteins and calcium play an important role in mediating mechanochemical signal transduction in osteoblasts.

The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

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

Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel

Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragmentmore » adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.« less

Mitochondrial heat shock protein (Hsp) 70 and Hsp10 cooperate in the formation of Hsp60 complexes.

PubMed

Böttinger, Lena; Oeljeklaus, Silke; Guiard, Bernard; Rospert, Sabine; Warscheid, Bettina; Becker, Thomas

2015-05-01

Mitochondrial Hsp70 (mtHsp70) mediates essential functions for mitochondrial biogenesis, like import and folding of proteins. In these processes, the chaperone cooperates with cochaperones, the presequence translocase, and other chaperone systems. The chaperonin Hsp60, together with its cofactor Hsp10, catalyzes folding of a subset of mtHsp70 client proteins. Hsp60 forms heptameric ring structures that provide a cavity for protein folding. How the Hsp60 rings are assembled is poorly understood. In a comprehensive interaction study, we found that mtHsp70 associates with Hsp60 and Hsp10. Surprisingly, mtHsp70 interacts with Hsp10 independently of Hsp60. The mtHsp70-Hsp10 complex binds to the unassembled Hsp60 precursor to promote its assembly into mature Hsp60 complexes. We conclude that coupling to Hsp10 recruits mtHsp70 to mediate the biogenesis of the heptameric Hsp60 rings. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Characterization of mediators of microbial virulence and innate immunity using the Caenorhabditis elegans host-pathogen model.

PubMed

Alegado, Rosanna A; Campbell, Marianne C; Chen, Will C; Slutz, Sandra S; Tan, Man-Wah

2003-07-01

The soil-borne nematode, Caenorhabditis elegans, is emerging as a versatile model in which to study host-pathogen interactions. The worm model has shown to be particularly effective in elucidating both microbial and animal genes involved in toxin-mediated killing. In addition, recent work on worm infection by a variety of bacterial pathogens has shown that a number of virulence regulatory genes mediate worm susceptibility. Many of these regulatory genes, including the PhoP/Q two-component regulators in Salmonella and LasR in Pseudomonas aeruginosa, have also been implicated in mammalian models suggesting that findings in the worm model will be relevant to other systems. In keeping with this concept, experiments aimed at identifying host innate immunity genes have also implicated pathways that have been suggested to play a role in plants and animals, such as the p38 MAP kinase pathway. Despite rapid forward progress using this model, much work remains to be done including the design of more sensitive methods to find effector molecules and further characterization of the exact interaction between invading pathogens and C. elegans' cellular components.

A microbial fuel cell operating at low pH using an acidophile, Acidiphilium cryptum.

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

Borole, Abhijeet P; Cesar, Scott A; O'Neill, Hugh Michael

2008-01-01

A microbial fuel cell using an acidophilic microorganism, Acidiphilium cryptum, as the anode biocatalyst was investigated. The mode of electron transfer by this organism to the electrode was studied. Electricity production in the presence of a mediator was demonstrated using its natural electron acceptor, iron, as well as phenosafranin as the electron mediating agent. Production of Fe(II), as a result of iron reduction, at a pH of 4.0 or below was found to support electricity production. Accumulation of the oxidized iron, Fe(III) as a result of electron donation to the electrode, however, restricted higher current output. Addition of nitrilotriacetic acidmore » helped resolve the problem by redissolution of deposited Fe(III). Further, use of phenosafranin as a secondary mediator resulted in improvement in power output. At a cell loading equivalent to OD600 of 1.0, a power output of 12.7 mW/m2 was obtained in a two-chamber air-sparged fuel cell. Potential for direct electron transfer was also investigated but not detected under the conditions studied.« less

Molecular imprinted hydrogel polymer (MIHP) as microbial immobilization media in artificial produced water treatment

NASA Astrophysics Data System (ADS)

Kardena, E.; Ridhati, S. L.; Helmy, Q.

2018-01-01

Produced water generated during oil and gas exploration and drilling, consists of many chemicals which used in drilling process. The production of produced water is over three fold of the oil production. The water-cut has increased over time and continues to do so because the fraction of oil in the reservoir decreases and it is more difficult to get the oil out from an old oil-field. It therefore requires more sea water to be injected in order to force the oil out; hence more produced water is generated. Produced water can pollute the environment if it is not treated properly. In this research, produced water will be treated biologically using bacterial consortium which is isolated from petroleum processing facility with Molecular Imprinted Hydrogel Polymer (MIHP) for microbial immobilization media. Microbial growth rate is determined by measuring the MLVSS and hydrogel mass, also by SEM-EDS analysis. SEM-EDS analysis is an analysis to evidence the presence of microbe trapped in hydrogel, and also to determine the types and weight of the molecules of hydrogel. From this research, suspended microbial growth rate was found at 0.1532/days and attached microbial growth rate was 0.3322/days. Furthermore, based on SEM analysis, microbe is entrapped inside the hydrogel. Effectiveness of microbial degradation activity was determined by measuring organic materials as COD. Based on COD measurement, degradation rate of organic materials in wastewater is 0.3089/days, with maximum COD removal efficiency of 76.67%.

Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

PubMed Central

Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

2014-01-01

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683

Forces Driving Chaperone Action

PubMed Central

Koldewey, Philipp; Stull, Frederick; Horowitz, Scott; Martin, Raoul; Bardwell, James C. A.

2016-01-01

SUMMARY It is still unclear what molecular forces drive chaperone-mediated protein folding. Here, we obtain a detailed mechanistic understanding of the forces that dictate the four key steps of chaperone-client interaction: initial binding, complex stabilization, folding, and release. Contrary to the common belief that chaperones recognize unfolding intermediates by their hydrophobic nature, we discover that the model chaperone Spy uses long-range electrostatic interactions to rapidly bind to its unfolded client protein Im7. Short-range hydrophobic interactions follow, which serve to stabilize the complex. Hydrophobic collapse of the client protein then drives its folding. By burying hydrophobic residues in its core, the client’s affinity to Spy decreases, which causes client release. By allowing the client to fold itself, Spy circumvents the need for client-specific folding instructions. This mechanism might help explain how chaperones can facilitate the folding of various unrelated proteins. PMID:27293188

Protozoan grazing reduces the current output of microbial fuel cells.

PubMed

Holmes, Dawn E; Nevin, Kelly P; Snoeyenbos-West, Oona L; Woodard, Trevor L; Strickland, Justin N; Lovley, Derek R

2015-10-01

Several experiments were conducted to determine whether protozoan grazing can reduce current output from sediment microbial fuel cells. When marine sediments were amended with eukaryotic inhibitors, the power output from the fuel cells increased 2-5-fold. Quantitative PCR showed that Geobacteraceae sequences were 120 times more abundant on anodes from treated fuel cells compared to untreated fuel cells, and that Spirotrichea sequences in untreated fuel cells were 200 times more abundant on anode surfaces than in the surrounding sediments. Defined studies with current-producing biofilms of Geobacter sulfurreducens and pure cultures of protozoa demonstrated that protozoa that were effective in consuming G. sulfurreducens reduced current production up to 91% when added to G. sulfurreducens fuel cells. These results suggest that anode biofilms are an attractive food source for protozoa and that protozoan grazing can be an important factor limiting the current output of sediment microbial fuel cells. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evaluation of Laminaria-based microbial fuel cells (LbMs) for electricity production.

PubMed

Gadhamshetty, Venkataramana; Belanger, Derek; Gardiner, Carly-Jeanne; Cummings, Anasha; Hynes, Anne

2013-01-01

Marine algae represents a sustainable feedstock in microbial fuel cells (MFCs) due to its low water and energy requirements for cultivation, higher capacity to sequester carbondioxide, and high carbohydrate content. Two-compartment MFCs were evaluated under batch-fed mode using Laminaria saccharina as the model for algae-based electron donor, and mixed microbial consortia as the biocatalyst, in the anode compartment. The Laminaria-based MFCs (LBMs) were studied with three different pretreatment conditions for the L. saccharina: (i) autoclaving (Auto), (ii) microwave irradiation (Micro), and (iii) as received treatment (No-Treat). A control was setup to establish base line performance for two-compartment MFCs using glucose as the electron donor in the anode. The performance of LBMs (250 mW/m(2) and 900 mA/m(2)) was on par with glucose-based MFCs. AC impedance analysis revealed that the charge transfer resistance was at least 50-fold higher than the corresponding ohmic losses in both LBMs and glucose-based MFCs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Microbial control of diatom bloom dynamics in the open ocean

NASA Astrophysics Data System (ADS)

Boyd, Philip W.; Strzepek, Robert; Chiswell, Steve; Chang, Hoe; DeBruyn, Jennifer M.; Ellwood, Michael; Keenan, Sean; King, Andrew L.; Maas, Elisabeth W.; Nodder, Scott; Sander, Sylvia G.; Sutton, Philip; Twining, Benjamin S.; Wilhelm, Steven W.; Hutchins, David A.

2012-09-01

Diatom blooms play a central role in supporting foodwebs and sequestering biogenic carbon to depth. Oceanic conditions set bloom initiation, whereas both environmental and ecological factors determine bloom magnitude and longevity. Our study reveals another fundamental determinant of bloom dynamics. A diatom spring bloom in offshore New Zealand waters was likely terminated by iron limitation, even though diatoms consumed <1/3 of the mixed-layer dissolved iron inventory. Thus, bloom duration and magnitude were primarily set by competition for dissolved iron between microbes and small phytoplankton versus diatoms. Significantly, such a microbial mode of control probably relies both upon out-competing diatoms for iron (i.e., K-strategy), and having high iron requirements (i.e., r-strategy). Such resource competition for iron has implications for carbon biogeochemistry, as, blooming diatoms fixed three-fold more carbon per unit iron than resident non-blooming microbes. Microbial sequestration of iron has major ramifications for determining the biogeochemical imprint of oceanic diatom blooms.

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

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

Roux, Simon; Hallam, Steven J.; Woyke, Tanja

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 newmore » viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.« less

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.

PubMed

Roux, Simon; Hallam, Steven J; Woyke, Tanja; Sullivan, Matthew B

2015-07-22

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

DOE PAGES

Roux, Simon; Hallam, Steven J.; Woyke, Tanja; ...

2015-07-22

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 newmore » viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.« less

Flamingos and drought as drivers of nutrients and microbial dynamics in a saline lake.

PubMed

Batanero, Gema L; León-Palmero, Elizabeth; Li, Linlin; Green, Andy J; Rendón-Martos, Manuel; Suttle, Curtis A; Reche, Isabel

2017-09-22

Waterbird aggregations and droughts affect nutrient and microbial dynamics in wetlands. We analysed the effects of high densities of flamingos on nutrients and microbial dynamics in a saline lake during a wet and a dry hydrological year, and explored the effects of guano on prokaryotic growth. Concentrations of dissolved organic carbon, total phosphorus and total nitrogen in the surface waters were 2-3 fold higher during the drought and were correlated with salinity. Flamingos stimulated prokaryotic heterotrophic production and triggered cascading effects on prokaryotic abundance, viruses and dissolved nitrogen. This stimulus of heterotrophic prokaryotes was associated with soluble phosphorus inputs from guano, and also from sediments. In the experiments, the specific growth rate and the carrying capacity were almost twice as high after guano addition than in the control treatments, and were coupled with soluble phosphorus assimilation. Flamingo guano was also rich in nitrogen. Dissolved N in lake water lagged behind the abundance of flamingos, but the causes of this lag are unclear. This study demonstrates that intense droughts could lead to increases in total nutrients in wetlands; however, microbial activity is likely constrained by the availability of soluble phosphorus, which appears to be more dependent on the abundance of waterbirds.

Amino acid production exceeds plant nitrogen demand in Siberian tundra

NASA Astrophysics Data System (ADS)

Wild, Birgit; Eloy Alves, Ricardo J.; Bárta, Jiři; Čapek, Petr; Gentsch, Norman; Guggenberger, Georg; Hugelius, Gustaf; Knoltsch, Anna; Kuhry, Peter; Lashchinskiy, Nikolay; Mikutta, Robert; Palmtag, Juri; Prommer, Judith; Schnecker, Jörg; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Richter, Andreas

2018-03-01

Arctic plant productivity is often limited by low soil N availability. This has been attributed to slow breakdown of N-containing polymers in litter and soil organic matter (SOM) into smaller, available units, and to shallow plant rooting constrained by permafrost and high soil moisture. Using 15N pool dilution assays, we here quantified gross amino acid and ammonium production rates in 97 active layer samples from four sites across the Siberian Arctic. We found that amino acid production in organic layers alone exceeded literature-based estimates of maximum plant N uptake 17-fold and therefore reject the hypothesis that arctic plant N limitation results from slow SOM breakdown. High microbial N use efficiency in organic layers rather suggests strong competition of microorganisms and plants in the dominant rooting zone. Deeper horizons showed lower amino acid production rates per volume, but also lower microbial N use efficiency. Permafrost thaw together with soil drainage might facilitate deeper plant rooting and uptake of previously inaccessible subsoil N, and thereby promote plant productivity in arctic ecosystems. We conclude that changes in microbial decomposer activity, microbial N utilization and plant root density with soil depth interactively control N availability for plants in the Arctic.

Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity.

PubMed

Owsianiak, Mikołaj; Szulc, Alicja; Chrzanowski, Łukasz; Cyplik, Paweł; Bogacki, Mariusz; Olejnik-Schmidt, Agnieszka K; Heipieper, Hermann J

2009-09-01

In this study, we elucidated the role of cell surface hydrophobicity (microbial adhesion to hydrocarbons method, MATH) and the effect of anionic rhamnolipids and nonionic Triton X-100 surfactants on biodegradation of diesel fuel employing 218 microbial consortia isolated from petroleum-contaminated soils. Applied enrichment procedure with floating diesel fuel as a sole carbon source in liquid cultures resulted in consortia of varying biodegradation potential and diametrically different cell surface properties, suggesting that cell surface hydrophobicity is a conserved parameter. Surprisingly, no correlations between cell surface hydrophobicity and biodegradation of diesel fuel were found. Nevertheless, both surfactants altered cell surface hydrophobicity of the consortia in similar manner: increased for the hydrophilic and decreased for the hydrophobic cultures. In addition to this, the surfactants exhibited similar influence on diesel fuel biodegradation: Increase was observed for initially slow-degrading cultures and the opposite for fast degraders. This indicates that in the surfactant-mediated biodegradation, effectiveness of surfactants depends on the specification of microorganisms and not on the type of surfactant. In contrary to what was previously reported for pure strains, cell surface hydrophobicity, as determined by MATH, is not a good descriptor of biodegrading potential for mixed cultures.

The development of Fe-nodules surrounding biological material mediated by microorganisms

NASA Astrophysics Data System (ADS)

Yoshida, Hidekazu; Yamamoto, Koshi; Murakami, Yuki; Katsuta, Nagayoshi; Hayashi, Toru; Naganuma, Takeshi

2008-09-01

Takashikozo is a phenomenon of Quaternary sediments in Japan. They are cylindrical Fe-oxyhydroxide nodules that form as plaques round plant roots, where Fe is preferentially concentrated to develop a solid wall. Structural features suggest that after the roots have decayed, the central space where the roots were situated acts as a flow path for oxidized water. Analysis of microbial 16S rDNA extracted from the nodules identified iron-oxidizing bacteria encrusted round the roots where they are the likely initiators of nodule formation. Direct microscopic observation revealed an accumulation of Fe-oxyhydroxides that fill the pore spaces and is also likely to be linked with the encrusting microbial colonies. Geological history and nanofossil evidence suggest that these Fe-nodules may have been buried at a depth of up to several tens of meters for at least 105 years in reducing Quaternary sediments. Thus Fe-oxyhydroxide nodules that have formed in a geological environment at the interfaces between water and rock by microbial mediation can persist under reducing conditions. If this is the case, the phenomenon is significant as an analogue of post-closure conditions in radioactive waste repositories, since it could influence nuclide migration.

Candida albicans Pathogenesis: Fitting within the Host-Microbe Damage Response Framework

PubMed Central

Kong, Eric F.; Tsui, Christina; Nguyen, M. Hong; Clancy, Cornelius J.; Fidel, Paul L.; Noverr, Mairi

2016-01-01

Historically, the nature and extent of host damage by a microbe were considered highly dependent on virulence attributes of the microbe. However, it has become clear that disease is a complex outcome which can arise because of pathogen-mediated damage, host-mediated damage, or both, with active participation from the host microbiota. This awareness led to the formulation of the damage response framework (DRF), a revolutionary concept that defined microbial virulence as a function of host immunity. The DRF outlines six classifications of host damage outcomes based on the microbe and the strength of the immune response. In this review, we revisit this concept from the perspective of Candida albicans, a microbial pathogen uniquely adapted to its human host. This fungus commonly colonizes various anatomical sites without causing notable damage. However, depending on environmental conditions, a diverse array of diseases may occur, ranging from mucosal to invasive systemic infections resulting in microbe-mediated and/or host-mediated damage. Remarkably, C. albicans infections can fit into all six DRF classifications, depending on the anatomical site and associated host immune response. Here, we highlight some of these diverse and site-specific diseases and how they fit the DRF classifications, and we describe the animal models available to uncover pathogenic mechanisms and related host immune responses. PMID:27430274

[Competition between redox mediator and oxygen in the microbial fuel cell].

PubMed

Alferov, S V; Vozchikova, S V; Arlyapov, V A; Alferov, V A; Reshetilov, A N

2017-01-01

The maximal rates and effective constants of 2,6-dichlorphenolindophenol and oxygen reduction by bacterim Gluconobacter oxydans in bacterial fuel cells under different conditions were evaluated. In an open-circuit mode, the rate of 2,6-dichlorphenolindophenol reduction coupled with ethanol oxidation under oxygen and nirogen atmospheres were 1.0 and 1.1 μM s–1 g–1, respectively. In closed-circuit mode, these values were 0.4 and 0.44 μM s–1 g–1, respectively. The initial rate of mediator reduction with the use of membrane fractions of bacteria in oxygen and nitrogen atmospheres in open-circuit mode were 6.3 and 6.9 μM s–1 g–1, whereas these values in closed-circuit mode comprised 2.2 and 2.4 μM s–1 g–1, respectively. The oxygen reduction rates in the presence and absence of 2,6-dichlorphenolindophenol were 0.31 and 0.32 μM s–1 g–1, respectively. The data obtained in this work demonstrated independent electron transfer from bacterial redox centers to the mediator and the absence of competition between the redox mediator and oxygen. The results can make it possible to reduce costs of microbial fuel cells based on activity of acetic acid bacteria G. oxydans.

Molecular chaperones and protein folding as therapeutic targets in Parkinson's disease and other synucleinopathies.

