Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

PubMed Central

Ben Said, Sami; Or, Dani

2017-01-01

The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of “microbial ecological power” observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to “discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems,” we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms

Engineering microbial hosts for production of bacterial natural products.

PubMed

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

2016-08-27

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

Impacts of engineered nanomaterials on microbial community structure and function in natural and engineered ecosystems.

PubMed

Mohanty, Anee; Wu, Yichao; Cao, Bin

2014-10-01

In natural and engineered environments, microorganisms often exist as complex communities, which are key to the health of ecosystems and the success of bioprocesses in various engineering applications. With the rapid development of nanotechnology in recent years, engineered nanomaterials (ENMs) have been considered one type of emerging contaminants that pose great potential risks to the proper function of microbial communities in natural and engineered ecosystems. The impacts of ENMs on microorganisms have attracted increasing research attentions; however, most studies focused on the antimicrobial activities of ENMs at single cell and population level. Elucidating the influence of ENMs on microbial communities represents a critical step toward a comprehensive understanding of the ecotoxicity of ENMs. In this mini-review, we summarize and discuss recent research work on the impacts of ENMs on microbial communities in natural and engineered ecosystems, with an emphasis on their influences on the community structure and function. We also highlight several important research topics which may be of great interest to the research community.

Engineering microbial fatty acid metabolism for biofuels and biochemicals.

PubMed

Marella, Eko Roy; Holkenbrink, Carina; Siewers, Verena; Borodina, Irina

2018-04-01

Traditional oleochemical industry chemically processes animal fats and plant oils to produce detergents, lubricants, biodiesel, plastics, coatings, and other products. Biotechnology offers an alternative process, where the same oleochemicals can be produced from abundant biomass feedstocks using microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining metabolites with different functionalities. The prospects of commercializing microbial oleochemicals are also discussed. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genome engineering for microbial natural product discovery.

PubMed

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

2018-03-03

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

Engineering microbial consortia to enhance biomining and bioremediation.

PubMed

Brune, Karl D; Bayer, Travis S

2012-01-01

In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage.

Engineering microbial consortia to enhance biomining and bioremediation

PubMed Central

Brune, Karl D.; Bayer, Travis S.

2012-01-01

In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage. PMID:22679443

Engineering microbial consortia for controllable outputs

PubMed Central

Lindemann, Stephen R; Bernstein, Hans C; Song, Hyun-Seob; Fredrickson, Jim K; Fields, Matthew W; Shou, Wenying; Johnson, David R; Beliaev, Alexander S

2016-01-01

Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into robust consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that, when combined with appropriate modeling frameworks, systems-level knowledge can markedly improve our ability to predict the fate and functioning of consortia. Here we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties. PMID:26967105

Engineering microbial consortia for controllable outputs

DOE PAGES

Lindemann, Stephen R.; Bernstein, Hans C.; Song, Hyun -Seob; ...

2016-03-11

In this study, much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into robust consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution globalmore » measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that, when combined with appropriate modeling frameworks, systems-level knowledge can markedly improve our ability to predict the fate and functioning of consortia. Here we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.« less

Neural Network Modeling of UH-60A Pilot Vibration

NASA Technical Reports Server (NTRS)

Kottapalli, Sesi

2003-01-01

Full-scale flight-test pilot