PubMed

Ebrahimi-Fakhari, Darius; Saidi, Laiq-Jan; Wahlster, Lara

2013-12-05

Changes in protein metabolism are key to disease onset and progression in many neurodegenerative diseases. As a prime example, in Parkinson's disease, folding, post-translational modification and recycling of the synaptic protein α-synuclein are clearly altered, leading to a progressive accumulation of pathogenic protein species and the formation of intracellular inclusion bodies. Altered protein folding is one of the first steps of an increasingly understood cascade in which α-synuclein forms complex oligomers and finally distinct protein aggregates, termed Lewy bodies and Lewy neurites. In neurons, an elaborated network of chaperone and co-chaperone proteins is instrumental in mediating protein folding and re-folding. In addition to their direct influence on client proteins, chaperones interact with protein degradation pathways such as the ubiquitin-proteasome-system or autophagy in order to ensure the effective removal of irreversibly misfolded and potentially pathogenic proteins. Because of the vital role of proper protein folding for protein homeostasis, a growing number of studies have evaluated the contribution of chaperone proteins to neurodegeneration. We herein review our current understanding of the involvement of chaperones, co-chaperones and chaperone-mediated autophagy in synucleinopathies with a focus on the Hsp90 and Hsp70 chaperone system. We discuss genetic and pathological studies in Parkinson's disease as well as experimental studies in models of synucleinopathies that explore molecular chaperones and protein degradation pathways as a novel therapeutic target. To this end, we examine the capacity of chaperones to prevent or modulate neurodegeneration and summarize the current progress in models of Parkinson's disease and related neurodegenerative disorders.

Immune indexes of larks from desert and temperate regions show weak associations with life history but stronger links to environmental variation in microbial abundance.

PubMed

Horrocks, Nicholas P C; Hegemann, Arne; Matson, Kevin D; Hine, Kathryn; Jaquier, Sophie; Shobrak, Mohammed; Williams, Joseph B; Tinbergen, Joost M; Tieleman, B Irene

2012-01-01

Immune defense may vary as a result of trade-offs with other life-history traits or in parallel with variation in antigen levels in the environment. We studied lark species (Alaudidae) in the Arabian Desert and temperate Netherlands to test opposing predictions from these two hypotheses. Based on their slower pace of life, the trade-off hypothesis predicts relatively stronger immune defenses in desert larks compared with temperate larks. However, as predicted by the antigen exposure hypothesis, reduced microbial abundances in deserts should result in desert-living larks having relatively weaker immune defenses. We quantified host-independent and host-dependent microbial abundances of culturable microbes in ambient air and from the surfaces of birds. We measured components of immunity by quantifying concentrations of the acute-phase protein haptoglobin, natural antibody-mediated agglutination titers, complement-mediated lysis titers, and the microbicidal ability of whole blood. Desert-living larks were exposed to significantly lower concentrations of airborne microbes than temperate larks, and densities of some bird-associated microbes were also lower in desert species. Haptoglobin concentrations and lysis titers were also significantly lower in desert-living larks, but other immune indexes did not differ. Thus, contrary to the trade-off hypothesis, we found little evidence that a slow pace of life predicted increased immunological investment. In contrast, and in support of the antigen exposure hypothesis, associations between microbial exposure and some immune indexes were apparent. Measures of antigen exposure, including assessment of host-independent and host-dependent microbial assemblages, can provide novel insights into the mechanisms underlying immunological variation.

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

PubMed

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

2014-01-01

Rivers in northern Chile have arsenic (As) concentrations at levels that are toxic for humans and other organisms. Microorganism-mediated redox reactions have a crucial role in the As cycle; the microbial oxidation of As (As(III) to As(V)) is a critical transformation because it favors the immobilization of As in the solid phase. We studied the role of microbial As oxidation for controlling the mobility of As in the extreme environment found in the Chilean Altiplano (i.e., > 4000 meters above sea level (masl) and < 310 mm annual rainfall), which are conditions that have rarely been studied. Our model system was the upper Azufre River sub-basin, where the natural attenuation of As from hydrothermal discharge (pH 4-6) was observed. As(III) was actively oxidized by a microbial consortium, leading to a significant decrease in the dissolved As concentrations and a corresponding increase in the sediment's As concentration downstream of the hydrothermal source. In-situ oxidation experiments demonstrated that the As oxidation required biological activity, and microbiological molecular analysis confirmed the presence of As(III)-oxidizing groups (aroA-like genes) in the system. In addition, the pH measurements and solid phase analysis strongly suggested that the As removal mechanism involved adsorption or coprecipitation with Fe-oxyhydroxides. Taken together, these results indicate that the microorganism-mediated As oxidation contributed to the attenuation of As concentrations and the stabilization of As in the solid phase, therefore controlling the amount of As transported downstream. This study is the first to demonstrate the microbial oxidation of As in Altiplano basins and its relevance in the immobilization of As. © 2013.

Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides.

PubMed

Thomson, Pamela; Medina, Daniel A; Ortúzar, Verónica; Gotteland, Martín; Garrido, Daniel

2018-07-01

The gut microbiome has a significant impact on host health, especially at the metabolic level. Dietary compounds arriving at the colon have a large influence on the composition of the gut microbiome. High fiber diets have been associated to health benefits that are mediated in great part by short chain fatty acids (SCFA). Gut microbial interactions are relevant for the utilization of complex carbohydrates in the gut microbiome. In this work we characterized the utilization of two dietary polysaccharides by combinations of representative adult gut microbes, and the impact of their activities on a cellular inflammation model. Paired combinations of Bifidobacterium adolescentis, Bacteroides dorei, Lactobacillus plantarum, Escherichia coli and Clostridium symbiosum were grown in inulin or xylan as carbon source. Their relative abundance, substrate consumption and major SCFAs produced were determined. Higher cell growth was observed during inulin consumption, and B. adolescentis and L. plantarum were dominant in co-cultures. The co-culture of B. dorei and C. symbiosum was dominant in xylan. In several cases the combined bacterial growth was lower in co-cultures than monocultures, with a few exceptions of synergistic growth between microorganisms. Inulin fermentation resulted in larger acetate and lactate concentrations, and several combinations grown in xylan containing C. symbiosum were characterized by high amounts of butyrate. These microbial consortia were scaled to batch bioreactor fermentations reaching high cell densities and similar profiles to co-culture experiments. Interestingly, a microbial combination producing high amounts of butyrate was able to reduce IL-8 expression in HT-29 cells co-incubated with TNFα. In summary, this work shows that microbial interactions during the utilization of dietary polysaccharides are complex and substrate dependent. Moreover, certain combinations deploy potent anti-inflammatory effects, which are independent of individual microbial growth, and could be mediated in part by higher butyrate production. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Effect of a Reduction in Microbial Diversity on Greenhouse Gas Production in Alaskan Tundra Soils.

NASA Astrophysics Data System (ADS)

Wagner, R.; Oechel, W. C.; Lipson, D.

2017-12-01

Atmospheric methane accounts for 20% of the warming potential of all greenhouse gases, has increased by 150% since pre-industrial times, and has the potential to double again over the next century. Microbially mediated CH4 emissions from natural wetlands represent the highest uncertainty in relative contributions to atmospheric CH4 levels of all CH4 sources, with Arctic wetlands currently experiencing twice the rate of warming as the rest of the planet. Notwithstanding the central role that the soil microbial community plays, and the high uncertainty in CH4 emissions from this ecosystem, surprisingly little research has been done to directly connect the microbial community structure to methane production rates. This is especially disconcerting given that most current CH4 emission models completely neglect microbial characteristics, despite the fact that the soil microbial community is predicted to be heavily impacted by a changing climate. Here, the effect of an artificial reduction in soil microbial α-diversity was investigated with regard to methane production and respiration rates. The microbial community was serially diluted followed by re-inoculation of sterilized Arctic soils in a mesocosm experiment. Methane production and respiration rates were measured, metagenomic sequencing was performed to determine microbial community diversity measures, and the effect of the oxidation state of iron was investigated. Preliminary results indicate that microbial communities with reduced α-diversity have lowered respiration rates in these soils. Analyses are ongoing and are expected to provide critical observations linking the role of soil microbial community diversity and greenhouse gas production in Arctic tundra ecosystems.

Comparison of Gene Expression by Sheep and Human Blood Stimulated with the TLR4 Agonists Lipopolysaccharide and Monophosphoryl Lipid A

PubMed Central

Enkhbaatar, Perenlei; Nelson, Christina; Salsbury, John R.; Carmical, Joseph R.; Torres, Karen E. O.; Herndon, David; Prough, Donald S.; Luan, Liming; Sherwood, Edward R.

2015-01-01

Background Animal models that mimic human biology are important for successful translation of basic science discoveries into the clinical practice. Recent studies in rodents have demonstrated the efficacy of TLR4 agonists as immunomodulators in models of infection. However, rodent models have been criticized for not mimicking important characteristics of the human immune response to microbial products. The goal of this study was to compare genomic responses of human and sheep blood to the TLR4 agonists lipopolysaccharide (LPS) and monophosphoryl lipid A (MPLA). Methods Venous blood, withdrawn from six healthy human adult volunteers (~ 28 years old) and six healthy adult female sheep (~3 years old), was mixed with 30 μL of PBS, LPS (1μg/mL) or MPLA (10μg/mL) and incubated at room temperature for 90 minutes on a rolling rocker. After incubation, 2.5 mL of blood was transferred to Paxgene Blood RNA tubes. Gene expression analysis was performed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip. Agilent gene expression microarrays were scanned with a G2565 Microarray Scanner. Differentially expressed genes were identified. Results 11,431 human and 4,992 sheep probes were detected above background. Among them 1,029 human and 175 sheep genes were differentially expressed at a stringency of 1.5-fold change (p<0.05). Of the 175 sheep genes, 54 had a known human orthologue. Among those genes, 22 had > 1.5-fold changes in human samples. Genes of major inflammatory mediators, such as IL-1, IL-6 and IL-8, TNF alpha, NF-kappaB, ETS2, PTGS2, PTX3, CXCL16, KYNU, and CLEC4E were similarly (>2-fold) upregulated by LPS and MPLA in both species. Conclusion The genomic responses of peripheral blood to LPS and MPLA in sheep are quite similar to those observed in humans, supporting the use of the ovine model for translational studies that mimic human inflammatory diseases and the study of TLR-based immunomodulators. PMID:26640957

Comparison of Gene Expression by Sheep and Human Blood Stimulated with the TLR4 Agonists Lipopolysaccharide and Monophosphoryl Lipid A.

PubMed

Enkhbaatar, Perenlei; Nelson, Christina; Salsbury, John R; Carmical, Joseph R; Torres, Karen E O; Herndon, David; Prough, Donald S; Luan, Liming; Sherwood, Edward R

2015-01-01

Animal models that mimic human biology are important for successful translation of basic science discoveries into the clinical practice. Recent studies in rodents have demonstrated the efficacy of TLR4 agonists as immunomodulators in models of infection. However, rodent models have been criticized for not mimicking important characteristics of the human immune response to microbial products. The goal of this study was to compare genomic responses of human and sheep blood to the TLR4 agonists lipopolysaccharide (LPS) and monophosphoryl lipid A (MPLA). Venous blood, withdrawn from six healthy human adult volunteers (~ 28 years old) and six healthy adult female sheep (~3 years old), was mixed with 30 μL of PBS, LPS (1μg/mL) or MPLA (10μg/mL) and incubated at room temperature for 90 minutes on a rolling rocker. After incubation, 2.5 mL of blood was transferred to Paxgene Blood RNA tubes. Gene expression analysis was performed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip. Agilent gene expression microarrays were scanned with a G2565 Microarray Scanner. Differentially expressed genes were identified. 11,431 human and 4,992 sheep probes were detected above background. Among them 1,029 human and 175 sheep genes were differentially expressed at a stringency of 1.5-fold change (p<0.05). Of the 175 sheep genes, 54 had a known human orthologue. Among those genes, 22 had > 1.5-fold changes in human samples. Genes of major inflammatory mediators, such as IL-1, IL-6 and IL-8, TNF alpha, NF-kappaB, ETS2, PTGS2, PTX3, CXCL16, KYNU, and CLEC4E were similarly (>2-fold) upregulated by LPS and MPLA in both species. The genomic responses of peripheral blood to LPS and MPLA in sheep are quite similar to those observed in humans, supporting the use of the ovine model for translational studies that mimic human inflammatory diseases and the study of TLR-based immunomodulators.

Bacterial Associates Modify Growth Dynamics of the Dinoflagellate Gymnodinium catenatum

PubMed Central

Bolch, Christopher J. S.; Bejoy, Thaila A.; Green, David H.

2017-01-01

Marine phytoplankton cells grow in close association with a complex microbial associate community known to affect the growth, behavior, and physiology of the algal host. The relative scale and importance these effects compared to other major factors governing algal cell growth remain unclear. Using algal-bacteria co-culture models based on the toxic dinoflagellate Gymnodinium catenatum, we tested the hypothesis that associate bacteria exert an independent effect on host algal cell growth. Batch co-cultures of G. catenatum were grown under identical environmental conditions with simplified bacterial communities composed of one-, two-, or three-bacterial associates. Modification of the associate community membership and complexity induced up to four-fold changes in dinoflagellate growth rate, equivalent to the effect of a 5°C change in temperature or an almost six-fold change in light intensity (20–115 moles photons PAR m-2 s-1). Almost three-fold changes in both stationary phase cell concentration and death rate were also observed. Co-culture with Roseobacter sp. DG874 reduced dinoflagellate exponential growth rate and led to a more rapid death rate compared with mixed associate community controls or co-culture with either Marinobacter sp. DG879, Alcanivorax sp. DG881. In contrast, associate bacteria concentration was positively correlated with dinoflagellate cell concentration during the exponential growth phase, indicating growth was limited by supply of dinoflagellate-derived carbon. Bacterial growth increased rapidly at the onset of declining and stationary phases due to either increasing availability of algal-derived carbon induced by nutrient stress and autolysis, or at mid-log phase in Roseobacter co-cultures potentially due to the onset of bacterial-mediated cell lysis. Co-cultures with the three bacterial associates resulted in dinoflagellate and bacterial growth dynamics very similar to more complex mixed bacterial community controls, suggesting that three-way co-cultures are sufficient to model interaction and growth dynamics of more complex communities. This study demonstrates that algal associate bacteria independently modify the growth of the host cell under non-limiting growth conditions and supports the concept that algal–bacterial interactions are an important structuring mechanism in phytoplankton communities. PMID:28469613

Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

NASA Astrophysics Data System (ADS)

Melle, C. J.; Darrouzet-Nardi, A.; Wallenstein, M. D.

2012-12-01

Soils of northern permafrost regions currently contain twice as much carbon as the entire Earth's atmosphere. Traditionally, environmental constraints have limited microbial activity resulting in restricted decomposition of soil organic matter in these systems and accumulation of massive amounts of soil organic carbon (SOC), however climate change is reducing the constraints of decomposition in arctic permafrost regions. Carbon cycling in nutrient poor, arctic ecosystems is tightly coupled to other biogeochemical cycles. Several studies have suggested strong nitrogen limitations of primary productivity and potentially warm-season microbial activity in these nutrient deficient soils. Nitrogen is required for microbial extracellular enzyme production which drives the decomposition of soil organic matter (SOM). Nitrogen limited arctic soils may also experience limitation via labile carbon availability despite the SOM rich environment due to low extracellular enzyme production. Few studies have directly addressed nutrient induced microbial limitation in SOC rich arctic tundra soils, and even less is known about the potential for nutrient co-limitation. Additionally, through the process of becoming deglaciated, sites within close proximity to one another may have experienced drastic differences in their effective soil ages due to the varied length of their active histories. Many soil properties and nutrient deficiencies are directly related to soil age, however this chronology has not previously been a focus of research on nutrient limitation of arctic soil microbial activity. Understanding of nutrient limitations, as well as potential co-limitation, on arctic soil microbial activity has important implications for carbon cycling and the ultimate fate of the current arctic SOC reservoir. Analyses of nutrient limitation on soils of a single site are not adequate for fully understanding the controls on soil microbial activity across a vast land mass with large variation in effective soil age. My research is focused on addressing the questions of the extent of microbial N limitation in arctic tundra soils, the potential for co-limitation of labile C despite a high SOC environment, and the dependence, if any, nutrient limitation may have on the effective age of the soil. I have addressed these questions by conducting a laboratory soil incubation of factorial design with treatments of amended glucose, amended ammonium nitrate, and a control consisting of an addition of an equivalent volume of deionized water. Moist acid tundra soils possessing similar soil properties from two arctic sites of close proximity yet with varying deglaciation chronologies were utilized in my study. Soil properties of C-mineralization via respiration, microbial biomass, and nitrogen content in the forms of ammonium, nitrate, and total free amino acids and microbial extra-cellular enzyme production were assayed to determine the microbial response to the experimental treatments. Through the results of this work, I hope to better our understanding of biogeochemical cycling within arctic tundra ecosystems and the response to climate change by contributing to existing knowledge of nutrient limitation on microbial mediated decomposition of SOC in the arctic and how this may differ in soils of varying effective age.

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

PubMed

He, Tianliang; Li, Hongyun; Zhang, Xiaobo

2017-07-11

Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival. Copyright © 2017 He et al.

E-cadherin suppression accelerates squamous cell carcinoma progression in three-dimensional, human tissue constructs.

PubMed

Margulis, Alexander; Zhang, Weitian; Alt-Holland, Addy; Crawford, Howard C; Fusenig, Norbert E; Garlick, Jonathan A

2005-03-01

We studied the link between loss of E-cadherin-mediated adhesion and acquisition of malignant properties in three-dimensional, human tissue constructs that mimicked the initial stages of squamous cell cancer progression. Suppression of E-cadherin expression in early-stage, skin-derived tumor cells (HaCaT-II-4) was induced by cytoplasmic sequestration of beta-catenin upon stable expression of a dominant-negative E-cadherin fusion protein (H-2Kd-Ecad). In monolayer cultures, expression of H-2Kd-Ecad resulted in decreased levels of E-cadherin, redistribution of beta-catenin to the cytoplasm, and complete loss of intercellular adhesion when compared with control II-4 cells. This was accompanied by a 7-fold decrease in beta-catenin-mediated transcription and a 12-fold increase in cell migration. In three-dimensional constructs, E-cadherin-deficient tissues showed disruption of architecture, loss of adherens junctional proteins from cell contacts, and focal tumor cell invasion. Invasion was linked to activation of matrix metalloproteinase (MMP)-mediated degradation of basement membrane in H-2Kd-Ecad-expressing tissue constructs that was blocked by MMP inhibition (GM6001). Quantitative reverse transcription-PCR showed a 2.5-fold increase in MMP-2 and an 8-fold increase in MMP-9 in cells expressing the H-2Kd-Ecad fusion protein when compared with controls, and gel zymography showed increased MMP protein levels. Following surface transplantation of three-dimensional tissues, suppression of E-cadherin expression greatly accelerated tumorigenesis in vivo by inducing a switch to high-grade carcinomas that resulted in a 5-fold increase in tumor size after 4 weeks. Suppression of E-cadherin expression and loss of its function fundamentally modified squamous cell carcinoma progression by activating a highly invasive, aggressive tumor phenotype, whereas maintenance of E-cadherin prevented invasion in vitro and limited tumor progression in vivo.

Task-Based Oral Computer-Mediated Communication and L2 Vocabulary Acquisition

ERIC Educational Resources Information Center

Yanguas, Inigo

2012-01-01

The present study adds to the computer-mediated communication (CMC) literature by exploring oral learner-to-learner interaction using Skype, a free and widely used Internet software program. In particular, this task-based study has a two-fold goal. Firstly, it explores possible differences between two modes of oral CMC (audio and video) and…

CCL2 and CCL3 are essential mediators of pelvic pain in experimental autoimmune prostatitis

PubMed Central

Quick, Marsha L.; Mukherjee, Soumi; Rudick, Charles N.; Done, Joseph D.; Schaeffer, Anthony J.

2012-01-01

Experimental autoimmune prostatitis (EAP) is a murine model of chronic prostatitis/chronic pelvic pain syndrome (CPPS) in men, a syndrome characterized by chronic pelvic pain. We have demonstrated that chemokine ligands CCL2 and CCL3 are biomarkers that correlate with pelvic pain symptoms. We postulated that CCL2 and CCL3 play a functional role in CPPS and therefore examined their expression in EAP. Upon examination of the prostate 5 days after induction of EAP, CCL2 mRNA was elevated 2- to 3-fold, CCL8 by 15-fold, CCL12 by 12- to 13-fold, and CXCL9 by 2- to 4-fold compared with control mice. At 10 days the major chemokines were CXCL13 and CXCL2; at 20 days CCL2 (1- to 2-fold), CCL3 (2- to 3-fold) and CCL11 (2- to 3-fold); and at 30 days, CCL12 (20- to 35-fold) and smaller increases in CCL2, CCL3, and XCL1. Chemokine elevations were accompanied by increases in mast cells and B cells at 5 days, monocytes and neutrophils at day 10, CD4+ T cells at day 20, and CD4+ and CD8+ T cells at day 30. Anti-CCL2 and anti-CCL3 neutralizing antibodies administered at EAP onset attenuated pelvic pain development, but only anti-CCL2 antibodies were effective therapeutically. CCL2- and its cognate receptor CCR2-deficient mice were completely protected from development of pain symptoms but assumed susceptibility after reconstitution with wild-type bone marrow. CCL3-deficient mice showed resistance to the maintenance of pelvic pain while CCR5-deficient mice did not show any lessening of pelvic pain severity. These results suggest that the CCL2-CCR2 axis and CCL3 are important mediators of chronic pelvic pain in EAP. PMID:22814670

Microbial proliferation on gill structures of juvenile European lobster ( Homarus gammarus) during a moult cycle

NASA Astrophysics Data System (ADS)

Middlemiss, Karen L.; Urbina, Mauricio A.; Wilson, Rod W.

2015-12-01

The morphology of gill-cleaning structures is not well described in European lobster ( Homarus gammarus). Furthermore, the magnitude and time scale of microbial proliferation on gill structures is unknown to date. Scanning electron microscopy was used to investigate development of setae in zoea, megalopa and juvenile stages (I-V). Microbes were classified and quantified on gill structures throughout a moult cycle from megalopa (stage IV) to juvenile (stage V). Epipodial serrulate setae, consisting of a naked proximal setal shaft with the distal portion possessing scale-like outgrowths (setules), occur only after zoea stage III. After moulting to megalopa (stage IV), gill structures were completely clean and no microbes were visible on days 1 or 5 postmoult. Microbial proliferation was first evident on day 10 postmoult, with a significant 16-fold increase from day 10 to 15. Rod-shaped bacteria were initially predominant (by day 10); however, by day 15 the microbial community was dominated by cocci-shaped bacteria. This research provides new insights into the morphology of gill-grooming structures, the timing of their development, and the magnitude, timescale and characteristics of gill microbial proliferation during a moult cycle. To some degree, the exponential growth of epibionts on gills found during a moult cycle will likely impair respiratory (gas exchange) and ion regulatory function, yet further research is needed to evaluate the physiological effects of the exponential bacterial proliferation documented here.

Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.

PubMed

Eichorst, Stephanie A; Joshua, Chijioke; Sathitsuksanoh, Noppadon; Singh, Seema; Simmons, Blake A; Singer, Steven W

2014-12-01

Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture.

PubMed

Qin, Yuan; Druzhinina, Irina S; Pan, Xueyu; Yuan, Zhilin

2016-11-15

Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

Bioelectrochemical ethanol production through mediated acetate reduction by mixed cultures.

PubMed

Steinbusch, Kirsten J J; Hamelers, Hubertus V M; Schaap, Joris D; Kampman, Christel; Buisman, Cees J N

2010-01-01

Biological acetate reduction with hydrogen is a potential method to convert wet biomass waste into ethanol. Since the ethanol concentration and reaction rates are low, this research studies the feasibility of using an electrode, in stead of hydrogen, as an electron donor for biological acetate reduction in conjunction of an electron mediator. Initially, the effect of three selected mediators on metabolic flows during acetate reduction with hydrogen was explored; subsequently, the best performing mediator was used in a bioelectrochemical system to stimulate acetate reduction at the cathode with mixed cultures at an applied cathode potential of -550 mV. In the batch test, methyl viologen (MV) was found to accelerate ethanol production 6-fold and increased ethanol concentration 2-fold to 13.5 +/- 0.7 mM compared to the control. Additionally, MV inhibited n-butyrate and methane formation, resulting in high ethanol production efficiency (74.6 +/- 6%). In the bioelectrochemical system, MV addition to an inoculated cathode led directly to ethanol production (1.82 mM). Hydrogen was coproduced at the cathode (0.0035 Nm(3) hydrogen m(-2) d(-1)), so it remained unclear whether acetate was reduced to ethanol by electrons supplied by the mediator or by hydrogen. As MV reacted irreversibly at the cathode, ethanol production stopped after 5 days.

Concepts and tools for predictive modeling of microbial dynamics.

PubMed

Bernaerts, Kristel; Dens, Els; Vereecken, Karen; Geeraerd, Annemie H; Standaert, Arnout R; Devlieghere, Frank; Debevere, Johan; Van Impe, Jan F

2004-09-01

Description of microbial cell (population) behavior as influenced by dynamically changing environmental conditions intrinsically needs dynamic mathematical models. In the past, major effort has been put into the modeling of microbial growth and inactivation within a constant environment (static models). In the early 1990s, differential equation models (dynamic models) were introduced in the field of predictive microbiology. Here, we present a general dynamic model-building concept describing microbial evolution under dynamic conditions. Starting from an elementary model building block, the model structure can be gradually complexified to incorporate increasing numbers of influencing factors. Based on two case studies, the fundamentals of both macroscopic (population) and microscopic (individual) modeling approaches are revisited. These illustrations deal with the modeling of (i) microbial lag under variable temperature conditions and (ii) interspecies microbial interactions mediated by lactic acid production (product inhibition). Current and future research trends should address the need for (i) more specific measurements at the cell and/or population level, (ii) measurements under dynamic conditions, and (iii) more comprehensive (mechanistically inspired) model structures. In the context of quantitative microbial risk assessment, complexity of the mathematical model must be kept under control. An important challenge for the future is determination of a satisfactory trade-off between predictive power and manageability of predictive microbiology models.

Analysis and assessment of microbial biofilm-mediated concrete deterioration.

DOT National Transportation Integrated Search

2008-10-01

Inspections of bridge substructures in Texas identified surface deterioration of reinforced concrete columns on : bridges continuously exposed water. Initial hypothesis were that the surface deterioration was a result of the : acidity of the water in...

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

PubMed Central

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

2017-01-01

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

Microbial shaping of wrinkle structures in siliciclastic deposits

NASA Astrophysics Data System (ADS)

Bosak, T.; Mariotti, G.; Pruss, S. B.; Perron, J.; O'Grady, M.

2013-12-01

Wrinkle structures are millimeter- to centimeter-scale elongated or reticulate sedimentary structures that resemble symmetric ripples. Sharp-crested and flat-topped wrinkle structures up to 1 cm wide occur on numerous bedding planes in the Neoproterozoic and Cambrian, as well as in some Archean and Phanerozoic siliciclastic deposits. Because similar, but unlithified structures occur in some modern, microbially-colonized sands, wrinkle structures are typically interpreted as microbially induced sedimentary structures. However, it is unclear if physical processes, such as the motion of suspended sand grains, can produce similar features in sand even before microbial colonization. We introduced mat fragments to the surface of silica sand in wave tanks and generated sharp-crested, flat-topped and pitted wrinkle structures. The abrasion of the sandy surface by rolling, low density, millimeter-size fragments of microbial mats produces wrinkle structures at extremely weak orbital velocities that cannot move sand grains in the absence of light particles. Wrinkle structures form in a few hours and can become colonized by microbial mats within weeks. Thus, wrinkle structures are patterns formed by microbially mediated sand motion at low orbital velocities in the absence of bioturbation. Once formed, wrinkle structures can be colonized and stabilized by microbial mats, but the shape of these mats does not dictate the shape of wrinkle structures. These experiments bolster the interpretation of wrinkle structures as morphological signatures of organic particles and early life in Archean and Proterozoic siliciclastic deposits.

Antibiofilm agents: A new perspective for antimicrobial strategy.

PubMed

Li, Xi-Hui; Lee, Joon-Hee

2017-10-01

Biofilms are complex microbial architectures that attach to surfaces and encase microorganisms in a matrix composed of self-produced hydrated extracellular polymeric substances (EPSs). In biofilms, microorganisms become much more resistant to antimicrobial treatments, harsh environmental conditions, and host immunity. Biofilm formation by microbial pathogens greatly enhances survival in hosts and causes chronic infections that result in persistent inflammation and tissue damages. Currently, it is believed over 80% of chronic infectious diseases are mediated by biofilms, and it is known that conventional antibiotic medications are inadequate at eradicating these biofilm-mediated infections. This situation demands new strategies for biofilm-associated infections, and currently, researchers focus on the development of antibiofilm agents that are specific to biofilms, but are nontoxic, because it is believed that this prevents the development of drug resistance. Here, we review the most promising antibiofilm agents undergoing intensive research and development.

Biopower generation from kitchen wastewater using a bioreactor.

PubMed

Khan, Abdul M; Naz, Shamsa

2014-01-01

This research provides a comparative study of the power output from mediator-less and mediator microbial fuel cells (MFCs) under aerobic and partially anaerobic conditions using kitchen wastewater (KWW) as a renewable energy source. The wastewater sample was subjected to different physical, chemical, biochemical, and microbial analysis. The chemical oxygen demand (COD), biochemical oxygen demand (BOD), and power output values were greater for the fermented samples than the non-fermented samples. The power output of samples was compared through the development of MFCs by using sand-salt bridge and agar-salt bridge. The H2 that was produced was converted to atomic hydrogen by using the nickel-coated zinc electrode. In addition, the power output was further enhanced by introducing air into the cathodic chamber, where oxygen reacts with the protons to form pure H2O. The study showed that the power output was increased with the increase in COD and BOD values.

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

DOEpatents

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji Won; Rondinone, Adam J.; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

2014-06-24

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component containing at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

Microbiota as a mediator of cancer progression and therapy.

PubMed

Pope, Jillian L; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbiota as a mediator of cancer progression and therapy

PubMed Central

Pope, Jillian L.; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. PMID:27554797

Inhibition of homodimerization of toll-like receptor 4 by 6-shogaol.

PubMed

Ahn, Sang-Il; Lee, Jun-Kyung; Youn, Hyung-Sun

2009-02-28

Toll-like receptors (TLRs) play a critical role in sensing microbial components and inducing innate immune and inflammatory responses by recognizing invading microbial pathogens. Lipopolysaccharide-induced dimerization of TLR4 is required for the activation of downstream signaling pathways including nuclear factor-kappa B (NF-kappaB). Therefore, TLR4 dimerization may be an early regulatory event in activating ligand-induced signaling pathways and induction of subsequent immune responses. Here, we report biochemical evidence that 6-shogaol, the most bioactive component of ginger, inhibits lipopolysaccharide-induced dimerization of TLR4 resulting in the inhibition of NF-kappaB activation and the expression of cyclooxygenase-2. Furthermore, we demonstrate that 6-shogaol can directly inhibit TLR-mediated signaling pathways at the receptor level. These results suggest that 6-shogaol can modulate TLR-mediated inflammatory responses, which may influence the risk of chronic inflammatory diseases.

Pathogen- and host-directed anti-inflammatory activities of macrolide antibiotics.

PubMed

Steel, Helen C; Theron, Annette J; Cockeran, Riana; Anderson, Ronald; Feldman, Charles

2012-01-01

Macrolide antibiotics possess several, beneficial, secondary properties which complement their primary antimicrobial activity. In addition to high levels of tissue penetration, which may counteract seemingly macrolide-resistant bacterial pathogens, these agents also possess anti-inflammatory properties, unrelated to their primary antimicrobial activity. Macrolides target cells of both the innate and adaptive immune systems, as well as structural cells, and are beneficial in controlling harmful inflammatory responses during acute and chronic bacterial infection. These secondary anti-inflammatory activities of macrolides appear to be particularly effective in attenuating neutrophil-mediated inflammation. This, in turn, may contribute to the usefulness of these agents in the treatment of acute and chronic inflammatory disorders of both microbial and nonmicrobial origin, predominantly of the airways. This paper is focused on the various mechanisms of macrolide-mediated anti-inflammatory activity which target both microbial pathogens and the cells of the innate and adaptive immune systems, with emphasis on their clinical relevance.

Pathogen- and Host-Directed Anti-Inflammatory Activities of Macrolide Antibiotics

PubMed Central

Steel, Helen C.; Theron, Annette J.; Cockeran, Riana; Anderson, Ronald; Feldman, Charles

2012-01-01

Macrolide antibiotics possess several, beneficial, secondary properties which complement their primary antimicrobial activity. In addition to high levels of tissue penetration, which may counteract seemingly macrolide-resistant bacterial pathogens, these agents also possess anti-inflammatory properties, unrelated to their primary antimicrobial activity. Macrolides target cells of both the innate and adaptive immune systems, as well as structural cells, and are beneficial in controlling harmful inflammatory responses during acute and chronic bacterial infection. These secondary anti-inflammatory activities of macrolides appear to be particularly effective in attenuating neutrophil-mediated inflammation. This, in turn, may contribute to the usefulness of these agents in the treatment of acute and chronic inflammatory disorders of both microbial and nonmicrobial origin, predominantly of the airways. This paper is focused on the various mechanisms of macrolide-mediated anti-inflammatory activity which target both microbial pathogens and the cells of the innate and adaptive immune systems, with emphasis on their clinical relevance. PMID:22778497

Construction and performance evaluation of mediator-less microbial fuel cell using carbon nanotubes as an anode material.

PubMed

Roh, Sung-Hee; Kim, Sun-Il

2012-05-01

A microbial fuel cell (MFC) is a device that converts chemical energy to electrical energy using the catalytic reaction of microorganisms. We investigated the performance of mediator-less MFC with carbon nanotubes (CNTs)/graphite felt composite electrodes. The addition of CNTs to a graphite felt electrode increases the specific surface area of the electrode and enhances the charge transfer capability so as to cause considerable improvement of the electrochemical activity for the anode reaction in a MFC. The performance of the MFC using CNTs/graphite felt electrode has been compared against a plain graphite felt electrode based MFC. A CNTs/graphite felt electrode showed as high as 15% increase in the power density (252 mW/m2) compared to graphite felt electrode (214 mW/m2). The CNTs/graphite felt anode therefore offers good prospects for application in MFCs.

Microbial secondary metabolites ameliorate growth, in planta contents and lignification in Withania somnifera (L.) Dunal.

PubMed

Singh, Akanksha; Gupta, Rupali; Srivastava, Madhumita; Gupta, M M; Pandey, Rakesh

2016-04-01

In the present investigation, metabolites of Streptomyces sp. MTN14 and Trichoderma harzianum ThU significantly enhanced biomass yield (3.58 and 3.48 fold respectively) in comparison to the control plants. The secondary metabolites treatments also showed significant augmentation (0.75-2.25 fold) in withanolide A, a plant secondary metabolite. Lignin deposition, total phenolic and flavonoid content in W. somnifera were maximally induced in treatment having T. harzianum metabolites. Also, Trichoderma and Streptomyces metabolites were found much better in invoking in planta contents and antioxidants compared with their live culture treatments. Therefore, identification of new molecular effectors from metabolites of efficient microbes may be used as biopesticide and biofertilizer for commercial production of W. somnifera globally.

Microbial response to space environment, part B

NASA Technical Reports Server (NTRS)

Taylor, G. R.; Chassay, C. E.; Ellis, W. L.; Foster, B. G.; Volz, P. A.; Spizizen, J.; Buecker, H.; Wrenn, R. T.; Simmonds, R. C.; Long, R. A.

1972-01-01

The performance of the microbial response to space environment experiment is considered excellent by all investigators. For most microbial systems, only preliminary survival data are available at this time. None of the available data indicate space flight-mediated changes in cell viability or recovery. One quite important observation has been made at this early date, however. The eggs produced after mice had been infected with N. dubius larvae demonstrated a significant decrease in hatchability when compared to identical ground controls. Except for the fact that the Apollo 16 flight larvae had been on board the command module, treatment of the flown larvae and ground control larvae was the same; neither had been exposed to UV irradiation. The significance and implications of this finding are currently being studied.

Magnesium Isotopic Evidence for Widespread Microbial Dolomite Precipitation in the Geological Record.

NASA Astrophysics Data System (ADS)

Carder, E. A.; Galy, A.; McKenzie, J. A.; Vasconcelos, C.; Elderfield, H.

2005-12-01

The enigma surrounding the `Dolomite Problem' is the relative abundance of dolomite in the geological record versus its very rare occurrence on the surface of the modern Earth despite a particularly favourable modern seawater chemistry. Recent studies of modern dolomite from hypersaline coastal lagoons in Brazil and Pleistocene dolomite from ODP cores collected during ODP Leg 201 on the Peru Margin suggest microbial mediation is an important factor [1]. Indeed, cultures of sulfate-reducing bacteria isolated from the lagoons mediate dolomite precipitation in the laboratory [2, 3]. In this study we report magnesium isotopic analyses of these modern microbial associated dolomites and ancient dolomites of a range of geological ages and environments. The application of stable magnesium isotopes to study dolomite formation and the nature of the processes involved represents a new frontier in isotope geochemistry. Highly accurate determination of the magnesium isotopic composition allows us to distinguish between kinetic and equilibrium isotope fractionation on the basis of the excess of 25Mg. A significant kinetic isotope fractionation is observed in laboratory cultures and surfical microbial mats from the Brazilian lagoons. Older dolomites (<3000 yrs.) taken from cores recovered from the lagoon are much closer to equilibrium. We interpret our data as evidencing an initial microbial mediated nucleation of dolomite that is a kinetic process and a subsequent inorganic addition of dolomite overprinting an equilibrium signature. This is in agreement with a previous major element and crystallographic study of the Brazilian dolomites [1]. The ancient dolomites analysed range in age from Neoproterozoic to Pleistocene and come from diverse geological environments including submarine diagenetic zones, platform carbonates and lagoonal environments. Magnesium isotopic analysis shows evidence of a varying component of kinetic fractionation, smaller than the kinetic end member as typified by the laboratory cultures. The ancient dolomites appear to evidence the same initial kinetic nucleation and subsequent equilibrium growth as the modern. In contrast, hydrothermal dolomite exhibits only equilibrium fractionation. Taken together, our results argue for a strong biological role in magnesium fixation into sedimentary dolomite in both the ancient and modern and suggest microbial processes are important in resolving the `Dolomite Problem'. References [1] Vasconcelos, C. and McKenzie, J.A., (1997), J. Sed. Res., 67, 378-390. [2] Vasconcelos, C., McKenzie, J.A., Bernasconi, S., Grujic, D. and Tien, A.J., (1995), Nature 377, 220-222. [3] Warthmann R., van Lith Y., Vasconcelos C., McKenzie J.A. and Karpoff A.M., (2000), Geology 28, 1091-1094.

Cellular content of biomolecules in sub-seafloor microbial communities

NASA Astrophysics Data System (ADS)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-09-01

Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

A SHORT SEQUENCE IMMEDIATELY UPSTREAM OF THE INTERNAL REPEAT ELEMENTS IS CRITICAL FOR KSHV LANA MEDIATED DNA REPLICATION AND IMPACTS EPISOME PERSISTENCE

PubMed Central

León Vázquez, Erika De; Juillard, Franceline; Rosner, Bernard; Kaye, Kenneth M.

2013-01-01

Kaposi’s sarcoma-associated herpesvirus LANA (1162 residues) mediates episomal persistence of viral genomes during latency. LANA mediates viral DNA replication and segregates episomes to daughter nuclei. A 59 residue deletion immediately upstream of the internal repeat elements rendered LANA highly deficient for DNA replication and modestly deficient for the ability to segregate episomes, while smaller deletions did not. The 59 amino acid deletion reduced LANA episome persistence by ~14-fold, while sequentially smaller deletions resulted in ~3-fold, or no deficiency. Three distinct LANA regions reorganized heterochromatin, one of which contains the deleted sequence, but the deletion did not abolish LANA’s ability to alter chromatin. Therefore, this work identifies a short internal LANA sequence that is critical for DNA replication, has modest effects on episome segregation, and substantially impacts episome persistence; this region may exert its effects through an interacting host cell protein(s). PMID:24314665

Colonic fermentation of polyphenolics from Sea buckthorn (Hippophae rhamnoides) berries: Assessment of effects on microbial diversity by Principal Component Analysis.

PubMed

Attri, Sampan; Sharma, Kavita; Raigond, Pinky; Goel, Gunjan

2018-03-01

The present study investigates the stability of polyphenolic in Sea buckthorn berries juice (SBJ) during different phases of digestion and its effect on colonic microbial diversity. At each stage, the Total polyphenolic content (TPC), Total antioxidant activity (TAA) and polyphenolic profile was determined. A 1.64 and 2.20 folds increase in TPC with 4.88 and 9.61 folds increase in TAA were observed during gastric and small intestine digestion (p<0.05) with the release of quercetin from food matrix. The digestion resulted in deformation of intact crystalline structure as indicated by scanning electron micrographs. The colonic fermentation resulted in an increase in quercetin, caffeic acid with decrease in rutin and chlorogenic acid after 36h of fermentation (p<0.05). The Shannon diversity index (H) of beneficial groups including Lactic acid bacteria (LAB), Bacteroides/Prevotella and Bifidobacteria was increased by 35%, 71% and 17%, respectively (p<0.05). The PCA analysis indicated that the presence and digestion of polyphenolics promote the proliferation of Bacteroides/Prevotella group as well as Lactic acid bacteria and Bifidobacteria. The results suggest that SBJ is good source of prebiotic substrate in terms of the proliferation of beneficial gut microbiota. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial communities in liquid and fiber fractions of food waste digestates are differentially resistant to inhibition by ammonia.

PubMed

Peng, Wei; Lü, Fan; Shao, Liming; He, Pinjing

2015-04-01

The effect of different concentrations of ammonia (1.0-7.0 g/L) during mesophilic anaerobic digestion with fiber or liquid digestate as inoculum was examined. Evolution of microbial community within fiber and liquid digestates was quantitatively assessed by the intact lipid analysis methods and qualitatively by DNA fingerprint methods in order to determine their resistance to ammonia inhibition. The results showed that an increased level of total ammonia nitrogen prolonged the lag phase of fiber digestates while reduced the metabolic rate of liquid digestates. Fiber digestates had 19.6-50.9-fold higher concentrations of phospholipid fatty acids (PLFA) compared to liquid digestates, whereas concentrations of phospholipid ether lipids (PLEL) in the fiber digestates were only 2.91-17.6-fold higher compared to liquid digestates. Although the cell concentration in liquid fraction was far lower than that in the fiber one, the ammonia-resistant ability and the methanization efficiency of the liquid digestate was superior to the fiber digestate. The bacterial profiles were affected more by the type of digestate inoculum compared to the concentration of ammonia. Principal component analysis indicated that the lipids technique was superior to the DNA technique for bacterial quantification but detected less archaeal diversity.

Comparing the responses of rumen ciliate protozoa and bacteria to excess carbohydrate.

PubMed

Teixeira, César R V; Lana, Rogério de Paula; Tao, Junyi; Hackmann, Timothy J

2017-06-01

When given excess carbohydrate, certain microbial species respond by storing energy (synthesizing reserve carbohydrate), but other species respond by dissipating the energy as heat (spilling energy). To determine the importance of these responses in the rumen microbial community, this study quantified the responses of mixed ciliate protozoa vs bacteria to glucose. We hypothesized that ciliates would direct more glucose to synthesis of reserve carbohydrate (and less to energy spilling) than would bacteria. Ciliates and bacteria were isolated from rumen fluid using filtration and centrifugation, resuspended in nitrogen-free buffer to limit growth, and dosed with 5 mM glucose. Compared with bacteria, ciliates consumed glucose >3-fold faster and synthesized reserve carbohydrate 4-fold faster. They incorporated 53% of glucose carbon into reserve carbohydrate-nearly double the value (27%) for bacteria. Energy spilling was not detected for ciliates, as all heat production (104%) was accounted by synthesis of reserve carbohydrate and endogenous metabolism. For bacteria, reserve carbohydrate and endogenous metabolism accounted for only 68% of heat production, and spilling was detected within 11 min of dosing glucose. These results suggest that ciliates alter the course of ruminal carbohydrate metabolism by outcompeting bacteria for excess carbohydrate, maximizing reserve carbohydrate synthesis, and minimizing energy spilling. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Biodegradability and ecological safety assessment of Stenotrophomonas sp. DDT-1 in the DDT-contaminated soil.

PubMed

Fang, Hua; Deng, Yanfei; Ge, Qiqing; Mei, Jiajia; Zhang, Houpu; Wang, Huifang; Yu, Yunlong

2018-04-18

The biodegradability and ecological safety assessment of the previously isolated DDT-degrading bacterial strain Stenotrophomonas sp. DDT-1 were investigated in the DDT-contaminated soil under laboratory and field conditions. Under laboratory conditions, the degradation rates of fresh p,p'-DDT in soil were enhanced by 2.0-3.0-fold with the introduction of the strain DDT-1 compared to those of the control treatments. A similar enhancement in the dissipation of DDTs (p,p'-DDT, p,p'-DDE, p,p'-DDD, and o,p'-DDT) in the aged DDT-contaminated field plot soils resulted from the inoculation with this strain. Meanwhile, the degradation rates of DDTs increased by 2.9-5.5- and 2.8-7.6-fold in the inoculated greenhouse and open field soils, respectively, after field demonstration application of strain DDT-1 preparation. Moreover, no significant differences in the soil enzyme activity, microbial functional diversity, and bacterial community structure were observed between the inoculated and un-inoculated field soils, but several soil microbial genera exhibited some fluctuations in abundance. It is concluded that strain DDT-1 could accelerate the removal of DDTs residues in field soils, and furthermore, its inoculation was ecologically safe. Copyright © 2018 Elsevier Inc. All rights reserved.

Post-fire interactions between soil water repellency, soil fertility and plant growth in soil collected from a burned piñon-juniper woodland

USGS Publications Warehouse

Fernelius, Kaitlynn J.; Madsen, Matthew D.; Hopkins, Bryan G.; Bansal, Sheel; Anderson, Val J.; Eggett, Dennis L.; Roundy, Bruce A.

2017-01-01

Woody plant encroachment can increase nutrient resources in the plant-mound zone. After a fire, this zone is often found to be water repellent. This study aimed to understand the effects of post-fire water repellency on soil water and inorganic nitrogen and their effects on plant growth of the introduced annual Bromus tectorum and native bunchgrass Pseudoroegneria spicata. Plots centered on burned Juniperus osteosperma trees were either left untreated or treated with surfactant to ameliorate water repellency. After two years, we excavated soil from the untreated and treated plots and placed it in zerotension lysimeter pots. In the greenhouse, half of the pots received an additional surfactant treatment. Pots were seeded separately with B. tectorum or P. spicata. Untreated soils had high runoff, decreased soilwater content, and elevated NO3eN in comparison to surfactant treated soils. The two plant species typically responded similar to the treatments. Above-ground biomass and microbial activity (estimated through soil CO2 gas emissions) was 16.8-fold and 9.5-fold higher in the surfactant-treated soils than repellent soils, respectably. This study demonstrates that water repellency can influence site recovery by decreasing soil water content, promoting inorganic N retention, and impairing plant growth and microbial activity.

Carbon nanotube dispersed conductive network for microbial fuel cells

NASA Astrophysics Data System (ADS)

Matsumoto, S.; Yamanaka, K.; Ogikubo, H.; Akasaka, H.; Ohtake, N.

2014-08-01

Microbial fuel cells (MFCs) are promising devices for capturing biomass energy. Although they have recently attracted considerable attention, their power densities are too low for practical use. Increasing their electrode surface area is a key factor for improving the performance of MFC. Carbon nanotubes (CNTs), which have excellent electrical conductivity and extremely high specific surface area, are promising materials for electrodes. However, CNTs are insoluble in aqueous solution because of their strong intertube van der Waals interactions, which make practical use of CNTs difficult. In this study, we revealed that CNTs have a strong interaction with Saccharomyces cerevisiae cells. CNTs attach to the cells and are dispersed in a mixture of water and S. cerevisiae, forming a three-dimensional CNT conductive network. Compared with a conventional two-dimensional electrode, such as carbon paper, the three-dimensional conductive network has a much larger surface area. By applying this conductive network to MFCs as an anode electrode, power density is increased to 176 μW/cm2, which is approximately 25-fold higher than that in the case without CNTs addition. Maximum current density is also increased to approximately 8-fold higher. These results suggest that three-dimensional CNT conductive network contributes to improve the performance of MFC by increasing surface area.

A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats

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

Beloglazova, Natalia; Brown, Greg; Zimmerman, Matthew D.

Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure ofmore » SSO1404 was solved at 1.6{angstrom} resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.« less

Leaching of Arsenic from Granular Ferric Hydroxide Residuals under Mature Landfill Conditions

PubMed Central

Ghosh, Amlan; Mukiibi, Muhammed; Sáez, A. Eduardo; Ela, Wendell P.

2008-01-01

Most arsenic bearing solid residuals (ABSR) from water treatment will be disposed in non-hazardous landfills. The lack of an appropriate leaching test to predict arsenic mobilization from ABSR creates a need to evaluate the magnitude and mechanisms of arsenic release under landfill conditions. This work studies the leaching of arsenic and iron from a common ABSR, granular ferric hydroxide, in a laboratory-scale column that simulates the biological and physicochemical conditions of a mature, mixed solid waste landfill. The column operated for approximately 900 days and the mode of transport as well as chemical speciation of iron and arsenic changed with column age. Both iron and arsenic were readily mobilized under the anaerobic, reducing conditions. During the early stages of operation, most arsenic and iron leaching (80% and 65%, respectively) was associated with suspended particulate matter and iron was lost proportionately faster than arsenic. In later stages, while the rate of iron leaching declined, the arsenic leaching rate increased greater than 7-fold. The final phase was characterized by dissolved species leaching. Future work on the development of standard batch leaching tests should take into account the dominant mobilization mechanisms identified in this work: solid associated transport, reductive sorbent dissolution, and microbially mediated arsenic reduction. PMID:17051802

Leaching of arsenic from granular ferric hydroxide residuals under mature landfill conditions.

PubMed

Ghosh, Amlan; Mukiibi, Muhammed; Sáez, A Eduardo; Ela, Wendell P

2006-10-01

Most arsenic bearing solid residuals (ABSR) from water treatment will be disposed in nonhazardous landfills. The lack of an appropriate leaching test to predict arsenic mobilization from ABSR creates a need to evaluate the magnitude and mechanisms of arsenic release under landfill conditions. This work studies the leaching of arsenic and iron from a common ABSR, granular ferric hydroxide, in a laboratory-scale column that simulates the biological and physicochemical conditions of a mature, mixed solid waste landfill. The column operated for approximately 900 days and the mode of transport as well as chemical speciation of iron and arsenic changed with column age. Both iron and arsenic were readily mobilized under the anaerobic, reducing conditions. During the early stages of operation, most arsenic and iron leaching (80% and 65%, respectively) was associated with suspended particulate matter, and iron was lost proportionately faster than arsenic. In later stages, while the rate of iron leaching declined, the arsenic leaching rate increased greater than 7-fold. The final phase was characterized by dissolved species leaching. Future work on the development of standard batch leaching tests should take into account the dominant mobilization mechanisms identified in this work: solid associated transport, reductive sorbent dissolution, and microbially mediated arsenic reduction.

Bacterial Cell Surface Adsorption of Rare Earth Elements

NASA Astrophysics Data System (ADS)

Jiao, Y.; Park, D.; Reed, D.; Fujita, Y.; Yung, M.; Anderko, A.; Eslamimanesh, A.

2015-12-01

Rare earth elements (REE) play a critical role in many emerging clean energy technologies, including high-power magnets, wind turbines, solar panels, hybrid/electric vehicle batteries and lamp phosphors. In order to sustain demand for such technologies given current domestic REE shortages, there is a need to develop new approaches for ore processing/refining and recycling of REE-containing materials. To this end, we have developed a microbially-mediated bioadsorption strategy with application towards enrichment of REE from complex mixtures. Specifically, the bacterium Caulobacter crescentus was genetically engineered to display lanthanide binding tags (LBTs), short peptides that possess high affinity and specificity for rare earth elements, on its cell surface S-layer protein. Under optimal conditions, LBT-displayed cells adsorbed greater than 5-fold more REE than control cells lacking LBTs. Competition binding experiments with a selection of REEs demonstrated that our engineered cells could facilitate separation of light- from heavy- REE. Importantly, binding of REE onto our engineered strains was much more favorable compared to non-REE metals. Finally, REE bound to the cell surface could be stripped off using citrate, providing an effective and non-toxic REE recovery method. Together, this data highlights the potential of our approach for selective REE enrichment from REE containing mixtures.

Bacterial expansins and related proteins from the world of microbes

DOE PAGES

Georgelis, Nikolaos; Nikolaidis, Nikolas; Cosgrove, Daniel J.

2015-04-02

The discovery of microbial expansins emerged from studies of the mechanism of plant cell growth and the molecular basis of plant cell wall extensibility. Expansins are wall-loosening proteins that are universal in the plant kingdom and are also found in a small set of phylogenetically diverse bacteria, fungi, and other organisms, most of which colonize plant surfaces. They loosen plant cell walls without detectable lytic activity. Bacterial expansins have attracted considerable attention recently for their potential use in cellulosic biomass conversion for biofuel production, as a means to disaggregate cellulosic structures by nonlytic means (“amorphogenesis”). Evolutionary analysis indicates that microbialmore » expansins originated by multiple horizontal gene transfers from plants. Crystallographic analysis of BsEXLX1, the expansin from Bacillus subtilis, shows that microbial expansins consist of two tightly packed domains: the N-terminal domain D1 has a double-ψ β-barrel fold similar to glycosyl hydrolase family-45 enzymes but lacks catalytic residues usually required for hydrolysis; the C-terminal domain D2 has a unique β-sandwich fold with three co-linear aromatic residues that bind β-1,4-glucans by hydrophobic interactions. Genetic deletion of expansin in Bacillus and Clavibacter cripples their ability to colonize plant tissues. In this paper, we assess reports that expansin addition enhances cellulose breakdown by cellulase and compare expansins with distantly related proteins named swollenin, cerato-platanin, and loosenin. Finally, we end in a speculative vein about the biological roles of microbial expansins and their potential applications. Advances in this field will be aided by a deeper understanding of how these proteins modify cellulosic structures.« less

Selective whole genome amplification for resequencing target microbial species from complex natural samples.

PubMed

Leichty, Aaron R; Brisson, Dustin

2014-10-01

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with <6.7-fold amplification of the background. SWGA-treated genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

Microbial response to different phytoplankton-derived dissolved organic matter sources in the Ross Sea, Antarctica

NASA Astrophysics Data System (ADS)

Sipler, R. E.; Spackeen, J.; McQuaid, J.; Bertrand, E. M.; Roberts, Q. N.; Baer, S. E.; Hutchins, D. A.; Allen, A. E.; Bronk, D. A.

2016-02-01

Western Antarctic shelves are highly productive regions that play an important role in global carbon and nitrogen cycles, specifically serving as a critical sink for carbon dioxide. Fixed carbon is stored within the phytoplankton cell as particulate organic matter or released into the surrounding water as dissolved organic matter (DOM). These phytoplankton-derived sources of organic matter support higher trophic levels as well as heterotrophic bacterial growth and respiration. The composition of the phytoplankton-derived organic matter is a function of the taxa as well as the environmental conditions under which it is produced. Phytoplankton community composition within western Antarctic Seas changes throughout Austral spring and summer with early production dominated by ice algae, switching to pelagic diatoms and flagellates later in the season. The goal of this study was to compare the response of Ross Sea microbial communities to DOM produced by ice algae or late season diatoms, specifically recent isolates of Pseudo nitzschia obtained from the Ross Sea. During 5-day bioassay studies, exudates from a natural ice algal community and from Pseudo nitzschia sp. isolates were added to natural microbial communities collected from two different Ross Sea locations, an ice-edge and an ice-covered site. The bacterial response to the DOM additions was greatest in the ice-covered community with a 5 and 3-fold higher bacterial abundance in the ice algae DOM and Pseudo nitzschia DOM treatments, respectively, relative to the control. The ice edge bacterial community responded similarly to both sources with a 2-fold increase in bacterial abundance compared to the control. Unlike the bacterial response, there was little difference in chlorophyll a concentrations between treatments, indicating that phytoplankton growth was not stimulated or inhibited by our additions.

Bacterial and fungal components in house dust of farm children, Rudolf Steiner school children and reference children--the PARSIFAL Study.

PubMed

Schram, D; Doekes, G; Boeve, M; Douwes, J; Riedler, J; Ublagger, E; von Mutius, E; Budde, J; Pershagen, G; Nyberg, F; Alm, J; Braun-Fahrländer, C; Waser, M; Brunekreef, B

2005-05-01

Growing up on a farm and an anthroposophic lifestyle are associated with a lower prevalence of allergic diseases in childhood. It has been suggested that the enhanced exposure to endotoxin is an important protective factor of farm environments. Little is known about exposure to other microbial components on farms and exposure in anthroposophic families. To assess the levels and determinants of bacterial endotoxin, mould beta(1,3)-glucans and fungal extracellular polysaccharides (EPS) in house dust of farm children, Steiner school children and reference children. Mattress and living room dust was collected in the homes of 229 farm children, 122 Steiner children and 60 and 67 of their respective reference children in five European countries. Stable dust was collected as well. All samples were analysed in one central laboratory. Determinants were assessed by questionnaire. Levels of endotoxin, EPS and glucans per gram of house dust in farm homes were 1.2- to 3.2-fold higher than levels in reference homes. For Steiner children, 1.1- to 1.6-fold higher levels were observed compared with their reference children. These differences were consistently found across countries, although mean levels varied considerably. Differences between groups and between countries were also significant after adjustment for home and family characteristics. Farm children are not only consistently exposed to higher levels of endotoxin, but also to higher levels of mould components. Steiner school children may also be exposed to higher levels of microbial agents, but differences with reference children are much less pronounced than for farm children. Further analyses are, however, required to assess the association between exposure to these various microbial agents and allergic and airway diseases in the PARSIFAL population.

Cation-limited kinetic model for microbial extracellular electron transport via an outer membrane cytochrome C complex

PubMed Central

Okamoto, Akihiro; Tokunou, Yoshihide; Saito, Junki

2016-01-01

Outer-membrane c-type cytochrome (OM c-Cyt) complexes in several genera of iron-reducing bacteria, such as Shewanella and Geobacter, are capable of transporting electrons from the cell interior to extracellular solids as a terminal step of anaerobic respiration. The kinetics of this electron transport has implications for controlling the rate of microbial electron transport during bioenergy or biochemical production, iron corrosion, and natural mineral cycling. Herein, we review the findings from in-vivo and in-vitro studies examining electron transport kinetics through single OM c-Cyt complexes in Shewanella oneidensis MR-1. In-vitro electron flux via a purified OM c-Cyt complex, comprised of MtrA, B, and C proteins from S. oneidensis MR-1, embedded in a proteoliposome system is reported to be 10- to 100-fold faster compared with in-vivo estimates based on measurements of electron flux per cell and OM c-Cyts density. As the proteoliposome system is estimated to have 10-fold higher cation flux via potassium channels than electrons, we speculate that the slower rate of electron-coupled cation transport across the OM is responsible for the significantly lower electron transport rate that is observed in-vivo. As most studies to date have primarily focused on the energetics or kinetics of interheme electron hopping in OM c-Cyts in this microbial electron transport mechanism, the proposed model involving cation transport provides new insight into the rate detemining step of EET, as well as the role of self-secreted flavin molecules bound to OM c-Cyt and proton management for energy conservation and production in S. oneidensis MR-1. PMID:27924259

Resistance to lambda-cyhalothrin in Spanish field populations of Ceratitis capitata and metabolic resistance mediated by P450 in a resistant strain.

PubMed

Arouri, Rabeh; Le Goff, Gaelle; Hemden, Hiethem; Navarro-Llopis, Vicente; M'saad, Mariem; Castañera, Pedro; Feyereisen, René; Hernández-Crespo, Pedro; Ortego, Félix

2015-09-01

The withdrawal of malathion in the European Union in 2009 resulted in a large increase in lambda-cyhalothrin applications for the control of the Mediterranean fruit fly, Ceratitis capitata, in Spanish citrus crops. Spanish field populations of C. capitata have developed resistance to lambda-cyhalothrin (6-14-fold), achieving LC50 values (129-287 ppm) higher than the recommended concentration for field treatments (125 ppm). These results contrast with the high susceptibility to lambda-cyhalothrin found in three Tunisian field populations. We have studied the mechanism of resistance in the laboratory-selected resistant strain W-1Kλ (205-fold resistance). Bioassays with synergists showed that resistance was almost completely suppressed by the P450 inhibitor PBO. The study of the expression of 53 P450 genes belonging to the CYP4, CYP6, CYP9 and CYP12 families in C. capitata revealed that CYP6A51 was overexpressed (13-18-fold) in the resistant strain. The W-1Kλ strain also showed high levels of cross-resistance to etofenprox (240-fold) and deltamethrin (150-fold). Field-evolved resistance to lambda-cyhalothrin has been found in C. capitata. Metabolic resistance mediated by P450 appears to be the main resistance mechanism in the resistant strain W-1Kλ. The levels of cross-resistance found may compromise the effectiveness of other pyrethroids for the control of this species. © 2014 Society of Chemical Industry. © 2014 Society of Chemical Industry.

Bacterial Community Analysis, New Exoelectrogen Isolation and Enhanced Performance of Microbial Electrochemical Systems Using Nano-Decorated Anodes

NASA Astrophysics Data System (ADS)

Xu, Shoutao

Microbial electrochemical systems (MESs) have attracted much research attention in recent years due to their promising applications in renewable energy generation, bioremediation, and wastewater treatment. In a MES, microorganisms interact with electrodes via electrons, catalyzing oxidation and reduction reactions at the anode and the cathode. The bacterial community of a high power mixed consortium MESs (maximum power density is 6.5W/m2) was analyzed by using denature gradient gel electrophoresis (DGGE) and 16S DNA clone library methods. The bacterial DGGE profiles were relatively complex (more than 10 bands) but only three brightly dominant bands in DGGE results. These results indicated there are three dominant bacterial species in mixed consortium MFCs. The 16S DNA clone library method results revealed that the predominant bacterial species in mixed culture is Geobacter sp (66%), Arcobacter sp and Citrobacter sp. These three bacterial species reached to 88% of total bacterial species. This result is consistent with the DGGE result which showed that three bright bands represented three dominant bacterial species. Exoelectrogenic bacterial strain SX-1 was isolated from a mediator-less microbial fuel cell by conventional plating techniques with ferric citrate as electron acceptor under anaerobic conditions. Phylogenetic analysis of the 16S rDNA sequence revealed that it was related to the members of Citrobacter genus with Citrobacter sp. sdy-48 being the most closely related species. The bacterial strain SX-1 produced electricity from citrate, acetate, glucose, sucrose, glycerol, and lactose in MFCs with the highest current density of 205 mA/m2 generated from citrate. Cyclic voltammetry analysis indicated that membrane associated proteins may play an important role in facilitating electron transfer from the bacteria to the electrode. This is the first study that demonstrates that Citrobacter species can transfer electrons to extracellular electron acceptors. Citrobacter strain SX-1 is capable of generating electricity from a wide range of substrates in MFCs. This finding increases the known diversity of power generating exoelectrogens and provids a new strain to explore the mechanisms of extracellular electron transfer from bacteria to electrode. The wide range of substrate utilization by SX-1 increases the application potential of MFCs in renewable energy generation and waste treatment. Anode properties are critical for the performance of microbial electrolysis cells (MECs). Inexpensive Fe nanoparticle modified graphite disks were used as anodes to preliminarily investigate the effects of nanoparticles on the performance of Shewanella oneidensis MR-1 in MECs. Results demonstrated that average current densities produced with Fe nanoparticle decorated anodes were up to 5.9-fold higher than plain graphite anodes. Whole genome microarray analysis of the gene expression showed that genes encoding biofilm formation were significantly up-regulated as a response to nanoparticle decorated anodes. Increased expression of genes related to nanowires, flavins and c-type cytochromes indicate that enhanced mechanisms of electron transfer to the anode may also have contributed to the observed increases in current density. The majority of the remaining differentially expressed genes were associated with electron transport and anaerobic metabolism demonstrating a systemic response to increased power loads. The carbon nanotube (CNT) is another form of nano materials. Carbon nanotube (CNT) modified graphite disks were used as anodes to investigate the effects of nanostructures on the performance S. oneidensis MR-1 in microbial electrolysis cells (MECs). The current densities produced with CNT decorated anodes were up to 5.6-fold higher than plain graphite anodes. Global transcriptome analysis showed that cytochrome c genes associated with extracellular electron transfer are up-expressed by CNT decorated anodes, which is the leading factor to contribute current increase in CNT decorated anode MECs. The up regulated genes encoded to flavin also contribute to current enhancement in CNT decorated anode MECs.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE PAGES

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; ...

2017-09-28

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

NASA Astrophysics Data System (ADS)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; Zhou, Xiaolu; Wang, Meng; Zhang, Kerou; Wang, Gangsheng

2017-10-01

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195 Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated by Xu et al. (2014). We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC), and mineral-associated organic carbon (MOC). However, our work represents the first step toward a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

PubMed Central

Zeglin, Lydia H.

2015-01-01

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors. PMID:26042102

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

PubMed

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

2016-01-01

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

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

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

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae

PubMed Central

Brennan, Timothy C. R.; Williams, Thomas C.; Schulz, Benjamin L.; Palfreyman, Robin W.; Nielsen, Lars K.

2015-01-01

Monoterpenes are liquid hydrocarbons with applications ranging from flavor and fragrance to replacement jet fuel. Their toxicity, however, presents a major challenge for microbial synthesis. Here we evolved limonene-tolerant Saccharomyces cerevisiae strains and sequenced six strains across the 200-generation evolutionary time course. Mutations were found in the tricalbin proteins Tcb2p and Tcb3p. Genomic reconstruction in the parent strain showed that truncation of a single protein (tTcb3p1-989), but not its complete deletion, was sufficient to recover the evolved phenotype improving limonene fitness 9-fold. tTcb3p1-989 increased tolerance toward two other monoterpenes (β-pinene and myrcene) 11- and 8-fold, respectively, and tolerance toward the biojet fuel blend AMJ-700t (10% cymene, 50% limonene, 40% farnesene) 4-fold. tTcb3p1-989 is the first example of successful engineering of phase tolerance and creates opportunities for production of the highly toxic C10 alkenes in yeast. PMID:25746998

A Constant Rate of Spontaneous Mutation in DNA-Based Microbes

NASA Astrophysics Data System (ADS)

Drake, John W.

1991-08-01

In terms of evolution and fitness, the most significant spontaneous mutation rate is likely to be that for the entire genome (or its nonfrivolous fraction). Information is now available to calculate this rate for several DNA-based haploid microbes, including bacteriophages with single- or double-stranded DNA, a bacterium, a yeast, and a filamentous fungus. Their genome sizes vary by ≈6500-fold. Their average mutation rates per base pair vary by ≈16,000-fold, whereas their mutation rates per genome vary by only ≈2.5-fold, apparently randomly, around a mean value of 0.0033 per DNA replication. The average mutation rate per base pair is inversely proportional to genome size. Therefore, a nearly invariant microbial mutation rate appears to have evolved. Because this rate is uniform in such diverse organisms, it is likely to be determined by deep general forces, perhaps by a balance between the usually deleterious effects of mutation and the physiological costs of further reducing mutation rates.

Sortase A-mediated crosslinked short-chain dehydrogenases/reductases as novel biocatalysts with improved thermostability and catalytic efficiency.

PubMed

Li, Kunpeng; Zhang, Rongzhen; Xu, Yan; Wu, Zhimeng; Li, Jing; Zhou, Xiaotian; Jiang, Jiawei; Liu, Haiyan; Xiao, Rong

2017-06-08

(S)-carbonyl reductase II (SCRII) from Candida parapsilosis is a short-chain alcohol dehydrogenase/reductase. It catalyses the conversion of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol with low efficiency. Sortase was reported as a molecular "stapler" for site-specific protein conjugation to strengthen or add protein functionality. Here, we describe Staphylococcus aureus sortase A-mediated crosslinking of SCRII to produce stable catalysts for efficient biotransformation. Via a native N-terminal glycine and an added GGGGSLPETGG peptide at C-terminus of SCRII, SCRII subunits were conjugated by sortase A to form crosslinked SCRII, mainly dimers and trimers. The crosslinked SCRII showed over 6-fold and 4-fold increases, respectively, in activity and k cat /K m values toward 2-hydroxyacetophenone compared with wild-type SCRII. Moreover, crosslinked SCRII was much more thermostable with its denaturation temperature (T m ) increased to 60 °C. Biotransformation result showed that crosslinked SCRII gave a product optical purity of 100% and a yield of >99.9% within 3 h, a 16-fold decrease in transformation duration with respect to Escherichia coli/pET-SCRII. Sortase A-catalysed ligation also obviously improved T m s and product yields of eight other short-chain alcohol dehydrogenases/reductases. This work demonstrates a generic technology to improve enzyme function and thermostability through sortase A-mediated crosslinking of oxidoreductases.

Characterization and mediation of microbial deterioration of concrete bridge structures.

DOT National Transportation Integrated Search

2013-04-01

Samples obtained from deteriorated bridge structures in Texas were cultured in growth medium containing thiosulfate as an energy source and investigated for acid production, type of acid produced by microbes and the bio-deterioration of concrete cyli...

Faculty Use of Culturally Mediated Instruction in a Community College Academic Enrichment Program

ERIC Educational Resources Information Center

Lacey, Charna L.

2009-01-01

The purpose of this study was to examine faculty use of Culturally Mediated Instructional (CMI) practices in a community college-based academic enrichment program. The intent of the study was two-fold: (a) to search for evidence that instructional practices were reflective of Hollins' (1996) theory of CMI, and (b) to explore faculty perceptions of…

Microbial Contamination of Ice Machines Is Mediated by Activated Charcoal Filtration Systems in a City Hospital.

PubMed

Yorioka, Katsuhiro; Oie, Shigeharu; Hayashi, Koji; Kimoto, Hiroo; Furukawa, Hiroyuki

2016-06-01

Although microbial contamination of ice machines has been reported, no previous study has addressed microbial contamination of ice produced by machines equipped with activated charcoal (AC) filters in hospitals. The aim of this study was to provide clinical data for evaluating AC filters to prevent microbial contamination of ice. We compared microbial contamination in ice samples produced by machines with (n = 20) and without an AC filter (n = 40) in Shunan City Shinnanyo Municipal Hospital. All samples from the ice machine equipped with an AC filter contained 10-116 CFUs/g of glucose nonfermenting gram-negative bacteria such as Pseudomonas aeruginosa and Chryseobacterium meningosepticum. No microorganisms were detected in samples from ice machines without AC filters. After the AC filter was removed from the ice machine that tested positive for Gram-negative bacteria, the ice was resampled (n = 20). Analysis found no contaminants. Ice machines equipped with AC filters pose a serious risk factor for ice contamination. New filter-use guidelines and regulations on bacterial detection limits to prevent contamination of ice in healthcare facilities are necessary.

Assessing the impact of nano- and micro-scale zerovalent iron particles on soil microbial activities: particle reactivity interferes with assay conditions and interpretation of genuine microbial effects.

PubMed

Cullen, Laurence G; Tilston, Emma L; Mitchell, Geoff R; Collins, Chris D; Shaw, Liz J

2011-03-01

The effects of nano-scale and micro-scale zerovalent iron (nZVI and mZVI) particles on general (dehydrogenase and hydrolase) and specific (ammonia oxidation potential, AOP) activities mediated by the microbial community in an uncontaminated soil were examined. nZVI (diameter 12.5 nm; 10 mg g⁻¹ soil) apparently inhibited AOP and nZVI and mZVI apparently stimulated dehydrogenase activity but had minimal influence on hydrolase activity. Sterile experiments revealed that the apparent inhibition of AOP could not be interpreted as such due to the confounding action of the particles, whereas, the nZVI-enhanced dehydrogenase activity could represent the genuine response of a stimulated microbial population or an artifact of ZVI reactivity. Overall, there was no evidence for negative effects of nZVI or mZVI on the processes studied. When examining the impact of redox active particles such as ZVI on microbial oxidation-reduction reactions, potential confounding effects of the test particles on assay conditions should be considered. Copyright © 2010 Elsevier Ltd. All rights reserved.

Phytoremediation of trichloroethene (TCE) using cottonwood trees

USGS Publications Warehouse

Jones, S.A.; Lee, R.W.; Kuniansky, E.L.; Leeson, Andrea; Alleman, Bruce C.

1999-01-01

Phytoremediation uses the natural ability of plants to degrade contaminants in ground water. A field demonstration designed to remediate aerobic shallow ground water that contains trichloroethene began in April 1996 with the planting of cottonwood trees over an approximately 0.2-hectare area at the Naval Air Station, Fort Worth, Tx. Ground water was sampled in July 1997, November 1997, February 1998, and June 1998. Analyses from samples indicate that tree roots have the potential to create anaerobic conditions in the ground water that will facilitate degradation of trichloroethene by microbially mediated reductive dichlorination. Dissolved oxygen concentrations, which varied across the site, were smallest near a mature cottonwood tree (about-20 years old) 60 meters southwest of the cottonwood plantings. Reduction of dissolved oxygen is the primary microbially mediated reaction occurring in the ground water beneath the planted trees, whereas near the mature cottonwood tree, data indicate that methanogenesis is the most probable reaction occurring. Reductive dichlorination either is not occurring or is not a primary process away from the mature tree. On the basis of isotopic analyses of carbon-13 at locations away from the mature tree, trichloroethene concentration is controlled by volatilization.Phytoremediation uses the natural ability of plants to degrade contaminants in ground water. A field demonstration designed to remediate aerobic shallow ground water that contains trichloroethene began in April 1996 with the planting of cottonwood trees over an approximately 0.2-hectare area at the Naval Air Station, Fort Worth, Tx. Ground water was sampled in July 1997, November 1997, February 1998, and June 1998. Analyses from samples indicate that tree roots have the potential to create anaerobic conditions in the ground water that will facilitate degradation of trichloroethene by microbially mediated reductive dichlorination. Dissolved oxygen concentrations, which varied across the site, were smallest near a mature cottonwood tree (about-20 years old) 60 meters southwest of the cottonwood plantings. Reduction of dissolved oxygen is the primary microbially mediated reaction occurring in the ground water beneath the planted trees, whereas near the mature cottonwood tree, data indicate that methanogenesis is the most probable reaction occurring. Reductive dichlorination either is not occurring or is not a primary process away from the mature tree. On the basis of isotopic analyses of carbon-13 at locations away from the mature tree, trichloroethene concentration is controlled by volatilization.

Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques (Macaca mulatta)

PubMed Central

Beisner, Brianne; Guan, Jiahui; Vandeleest, Jessica; Fushing, Hsieh; Atwill, Edward; McCowan, Brenda

2018-01-01

In group-living animals, heterogeneity in individuals’ social connections may mediate the sharing of microbial infectious agents. In this regard, the genetic relatedness of individuals’ commensal gut bacterium Escherichia coli may be ideal to assess the potential for pathogen transmission through animal social networks. Here we use microbial phylogenetics and population genetics approaches, as well as host social network reconstruction, to assess evidence for the contact-mediated sharing of E. coli among three groups of captively housed rhesus macaques (Macaca mulatta), at multiple organizational scales. For each group, behavioral data on grooming, huddling, and aggressive interactions collected for a six-week period were used to reconstruct social network communities via the Data Cloud Geometry (DCG) clustering algorithm. Further, an E. coli isolate was biochemically confirmed and genotypically fingerprinted from fecal swabs collected from each macaque. Population genetics approaches revealed that Group Membership, in comparison to intrinsic attributes like age, sex, and/or matriline membership of individuals, accounted for the highest proportion of variance in E. coli genotypic similarity. Social network approaches revealed that such sharing was evident at the community-level rather than the dyadic level. Specifically, although we found no links between dyadic E. coli similarity and social contact frequencies, similarity was significantly greater among macaques within the same social network communities compared to those across different communities. Moreover, tests for one of our study-groups confirmed that E. coli isolated from macaque rectal swabs were more genotypically similar to each other than they were to isolates from environmentally deposited feces. In summary, our results suggest that among frequently interacting, spatially constrained macaques with complex social relationships, microbial sharing via fecal-oral, social contact-mediated routes may depend on both individuals’ direct connections and on secondary network pathways that define community structure. They lend support to the hypothesis that social network communities may act as bottlenecks to contain the spread of infectious agents, thereby encouraging disease control strategies to focus on multiple organizational scales. Future directions includeincreasing microbial sampling effort per individual to better-detect dyadic transmission events, and assessments of the co-evolutionary links between sociality, infectious agent risk, and host immune function. PMID:29372120

Active dry Saccharomyces cerevisiae can alleviate the effect of subacute ruminal acidosis in lactating dairy cows.

PubMed

AlZahal, O; Dionissopoulos, L; Laarman, A H; Walker, N; McBride, B W

2014-12-01

The objective of the study was to determine the effect of active dry Saccharomyces cerevisiae (ADSC) supplementation on dry matter intake, milk yield, milk components, ruminal pH, and microbial community during a dietary regimen that leads to subacute ruminal acidosis (SARA). Sixteen multiparous, rumen-cannulated lactating Holstein cows were randomly assigned to 1 of 2 dietary treatments that included ADSC (Biomate; AB Vista, Marlborough, UK; 8 × 10(10) cfu/head per day) or control. During wk 1 to 6, all cows received a high-forage (HF) diet (77:23, forage:concentrate). Cows were then abruptly switched during wk 7 to a high-grain (HG) diet (49:51, forage:concentrate) and remained on the HG until the end of wk 10. Feed intake and milk yields were recorded daily. Ruminal pH was recorded continuously using an indwelling system for 1 to 2 d per week during the pre-experimental phase, and wk 6, 7, and 10. Ruminal digesta samples were collected at the end of the experiment and analyzed for relative change in microbial communities using real-time quantitative PCR. Cows were considered to have SARA if the duration below pH 5.6 was ≥300 min/d. Ruminal pH during wk 6 (HF plateau) was not different across treatments (15 ± 46 min/d at pH <5.6). The dietary regimen successfully induced SARA during wk 7 (transition from HF to HG diet), and ruminal pH (551 ± 46 min/d at pH <5.6) was not different across treatments. However, cows receiving ADSC had an improved ruminal pH (122 ± 57 vs. 321 ± 53 min/d at pH <5.6) during wk 10 (HG plateau) compared with control. Additionally, cows receiving ADSC had a better dry matter intake (23.3 ± 0.66 vs. 21.6 ± 0.61 kg/d) and 4% fat-corrected milk yield (29.6 ± 1.2 vs. 26.5 ± 1.2 kg/d) than control cows during the HG phase (wk 8 to 10). During HG feeding, cows receiving ADSC had greater total volatile fatty acid and propionate concentrations (175 ± 7.5 vs. 154 ± 7.5 and 117 ± 6.1 vs. 94 ± 5.7 mM for ADSC and control, respectively) and lower acetate:propionate ratio (0.26 ± 0.5 vs. 0.36 ± 0.05 for ADSC and control, respectively). Microbial analyses conducted on samples collected during wk 10 showed that cows supplemented with S. cerevisiae had a 9-fold, 2-fold, 6-fold, 1.3-fold, and 8-fold increase in S. cerevisiae, Fibrobacter succinogenes, Anaerovibrio lipolytica, Ruminococcus albus, and anaerobic fungi, respectively, which suggested an increase in cellulolytic microbes within the rumen. Cows supplemented with ADSC had 2.2-fold reduction in Prevotella albensis, which is a gram-negative bacterium predominant during SARA. Prevotella spp. are suggested to be an important source of lipopolysaccharide responsible for inflammation within the rumen. Cows supplemented with ADSC had a 2.3-fold increase in Streptococcus bovis and a 12-fold reduction in Megasphaera elsdenii. The reduction in M. elsdenii may reflect lower concentration of lactic acid within the rumen for ADSC cows. In conclusion, ADSC supplementation to dairy cows was demonstrated to alleviate the condition of SARA caused by abrupt dietary changes from HF to HG, and can potentially improve rumen function, as indicated by greater numbers of cellulolytic microorganisms within the rumen. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Architecture engineering of hierarchically porous chitosan/vacuum-stripped graphene scaffold as bioanode for high performance microbial fuel cell.

PubMed

He, Ziming; Liu, Jing; Qiao, Yan; Li, Chang Ming; Tan, Timothy Thatt Yang

2012-09-12

The bioanode is the defining feature of microbial fuel cell (MFC) technology and often limits its performance. In the current work, we report the engineering of a novel hierarchically porous architecture as an efficient bioanode, consisting of biocompatible chitosan and vacuum-stripped graphene (CHI/VSG). With the hierarchical pores and unique VSG, an optimized bioanode delivered a remarkable maximum power density of 1530 mW m(-2) in a mediator-less MFC, 78 times higher than a carbon cloth anode.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

PubMed Central

Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

2014-01-01

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material. PMID:24705618

Isolation and Characterization of Microbes Mediating Thermodynamically Favorable Coupling of Anaerobic Oxidation of Methane and Metal Reduction

NASA Astrophysics Data System (ADS)

Glass, J. B.; Reed, B. C.; Sarode, N. D.; Kretz, C. B.; Bray, M. S.; DiChristina, T. J.; Stewart, F. J.; Fowle, D. A.; Crowe, S.

2014-12-01

Methane is the third most reduced environmentally relevant electron donor for microbial metabolisms after organic carbon and hydrogen. In anoxic ecosystems, the major sink for methane is anaerobic oxidation of methane (AOM) mediated by syntrophic microbial consortia that couple AOM to reduction of an oxidized electron acceptor to yield free energy. In marine sediments, AOM is generally coupled to reduction of sulfate despite an extremely small amount of free energy yield because sulfate is the most abundant electron acceptor in seawater. While AOM coupled to Fe(III) and Mn(IV) reduction (Fe- and Mn-AOM) is 10-30x more thermodynamically favorable than sulfate-AOM, and geochemical data suggests that it occurs in diverse environments, the microorganisms mediating Fe- and Mn-AOM remain unknown. Lake Matano, Indonesia is an ideal ecosystem to enrich for Fe- and Mn-AOM microbes because its anoxic ferruginous deep waters and sediments contain abundant Fe(III), Mn(IV) and methane, and extremely low sulfate and nitrate. Our research aims to isolate and characterize the microbes mediating Fe- and Mn-AOM from three layers of Lake Matano sediments through serial enrichment cultures in minimal media lacking nitrate and sulfate. 16S rRNA amplicon sequencing of sediment inoculum revealed the presence of the Fe(III)-reducing bacterium Geobacter (5-10% total microbial community in shallow sediment and 35-60% in deeper sediment) as well as 1-2% Euryarchaeota implicated in methane cycling, including ANME-1 and 2d and Methanosarcinales. After 90 days of primary enrichment, all three sediment layers showed high levels of Fe(III) reduction (60-90 μM Fe(II) d-1) in the presence of methane compared to no methane and heat-killed controls. Treatments with added Fe(III) as goethite contained higher abundances of Geobacter than the inoculum (60-80% in all layers), suggesting that Geobacter may be mediating Fe(III) reduction in these enrichments. Quantification of AOM rates is underway, and will be used to estimate the plausibility of metal-AOM as a thermodynamically favorable methane sink in anoxic ecosystems of both the modern and ancient Earth.

Type I diabetes mellitus decreases in vivo macrophage-to-feces reverse cholesterol transport despite increased biliary sterol secretion in mice

PubMed Central

Freark de Boer, Jan; Annema, Wijtske; Schreurs, Marijke; van der Veen, Jelske N.; van der Giet, Markus; Nijstad, Niels; Kuipers, Folkert; Tietge, Uwe J. F.

2012-01-01

Type I diabetes mellitus (T1DM) increases atherosclerotic cardiovascular disease; however, the underlying pathophysiology is still incompletely understood. We investigated whether experimental T1DM impacts HDL-mediated reverse cholesterol transport (RCT). C57BL/6J mice with alloxan-induced T1DM had higher plasma cholesterol levels (P < 0.05), particularly within HDL, and increased hepatic cholesterol content (P < 0.001). T1DM resulted in increased bile flow (2.1-fold; P < 0.05) and biliary secretion of bile acids (BA, 10.5-fold; P < 0.001), phospholipids (4.5-fold; P < 0.001), and cholesterol (5.5-fold; P < 0.05). Hepatic cholesterol synthesis was unaltered, whereas BA synthesis was increased in T1DM (P < 0.001). Mass fecal BA output was significantly higher in T1DM mice (1.5-fold; P < 0.05), fecal neutral sterol excretion did not change due to increased intestinal cholesterol absorption (2.1-fold; P < 0.05). Overall in vivo macrophage-to-feces RCT, using [3H]cholesterol-loaded primary mouse macrophage foam cells, was 20% lower in T1DM (P < 0.05), mainly due to reduced tracer excretion within BA (P < 0.05). In vitro experiments revealed unchanged cholesterol efflux toward T1DM HDL, whereas scavenger receptor class BI-mediated selective uptake from T1DM HDL was lower in vitro and in vivo (HDL kinetic experiments) (P < 0.05), conceivably due to increased glycation of HDL-associated proteins (+65%, P < 0.01). In summary, despite higher mass biliary sterol secretion T1DM impairs macrophage-to-feces RCT, mainly by decreasing hepatic selective uptake, a mechanism conceivably contributing to increased cardiovascular disease in T1DM. PMID:22180634

M1 RNA is important for the in-cell solubility of its cognate C5 protein: Implications for RNA-mediated protein folding

PubMed Central

Son, Ahyun; Choi, Seong Il; Han, Gyoonhee; Seong, Baik L

2015-01-01

It is one of the fundamental questions in biology how proteins efficiently fold into their native conformations despite off-pathway events such as misfolding and aggregation in living cells. Although molecular chaperones have been known to assist the de novo folding of certain types of proteins, the role of a binding partner (or a ligand) in the folding and in-cell solubility of its interacting protein still remains poorly defined. RNase P is responsible for the maturation of tRNAs as adaptor molecules of amino acids in ribosomal protein synthesis. The RNase P from Escherichia coli, composed of M1 RNA and C5 protein, is a prototypical ribozyme in which the RNA subunit contains the catalytic activity. Using E. coli RNase P, we demonstrate that M1 RNA plays a pivotal role in the in-cell solubility of C5 protein both in vitro and in vivo. Mutations in either the C5 protein or M1 RNA that affect their interactions significantly abolished the folding of C5 protein. Moreover, we find that M1 RNA provides quality insurance of interacting C5 protein, either by promoting the degradation of C5 mutants in the presence of functional proteolytic machinery, or by abolishing their solubility if the machinery is non-functional. Our results describe a crucial role of M1 RNA in the folding, in-cell solubility, and, consequently, the proteostasis of the client C5 protein, giving new insight into the biological role of RNAs as chaperones and mediators that ensure the quality of interacting proteins. PMID:26517763

Minichaperone (GroEL191-345) mediated folding of MalZ proceeds by binding and release of native and functional intermediates.

PubMed

Jain, Neha; Knowles, Timothy J; Lund, Peter A; Chaudhuri, Tapan K

2018-06-02

The isolated apical domain of GroEL consisting of residues 191-345 (known as "minichaperone") binds and assists the folding of a wide variety of client proteins without GroES and ATP, but the mechanism of its action is still unknown. In order to probe into the matter, we have examined minichaperone-mediated folding of a large aggregation prone protein Maltodextrin-glucosidase (MalZ). The key objective was to identify whether MalZ exists free in solution, or remains bound to, or cycling on and off the minichaperone during the refolding process. When GroES was introduced during refolding process, production of the native MalZ was inhibited. We also observed the same findings with a trap mutant of GroEL, which stably captures a predominantly non-native MalZ released from minichaperone during refolding process, but does not release it. Tryptophan and ANS fluorescence measurements indicated that refolded MalZ has the same structure as the native MalZ, but that its structure when bound to minichaperone is different. Surface plasmon resonance measurements provide an estimate for the equilibrium dissociation constant KD for the MalZ-minichaperone complex of 0.21 ± 0.04 μM, which are significantly higher than for most GroEL clients. This showed that minichaperone interacts loosely with MalZ to allow the protein to change its conformation and fold while bound during the refolding process. These observations suggest that the minichaperone works by carrying out repeated cycles of binding aggregation-prone protein MalZ in a relatively compact conformation and in a partially folded but active state, and releasing them to attempt to fold in solution. Copyright © 2018 Elsevier B.V. All rights reserved.

A prospective microbiome-wide association study of food sensitization and food allergy in early childhood.

PubMed

Savage, Jessica H; Lee-Sarwar, Kathleen A; Sordillo, Joanne; Bunyavanich, Supinda; Zhou, Yanjiao; O'Connor, George; Sandel, Megan; Bacharier, Leonard B; Zeiger, Robert; Sodergren, Erica; Weinstock, George M; Gold, Diane R; Weiss, Scott T; Litonjua, Augusto A

2018-01-01

Alterations in the intestinal microbiome are prospectively associated with the development of asthma; less is known regarding the role of microbiome alterations in food allergy development. Intestinal microbiome samples were collected at age 3-6 months in children participating in the follow-up phase of an interventional trial of high-dose vitamin D given during pregnancy. At age 3, sensitization to foods (milk, egg, peanut, soy, wheat, walnut) was assessed. Food allergy was defined as caretaker report of healthcare provider-diagnosed allergy to the above foods prior to age 3 with evidence of IgE sensitization. Analysis was performed using Phyloseq and DESeq2; P-values were adjusted for multiple comparisons. Complete data were available for 225 children; there were 87 cases of food sensitization and 14 cases of food allergy. Microbial diversity measures did not differ between food sensitization and food allergy cases and controls. The genera Haemophilus (log 2 fold change -2.15, P=.003), Dialister (log 2 fold change -2.22, P=.009), Dorea (log 2 fold change -1.65, P=.02), and Clostridium (log 2 fold change -1.47, P=.002) were underrepresented among subjects with food sensitization. The genera Citrobacter (log 2 fold change -3.41, P=.03), Oscillospira (log 2 fold change -2.80, P=.03), Lactococcus (log 2 fold change -3.19, P=.05), and Dorea (log 2 fold change -3.00, P=.05) were underrepresented among subjects with food allergy. The temporal association between bacterial colonization and food sensitization and allergy suggests that the microbiome may have a causal role in the development of food allergy. Our findings have therapeutic implications for the prevention and treatment of food allergy. © 2017 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.

Folding of the four-helix bundle FF domain from a compact on-pathway intermediate state is governed predominantly by water motion.

PubMed

Sekhar, Ashok; Vallurupalli, Pramodh; Kay, Lewis E

2012-11-20

Friction plays a critical role in protein folding. Frictional forces originating from random solvent and protein fluctuations both retard motion along the folding pathway and activate protein molecules to cross free energy barriers. Studies of friction thus may provide insights into the driving forces underlying protein conformational dynamics. However, the molecular origin of friction in protein folding remains poorly understood because, with the exception of the native conformer, there generally is little detailed structural information on the other states participating in the folding process. Here, we study the folding of the four-helix bundle FF domain that proceeds via a transiently formed, sparsely populated compact on-pathway folding intermediate whose structure was elucidated previously. Because the intermediate is stabilized by both native and nonnative interactions, friction in the folding transition between intermediate and folded states is expected to arise from intrachain reorganization in the protein. However, the viscosity dependencies of rates of folding from or unfolding to the intermediate, as established by relaxation dispersion NMR spectroscopy, clearly indicate that contributions from internal friction are small relative to those from solvent, so solvent frictional forces drive the folding process. Our results emphasize the importance of solvent dynamics in mediating the interconversion between protein configurations, even those that are highly compact, and in equilibrium folding/unfolding fluctuations in general.

Humic acids enhance the microbially mediated release of sedimentary ferrous iron.

PubMed

Chang, Chun-Han; Wei, Chia-Cheng; Lin, Li-Hung; Tu, Tzu-Hsuan; Liao, Vivian Hsiu-Chuan

2016-03-01

Iron (Fe) is an essential element for many organisms, but high concentrations of iron can be toxic. The complex relation between iron, arsenic (As), bacteria, and organic matter in sediments and groundwater is still an issue of environmental concern. The present study addresses the effects of humic acids and microorganisms on the mobilization of iron in sediments from an arsenic-affected area, and the microbial diversity was analyzed. The results showed that the addition of 50, 100, and 500 mg/L humic acids enhanced ferrous iron (Fe(II)) release in a time-dependent and dose-dependent fashion under anaerobic conditions. A significant increase in the soluble Fe(II) concentrations occurred in the aqueous phases of the samples during the first 2 weeks, and aqueous Fe(II) reached its maximum concentrations after 8 weeks at the following Fe(II) concentrations: 28.95 ± 1.16 mg/L (original non-sterilized sediments), 32.50 ± 0.71 mg/L (50 mg/L humic acid-amended, non-sterilized sediments), 37.50 ± 1.85 mg/L (100 mg/L humic acid-amended, non-sterilized sediments), and 39.00 ± 0.43 mg/L (500 mg/L humic acid-amended, non-sterilized sediments). These results suggest that humic acids can further enhance the microbially mediated release of sedimentary iron under anaerobic conditions. By contrast, very insignificant amounts of iron release were observed from sterilized sediments (the abiotic controls), even with the supplementation of humic acids under anaerobic incubation. In addition, the As(III) release was increased from 50 ± 10 μg/L (original non-sterilized sediments) to 110 ± 45 μg/L (100 mg/L humic acid-amended, non-sterilized sediments) after 8 weeks of anaerobic incubation. Furthermore, a microbial community analysis indicated that the predominant class was changed from Alphaproteobacteria to Deltaproteobacteria, and clearly increased populations of Geobacter sp., Paludibacter sp., and Methylophaga sp. were found after adding humic acids along with the increased release of iron and arsenic. Our findings provide evidence that humic acids can enhance the microbially mediated release of sedimentary ferrous iron in an arsenic-affected area. It is thus suggested that the control of anthropogenic humic acid use and entry into the environment is important for preventing the subsequent iron contamination in groundwater.

The Est3 protein associates with yeast telomerase through an OB-fold domain

PubMed Central

Lee, Jaesung S.; Mandell, Edward K.; Tucey, Timothy M.; Morris, Danna K.; Victoria, Lundblad

2009-01-01

The Est3 protein is a small regulatory subunit of yeast telomerase which is dispensable for enzyme catalysis but essential for telomere replication in vivo. Using structure prediction combined with in vivo characterization, we show here that Est3 consists of a predicted OB (oligo-saccharide/oligo-nucleotide binding) fold. Mutagenesis of predicted surface residues was used to generate a functional map of one surface of Est3, which identified a site that mediates association with the telomerase complex. Surprisingly, the predicted OB-fold of Est3 is structurally similar to the OB-fold of the mammalian TPP1 protein, despite the fact that Est3 and TPP1, as components of telomerase and a telomere capping complex, respectively, perform functionally distinct tasks at chromosome ends. The analysis performed on Est3 may be instructive in generating comparable missense mutations on the surface of the OB-fold domain of TPP1. PMID:19172754

Cross-system excision of chaperone-mediated proteolysis in chaperone-assisted recombinant protein production

PubMed Central

Martínez-Alonso, Mónica; Villaverde, Antonio

2010-01-01

Main Escherichia coli cytosolic chaperones such as DnaK are key components of the control quality network designed to minimize the prevalence of polypeptides with aberrant conformations. This is achieved by both favoring refolding activities but also stimulating proteolytic degradation of folding reluctant species. This last activity is responsible for the decrease of the proteolytic stability of recombinant proteins when co-produced along with DnaK, where an increase in solubility might be associated to a decrease in protein yield. However, when DnaK and its co-chaperone DnaJ are co-produced in cultured insect cells or whole insect larvae (and expectedly, in other heterologous hosts), only positive, folding-related effects of these chaperones are observed, in absence of proteolysis-mediated reduction of recombinant protein yield. PMID:21326941

Aromatic thiol-mediated cleavage of N-O bonds enables chemical ubiquitylation of folded proteins

NASA Astrophysics Data System (ADS)

Weller, Caroline E.; Dhall, Abhinav; Ding, Feizhi; Linares, Edlaine; Whedon, Samuel D.; Senger, Nicholas A.; Tyson, Elizabeth L.; Bagert, John D.; Li, Xiaosong; Augusto, Ohara; Chatterjee, Champak

2016-09-01

Access to protein substrates homogenously modified by ubiquitin (Ub) is critical for biophysical and biochemical investigations aimed at deconvoluting the myriad biological roles for Ub. Current chemical strategies for protein ubiquitylation, however, employ temporary ligation auxiliaries that are removed under harsh denaturing conditions and have limited applicability. We report an unprecedented aromatic thiol-mediated N-O bond cleavage and its application towards native chemical ubiquitylation with the ligation auxiliary 2-aminooxyethanethiol. Our interrogation of the reaction mechanism suggests a disulfide radical anion as the active species capable of cleaving the N-O bond. The successful semisynthesis of full-length histone H2B modified by the small ubiquitin-like modifier-3 (SUMO-3) protein further demonstrates the generalizability and compatibility of our strategy with folded proteins.

Cytokinin production by Pseudomonas fluorescens G20-18 determines biocontrol activity against Pseudomonas syringae in Arabidopsis

PubMed Central

Großkinsky, Dominik K.; Tafner, Richard; Moreno, María V.; Stenglein, Sebastian A.; García de Salamone, Inés E.; Nelson, Louise M.; Novák, Ondřej; Strnad, Miroslav; van der Graaff, Eric; Roitsch, Thomas

2016-01-01

Plant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. Although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. Here we identify the ability of Pseudomonas fluorescens G20-18 to efficiently control P. syringae infection in Arabidopsis, allowing maintenance of tissue integrity and ultimately biomass yield. Microbial cytokinin production was identified as a key determinant for this biocontrol effect on the hemibiotrophic bacterial pathogen. While cytokinin-deficient loss-of-function mutants of G20-18 exhibit impaired biocontrol, functional complementation with cytokinin biosynthetic genes restores cytokinin-mediated biocontrol, which is correlated with differential cytokinin levels in planta. Arabidopsis mutant analyses revealed the necessity of functional plant cytokinin perception and salicylic acid-dependent defence signalling for this biocontrol mechanism. These results demonstrate microbial cytokinin production as a novel microbe-based, hormone-mediated concept of biocontrol. This mechanism provides a basis to potentially develop novel, integrated plant protection strategies combining promotion of growth, a favourable physiological status and activation of fine-tuned direct defence and abiotic stress resilience. PMID:26984671

Cytokinin production by Pseudomonas fluorescens G20-18 determines biocontrol activity against Pseudomonas syringae in Arabidopsis.

PubMed

Großkinsky, Dominik K; Tafner, Richard; Moreno, María V; Stenglein, Sebastian A; García de Salamone, Inés E; Nelson, Louise M; Novák, Ondřej; Strnad, Miroslav; van der Graaff, Eric; Roitsch, Thomas

2016-03-17

Plant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. Although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. Here we identify the ability of Pseudomonas fluorescens G20-18 to efficiently control P. syringae infection in Arabidopsis, allowing maintenance of tissue integrity and ultimately biomass yield. Microbial cytokinin production was identified as a key determinant for this biocontrol effect on the hemibiotrophic bacterial pathogen. While cytokinin-deficient loss-of-function mutants of G20-18 exhibit impaired biocontrol, functional complementation with cytokinin biosynthetic genes restores cytokinin-mediated biocontrol, which is correlated with differential cytokinin levels in planta. Arabidopsis mutant analyses revealed the necessity of functional plant cytokinin perception and salicylic acid-dependent defence signalling for this biocontrol mechanism. These results demonstrate microbial cytokinin production as a novel microbe-based, hormone-mediated concept of biocontrol. This mechanism provides a basis to potentially develop novel, integrated plant protection strategies combining promotion of growth, a favourable physiological status and activation of fine-tuned direct defence and abiotic stress resilience.

Temperature-driven decoupling of key phases of organic matter degradation in marine sediments.

PubMed

Weston, Nathaniel B; Joye, Samantha B

2005-11-22

The long-term burial of organic carbon in sediments results in the net accumulation of oxygen in the atmosphere, thereby mediating the redox state of the Earth's biosphere and atmosphere. Sediment microbial activity plays a major role in determining whether particulate organic carbon is recycled or buried. A diverse consortium of microorganisms that hydrolyze, ferment, and terminally oxidize organic compounds mediates anaerobic organic matter mineralization in anoxic sediments. Variable temperature regulation of the sequential processes, leading from the breakdown of complex particulate organic carbon to the production and subsequent consumption of labile, low-molecular weight, dissolved intermediates, could play a key role in controlling rates of overall organic carbon mineralization. We examined sediment organic carbon cycling in a sediment slurry and in flow through bioreactor experiments. The data show a variable temperature response of the microbial functional groups mediating organic matter mineralization in anoxic marine sediments, resulting in the temperature-driven decoupling of the production and consumption of organic intermediates. This temperature-driven decoupling leads to the accumulation of labile, low-molecular weight, dissolved organic carbon at low temperatures and low-molecular weight dissolved organic carbon limitation of terminal metabolism at higher temperatures.

Inflammation: Friend or foe for animal production?

USDA-ARS?s Scientific Manuscript database

Inflammation is an essential immune response that seeks to contain microbial infection and repair damaged tissue. Increased pro-inflammatory mediators have been associated with enhanced resistance to a range of important poultry and pig pathogens. However, inflammation may also have undesirable co...

ENVIRONMENTAL CHARACTERISTICS AFFECTING REDUCTIVE TRANSFORMATION OF ORGANIC POLLUTANTS IN ANOXIC SEDIMENTS

EPA Science Inventory

Reductive transformations are important processes for determining the fate of organic pollutants in anoxic environments. These processes are most often microbially mediated by both direct and indirect means. For example, specific bacteria transform organic pollutants directly as ...

Metagenomic insights into zooplankton‐associated bacterial communities

PubMed Central

Srivastava, Abhishek; Koski, Marja; Garcia, Juan Antonio L.; Takaki, Yoshihiro; Yokokawa, Taichi; Nunoura, Takuro; Elisabeth, Nathalie H.; Sintes, Eva; Herndl, Gerhard J.

2017-01-01

Summary Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton‐associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton‐associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton‐associated microbiome suggests that this zooplankton‐associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. PMID:28967193

Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease

PubMed Central

Casey, Jordan M.; Ainsworth, Tracy D.; Choat, J. Howard; Connolly, Sean R.

2014-01-01

Microbial community structure on coral reefs is strongly influenced by coral–algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes, mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease. PMID:24966320

Microbial CH4 and N2O Consumption in Acidic Wetlands

PubMed Central

Kolb, Steffen; Horn, Marcus A.

2012-01-01

Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH4), and nitrous oxide (N2O). Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH4 is consumed in sub soil by aerobic methanotrophs at anoxic–oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots). Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH4 in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH4 consumption have not been systematically evaluated. N2O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N2O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N2O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N2O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and denitrifiers that consume atmospheric CH4 and N2O in acidic wetlands. PMID:22403579

Interactive effects of global climate change and pollution on marine microbes: the way ahead.

PubMed

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Angela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-06-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

Interactive effects of global climate change and pollution on marine microbes: the way ahead

PubMed Central

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Ângela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-01-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future. PMID:23789087

Mechanism-based inactivation of CYP2C8 by gemfibrozil occurs rapidly in humans.

PubMed

Honkalammi, J; Niemi, M; Neuvonen, P J; Backman, J T

2011-04-01

To study the time to onset of mechanism-based inactivation of cytochrome P450 (CYP) 2C8 by gemfibrozil in vivo, we conducted a randomized five-phase crossover study in 10 healthy volunteers. In one phase the volunteers ingested 0.25 mg of repaglinide alone (control), and in the other phases they received 600 mg of gemfibrozil 0-6 h prior to the repaglinide dose. When gemfibrozil was taken 0, 1, 3, or 6 h before repaglinide, the geometric mean ratio relative to control (90% confidence interval (CI)) of repaglinide area under the plasma concentration-time curve (AUC(0-∞)) was 5.0-fold (4.3-5.7-fold), 6.3-fold (5.4-7.5-fold), 6.6-fold (5.6-7.7-fold), and 5.4-fold (4.8-6.1-fold), respectively (P < 0.001 vs. control). The geometric mean ratio relative to control (90% CI) of the maximum plasma concentration (C(max)) of the CYP2C8-mediated metabolite M4 was 1.0-fold (0.8-1.3-fold), 0.10-fold (0.06-0.17-fold, P < 0.001), 0.06-fold (0.04-0.10-fold, P < 0.001), and 0.09-fold (0.05-0.14-fold, P < 0.001), respectively. The strong inactivation of CYP2C8, evident as soon as 1 h after gemfibrozil dosing, has implications in clinical practice and in studies with gemfibrozil as a CYP2C8 model inhibitor.

Exploring the Metabolic Potential of Microbial Communities in Ultra-basic Reducing Spring at The Cedars, CA: Evidence of Microbial Methanogenesis and Heterotrophic Acetogenesis

NASA Astrophysics Data System (ADS)

Kohl, L.; Cummings, E.; Cox, A.; Suzuki, S.; Morrrissey, L.; Lang, S. Q.; Richter, A.; Nealson, K. H.; Morrill, P. L.

2015-12-01

The Cedars is a complex of ultra-basic, reducing springs located in the Coastal Range Ophiolite (CA, USA), a site of present day serpentinization. Similar to other serpentinization-associated fluids, the groundwaters discharging at The Cedars contain elevated concentrations of C1-C6 alkanes and volatile organic acids (VOAs) which may originate from abiotic or thermogenic processes but can also be produced, consumed, or transformed by microbial activity. In contrast to other continental sites of serpentinization, geochemical indicators (δ13CCH4, δ2HCH4, CH4/C2-C6 alkanes) are consistent with a partial microbial origin of methane at The Cedars. These indicators, however, can provide only indirect evidence of microbial methanogenesis. To further explore the metabolic potential of the indigenous microbial communities at The Cedars, we conducted a series of microcosm experiments in which fluids and sediments collected at The Cedars were incubated with 13C labeled substrates (formate, acetate, bicarbonate, methanol) under anaerobic conditions. 13C from all amended substrates was incorporated into CH4 demonstrating that these microbial communities can convert both organic and inorganic substrates to CH4. The apparent fractionation of 13C between methane and potential substrates indicated that carbonate reduction was the dominant pathway of methanogenesis, and 16S rDNA based community profiling revealed the presence of an OTU closest related to Methanobacterium sp., an autotrophic (CO2/H2) methanogen. Concentrations of C1-C4 VOAs increased 5-fold over the course of the experiment indicating the microbial production of VOAs. This acetogenesis occurred heterotrophically as autotrophic acetogenesis can be excluded because (a) δ13C values of acetate were similar to those of inorganic carbon (inconsistent with the strong discrimination against 13C observed in autotrophic acetogenesis) and (b) no incorporation of 13C from labeled bicarbonate was into acetate was observed.

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

DOE PAGES

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; ...

2015-03-17

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms weremore » mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.« less

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

PubMed Central

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; Mahnert, Alexander; Tom, Lauren; Piceno, Yvette; Andersen, Gary L.; Venkateswaran, Kasthuri; Rettberg, Petra; Barczyk, Simon; Pukall, Rüdiger; Berg, Gabriele

2015-01-01

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms. PMID:25778463

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

NASA Astrophysics Data System (ADS)

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.; Mahnert, Alexander; Tom, Lauren; Piceno, Yvette; Andersen, Gary L.; Venkateswaran, Kasthuri; Rettberg, Petra; Barczyk, Simon; Pukall, Rüdiger; Berg, Gabriele

2015-03-01

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll

NASA Astrophysics Data System (ADS)

Jeffries, Thomas C.; Ostrowski, Martin; Williams, Rohan B.; Xie, Chao; Jensen, Rachelle M.; Grzymski, Joseph J.; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K.; Neches, Russell Y.; Drautz-Moses, Daniela I.; Chénard, Caroline; Paulsen, Ian T.; Lauro, Federico M.

2015-10-01

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll.

PubMed

Jeffries, Thomas C; Ostrowski, Martin; Williams, Rohan B; Xie, Chao; Jensen, Rachelle M; Grzymski, Joseph J; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K; Neches, Russell Y; Drautz-Moses, Daniela I; Chénard, Caroline; Paulsen, Ian T; Lauro, Federico M

2015-10-20

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a 'citizen oceanography' approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland

NASA Astrophysics Data System (ADS)

Bomberg, Malin; Lamminmäki, Tiina; Itävaara, Merja

2016-11-01

The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7 × 104 and 1.2 × 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99 % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3- and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.

Superiority of Graphene over Polymer Coatings for Prevention of Microbially Induced Corrosion

NASA Astrophysics Data System (ADS)

Krishnamurthy, Ajay; Gadhamshetty, Venkataramana; Mukherjee, Rahul; Natarajan, Bharath; Eksik, Osman; Ali Shojaee, S.; Lucca, Don A.; Ren, Wencai; Cheng, Hui-Ming; Koratkar, Nikhil

2015-09-01

Prevention of microbially induced corrosion (MIC) is of great significance in many environmental applications. Here, we report the use of an ultra-thin, graphene skin (Gr) as a superior anti-MIC coating over two commercial polymeric coatings, Parylene-C (PA) and Polyurethane (PU). We find that Nickel (Ni) dissolution in a corrosion cell with Gr-coated Ni is an order of magnitude lower than that of PA and PU coated electrodes. Electrochemical analysis reveals that the Gr coating offers ~10 and ~100 fold improvement in MIC resistance over PU and PA coatings respectively. This finding is remarkable considering that the Gr coating (1-2 nm) is ~25 and ~4000 times thinner than the PA (40-50 nm), and PU coatings (20-80 μm), respectively. Conventional polymer coatings are either non-conformal when deposited or degrade under the action of microbial processes, while the electro-chemically inert graphene coating is both resistant to microbial attack and is extremely conformal and defect-free. Finally, we provide a brief discussion regarding the effectiveness of as-grown vs. transferred graphene films for anti-MIC applications. While the as-grown graphene films are devoid of major defects, wet transfer of graphene is shown to introduce large scale defects that make it less suitable for the current application.

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll

PubMed Central

Jeffries, Thomas C.; Ostrowski, Martin; Williams, Rohan B.; Xie, Chao; Jensen, Rachelle M.; Grzymski, Joseph J.; Senstius, Svend Jacob; Givskov, Michael; Hoeke, Ron; Philip, Gayle K.; Neches, Russell Y.; Drautz-Moses, Daniela I.; Chénard, Caroline; Paulsen, Ian T.; Lauro, Federico M.

2015-01-01

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system. PMID:26481089

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

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

Moissl-Eichinger, Christine; Auerbach, Anna K.; Probst, Alexander J.

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms weremore » mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.« less

Streptomyces Exploration: Competition, Volatile Communication and New Bacterial Behaviours.

PubMed

Jones, Stephanie E; Elliot, Marie A

2017-07-01

Streptomyces bacteria are prolific producers of specialized metabolites, and have a well studied, complex life cycle. Recent work has revealed a new type of Streptomyces growth termed 'exploration' - so named for the ability of explorer cells to rapidly traverse solid surfaces. Streptomyces exploration is stimulated by fungal interactions, and is associated with the production of an alkaline volatile organic compound (VOC) capable of inducing exploration by other streptomycetes. Here, we examine Streptomyces exploration from the perspectives of interkingdom interactions, pH-induced morphological switches, and VOC-mediated communication. The phenotypic diversity that can be revealed through microbial interactions and VOC exposure is providing us with insight into novel modes of microbial development, and an opportunity to exploit VOCs to stimulate desired microbial behaviours. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inhibitory effects of hepatocyte growth factor and interleukin-6 on transforming growth factor-beta1 mediated vocal fold fibroblast-myofibroblast differentiation.

PubMed

Vyas, Bimal; Ishikawa, Keiko; Duflo, Suzy; Chen, Xia; Thibeault, Susan L

2010-05-01

The role of myofibroblasts in vocal fold scarring has not been extensively studied, partly because of the lack of a robust in vitro model. The objective of this investigation was to develop and characterize a myofibroblast in vitro model that could be utilized to investigate the molecular mechanism of myofibroblast differentiation and function in injured vocal fold tissue. Differentiation of human primary vocal fold fibroblasts (hVFFs) to myofibroblasts was stimulated with 5, 10, or 20 ng/mL of recombinant transforming growth factor-beta1 (TGF-beta1). Cultures were analyzed by immunofluorescence and Western blotting, with an alpha-smooth muscle actin (alpha-SMA) antibody used as a myofibroblast marker. Normal rabbit vocal folds were treated with 10 ng/mL of TGF-beta1 for 7 days for in vivo corroboration. The effects of interleukin-6 (IL-6) and hepatocyte growth factor (HGF) on myofibroblast differentiation were studied with Western blots. The hVFFs demonstrated positive alpha-SMA labeling in cells stimulated by 10 and 20 ng/mL TGF-beta1, indicating that hVFFs were capable of differentiation to myofibroblasts. Transforming growth factor-beta1 induced the largest increase in alpha-SMA at 10 ng/mL on day 5 of treatment. Both HGF and IL-6 suppressed the expression of TGF-beta1-induced alpha-SMA. Our work characterizes a useful in vitro model of TGF-beta1-mediated vocal fold fibroblast-myofibroblast differentiation. The extent of differentiation appears to be attenuated by HGF, suggesting a potential mechanism to support prior work indicating that HGF plays a protective role in reducing scar formation in vocal fold injuries. Paradoxically, IL-6, which has been shown to play a profibrotic role in dermal studies, also attenuated the TGF-beta1 response.

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

Microbial dormancy improves development and experimental validation of ecosystem model

DOE PAGES

Wang, Gangsheng; Jagadamma, Sindhu; Mayes, Melanie; ...

2014-07-11

Climate feedbacks from soils can result from environmental change followed by response of plant and microbial communities, and/or associated changes in nutrient cycling. Explicit consideration of microbial life history traits and functions may be necessary to predict climate feedbacks due to changes in the physiology and community composition of microbes and their associated effect on carbon cycling. Here, we enhanced the Microbial-Enzyme-mediated Decomposition (MEND) model by incorporating microbial dormancy and the ability to track multiple isotopes of carbon. We tested two versions of MEND, i.e., MEND with dormancy and MEND without dormancy, against long-term (270 d) lab incubations of fourmore » soils with isotopically-labeled substrates. MEND without dormancy adequately fitted multiple observations (total and 14C respiration, and dissolved organic carbon), but at the cost of significantly underestimating the total microbial biomass. The MEND with dormancy improved estimates of microbial biomass by 20 71% over the MEND without dormancy. We observed large differences for two fitted model parameters, the specific maintenance and growth rates for active microbes, depending on whether dormancy was considered. Together our model extrapolations of the incubation study show that long-term soil incubations with observations in multiple carbon pools are necessary to estimate both decomposition and microbial parameters. These efforts should provide essential support to future field- and global-scale simulations and enable more confident predictions of feedbacks between environmental change and carbon cycling.« less

Mediation analysis allowing for exposure-mediator interactions and causal interpretation: theoretical assumptions and implementation with SAS and SPSS macros

PubMed Central

Valeri, Linda; VanderWeele, Tyler J.

2012-01-01

Mediation analysis is a useful and widely employed approach to studies in the field of psychology and in the social and biomedical sciences. The contributions of this paper are several-fold. First we seek to bring the developments in mediation analysis for non linear models within the counterfactual framework to the psychology audience in an accessible format and compare the sorts of inferences about mediation that are possible in the presence of exposure-mediator interaction when using a counterfactual versus the standard statistical approach. Second, the work by VanderWeele and Vansteelandt (2009, 2010) is extended here to allow for dichotomous mediators and count outcomes. Third, we provide SAS and SPSS macros to implement all of these mediation analysis techniques automatically and we compare the types of inferences about mediation that are allowed by a variety of software macros. PMID:23379553

Mediation analysis allowing for exposure-mediator interactions and causal interpretation: theoretical assumptions and implementation with SAS and SPSS macros.

PubMed

Valeri, Linda; Vanderweele, Tyler J

2013-06-01

Mediation analysis is a useful and widely employed approach to studies in the field of psychology and in the social and biomedical sciences. The contributions of this article are several-fold. First we seek to bring the developments in mediation analysis for nonlinear models within the counterfactual framework to the psychology audience in an accessible format and compare the sorts of inferences about mediation that are possible in the presence of exposure-mediator interaction when using a counterfactual versus the standard statistical approach. Second, the work by VanderWeele and Vansteelandt (2009, 2010) is extended here to allow for dichotomous mediators and count outcomes. Third, we provide SAS and SPSS macros to implement all of these mediation analysis techniques automatically, and we compare the types of inferences about mediation that are allowed by a variety of software macros. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Dynamics of Cathode-Associated Microbial Communities and Metabolite Profiles in a Glycerol-Fed Bioelectrochemical System

PubMed Central

Dennis, Paul G.; Harnisch, Falk; Yeoh, Yun Kit; Tyson, Gene W.

2013-01-01

Electrical current can be used to supply reducing power to microbial metabolism. This phenomenon is typically studied in pure cultures with added redox mediators to transfer charge. Here, we investigate the development of a current-fed mixed microbial community fermenting glycerol at the cathode of a bioelectrochemical system in the absence of added mediators and identify correlations between microbial diversity and the respective product outcomes. Within 1 week of inoculation, a Citrobacter population represented 95 to 99% of the community and the metabolite profiles were dominated by 1,3-propanediol and ethanol. Over time, the Citrobacter population decreased in abundance while that of a Pectinatus population and the formation of propionate increased. After 6 weeks, several Clostridium populations and the production of valerate increased, which suggests that chain elongation was being performed. Current supply was stopped after 9 weeks and was associated with a decrease in glycerol degradation and alcohol formation. This decrease was reversed by resuming current supply; however, when hydrogen gas was bubbled through the reactor during open-circuit operation (open-circuit potential) as an alternative source of reducing power, glycerol degradation and metabolite production were unaffected. Cyclic voltammetry revealed that the community appeared to catalyze the hydrogen evolution reaction, leading to a +400-mV shift in its onset potential. Our results clearly demonstrate that current supply can alter fermentation profiles; however, further work is needed to determine the mechanisms behind this effect. In addition, operational conditions must be refined to gain greater control over community composition and metabolic outcomes. PMID:23603684

Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster

PubMed Central

Douglas, Angela E.

2014-01-01

The animal gut is perpetually exposed to microorganisms, and this microbiota affects development, nutrient allocation, and immune homeostasis. A major challenge is to understand the contribution of individual microbial species and interactions among species in shaping these microbe-dependent traits. Using the Drosophila melanogaster gut microbiota, we tested whether microbe-dependent performance and nutritional traits of Drosophila are functionally modular, i.e., whether the impact of each microbial taxon on host traits is independent of the presence of other microbial taxa. Gnotobiotic flies were constructed with one or a set of five of the Acetobacter and Lactobacillus species which dominate the gut microbiota of conventional flies (Drosophila with untreated microbiota). Axenic (microbiota-free) flies exhibited prolonged development time and elevated glucose and triglyceride contents. The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. In contrast, the development rates and triglyceride levels in monocolonized flies varied depending on the taxon present: Acetobacter species supported the largest reductions, while most Lactobacillus species had no effect. Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. This could be attributed to two processes: Lactobacillus-mediated promotion of Acetobacter abundance in the fly and a significant negative correlation between fly triglyceride content and Acetobacter abundance. We conclude that the microbial basis of host traits varies in both specificity and modularity; microbe-mediated reduction in glucose is relatively nonspecific and modular, while triglyceride content is influenced by interactions among microbes. PMID:24242251

Lipidomic analysis of patients with microbial invasion of the amniotic cavity reveals up-regulation of leukotriene B4

PubMed Central

Maddipati, Krishna Rao; Romero, Roberto; Chaiworapongsa, Tinnakorn; Chaemsaithong, Piya; Zhou, Sen-Lin; Xu, Zhonghui; Tarca, Adi L.; Kusanovic, Juan Pedro; Gomez, Ricardo; Chaiyasit, Noppadol; Honn, Kenneth V.

2016-01-01

Bioactive lipids derived from the metabolism of polyunsaturated fatty acids are important mediators of the inflammatory response. Labor per se is considered a sterile inflammatory process. Intra-amniotic inflammation (IAI) due to microorganisms (i.e., intra-amniotic infection) or danger signals (i.e., sterile IAI) has been implicated in the pathogenesis of preterm labor and clinical chorioamnionitis at term. Early and accurate diagnosis of microbial invasion of the amniotic cavity (MIAC) requires analysis of amniotic fluid (AF). It is possible that IAI caused by microorganisms is associated with a stereotypic lipidomic profile, and that analysis of AF may help in the identification of patients with this condition. To test this hypothesis, we analyzed the fatty acyl lipidome of AF by liquid chromatography—mass spectrometry from patients in spontaneous labor at term and preterm gestations. We report that the AF concentrations of proinflammatory lipid mediators of the 5-lipoxygenase pathway are significantly higher in MIAC than in cases of sterile IAI. These results suggest that the concentrations of 5-lipoxygenase metabolites of arachidonic acid, 5-hydroxyeicosatetraenoic acid, and leukotriene B4 in particular could serve as potential biomarkers of MIAC. This finding could have important implications for the rapid identification of patients who may benefit from anti-microbial treatment.—Maddipati, K. R., Romero, R., Chaiworapongsa ,T., Chaemsaithong, P., Zhou, S.-L., Xu, Z., Tarca, A. L., Kusanovic, J. P., Gomez, R., Chaiyasit, N., Honn, K. V. Lipidomic analysis of patients with microbial invasion of the amniotic cavity reveals up-regulation of leukotriene B4. PMID:27312808

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.

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.

Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability.

PubMed

Bryant, Lee D; Little, John C; Bürgmann, Helmut

2012-04-01

Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Quasi-equilibrium analysis of the ion-pair mediated membrane transport of low-permeability drugs.

PubMed

Miller, Jonathan M; Dahan, Arik; Gupta, Deepak; Varghese, Sheeba; Amidon, Gordon L

2009-07-01

The aim of this research was to gain a mechanistic understanding of ion-pair mediated membrane transport of low-permeability drugs. Quasi-equilibrium mass transport analyses were developed to describe the ion-pair mediated octanol-buffer partitioning and hydrophobic membrane permeation of the model basic drug phenformin. Three lipophilic counterions were employed: p-toluenesulfonic acid, 2-naphthalenesulfonic acid, and 1-hydroxy-2-naphthoic acid (HNAP). Association constants and intrinsic octanol-buffer partition coefficients (Log P(AB)) of the ion-pairs were obtained by fitting a transport model to double reciprocal plots of apparent octanol-buffer distribution coefficients versus counterion concentration. All three counterions enhanced the lipophilicity of phenformin, with HNAP providing the greatest increase in Log P(AB), 3.7 units over phenformin alone. HNAP also enhanced the apparent membrane permeability of phenformin, 27-fold in the PAMPA model, and 4.9-fold across Caco-2 cell monolayers. As predicted from a quasi-equilibrium analysis of ion-pair mediated membrane transport, an order of magnitude increase in phenformin flux was observed per log increase in counterion concentration, such that log-log plots of phenformin flux versus HNAP concentration gave linear relationships. These results provide increased understanding of the underlying mechanisms of ion-pair mediated membrane transport, emphasizing the potential of this approach to enable oral delivery of low-permeability drugs.

Intestinal absorption and activation of decitabine amino acid ester prodrugs mediated by peptide transporter PEPT1 and enterocyte enzymes.

PubMed

Tao, Wenhui; Zhao, Dongyang; Sun, Mengchi; Wang, Ziyu; Lin, Bin; Bao, Yu; Li, Yingying; He, Zhonggui; Sun, Yinghua; Sun, Jin

2018-04-25

Decitabine (DAC), a potent DNA methyltransferase (DNMT) inhibitor, has a limited oral bioavailability. Its 5'-amino acid ester prodrugs could improve its oral delivery but the specific absorption mechanism is not yet fully understood. The aim of this present study was to investigate the in vivo absorption and activation mechanism of these prodrugs using in situ intestinal perfusion and pharmacokinetics studies in rats. Although PEPT1 transporter is pH dependent, there appeared to be no proton cotransport in the perfusion experiment with a preferable transport at pH 7.4 rather than pH 6.5. This suggested that the transport was mostly dependent on the dissociated state of the prodrugs and the proton gradient might play only a limited role. In pH 7.4 HEPES buffer, an increase in P eff was observed for L-val-DAC, D-val-DAC, L-phe-DAC and L-trp-DAC (2.89-fold, 1.2-fold, 2.73-fold, and 1.90-fold, respectively), compared with the parent drug. When co-perfusing the prodrug with Glysar, a known substrate of PEPT1, the permeabilities of the prodrugs were significantly inhibited compared with the control. To further investigate the absorption of the prodrugs, L-val-DAC was selected and found to be concentration-dependent and saturable, suggesting a carrier-mediated process (intrinsic K m : 7.80 ± 2.61 mM) along with passive transport. Determination of drug in intestinal homogenate after perfusion further confirmed that the metabolic activation mainly involved an intestinal first-pass effect. In a pharmacokinetic evaluation, the oral bioavailability of L-val-DAC, L-phe-DAC and L-trp-DAC were nearly 1.74-fold, 1.69-fold and 1.49-fold greater than that of DAC. The differences in membrane permeability and oral bioavailability might be due to the different stability in the intestinal lumen and the distinct PEPT1 affinity which is mainly caused by the stereochemistry, hydrophobicity and steric hindrance of the side chains. In summary, the detailed investigation of the absorption mechanism by in vivo intestinal perfusion and pharmacokinetic studies showed that the prodrugs of DAC exhibited excellent permeability and oral bioavailability, which might be attributed to a hybrid (partly PEPT1-mediated and partly passive) transport mode and a rapid activation process in enterocytes. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Effect of light on the production of bioelectricity and added-value microalgae biomass in a Photosynthetic Alga Microbial Fuel Cell.

PubMed

Gouveia, Luísa; Neves, Carole; Sebastião, Diogo; Nobre, Beatriz P; Matos, Cristina T

2014-02-01

This study demonstrates the simultaneous production of bioelectricity and added-value pigments in a Photosynthetic Alga Microbial Fuel Cell (PAMFC). A PAMFC was operated using Chlorella vulgaris in the cathode compartment and a bacterial consortium in the anode. The system was studied at two different light intensities and the maximum power produced was 62.7 mW/m(2) with a light intensity of 96 μE/(m(2)s). The results showed that increasing light intensity from 26 to 96 μE/(m(2)s) leads to an increase of about 6-folds in the power produced. Additionally, the pigments produced by the microalga were analysed and the results showed that the light intensity and PAMFC operation potentiated the carotenogenesis in the cathode compartment. The demonstrated possibility of producing added-value microalgae biomass in microbial fuel cell cathodes will increase the economic feasibility of these bioelectrochemical systems, allowing the development of energy efficient systems for wastewater treatment and carbon fixation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Photo-switchable microbial fuel-cells.

PubMed

Schlesinger, Orr; Dandela, Rambabu; Bhagat, Ashok; Adepu, Raju; Meijler, Michael M; Xia, Lin; Alfonta, Lital

2018-05-01

Regulation of Bio-systems in a clean, simple, and efficient way is important for the design of smart bio-interfaces and bioelectronic devices. Light as a non-invasive mean to control the activity of a protein enables spatial and temporal control far superior to other chemical and physical methods. The ability to regulate the activity of a catalytic enzyme in a biofuel-cell reduces the waste of resources and energy and turns the fuel-cell into a smart and more efficient device for power generation. Here we present a microbial-fuel-cell based on a surface displayed, photo-switchable alcohol dehydrogenase. The enzyme was modified near the active site using non-canonical amino acids and a small photo-reactive molecule, which enables reversible control of enzymatic activity. Depending on the modification site, the enzyme exhibits reversible behavior upon irradiation with UV and visible light, in both biochemical, and electrochemical assays. The change observed in power output of a microbial fuel cell utilizing the modified enzyme was almost five-fold, between inactive and active states. © 2018 Wiley Periodicals, Inc.

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

PubMed Central

Roux, Simon; Hallam, Steven J; Woyke, Tanja; Sullivan, Matthew B

2015-01-01

The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes. DOI: http://dx.doi.org/10.7554/eLife.08490.001 PMID:26200428

Community structure dynamics during startup in microbial fuel cells - The effect of phosphate concentrations.

PubMed

Yanuka-Golub, Keren; Reshef, Leah; Rishpon, Judith; Gophna, Uri

2016-07-01

For microbial fuel cells (MFCs) to become a cost-effective wastewater treatment technology, they must produce a stable electro-active microbial community quickly and operate under realistic wastewater nutrient conditions. The composition of the anodic-biofilm and planktonic-cells communities was followed temporally for MFCs operated under typical laboratory phosphate concentrations (134mgL(-1)P) versus wastewater phosphate concentrations (16mgL(-1)P). A stable peak voltage was attained two-fold faster in MFCs operating under lower phosphate concentration. All anodic-biofilms were composed of well-known exoelectrogenic bacterial families; however, MFCs showing faster startup and a stable voltage had a Desulfuromonadaceae-dominated-biofilm, while biofilms co-dominated by Desulfuromonadaceae and Geobacteraceae characterized slower or less stable MFCs. Interestingly,planktonic-cell concentrations of these bacteria followed a similar trend as the anodic-biofilm and could therefore serve as a biomarker for its formation. These results demonstrate that wastewater-phosphate concentrations do not compromise MFCs efficiency, and considerably speed up startup times. Copyright © 2016 Elsevier Ltd. All rights reserved.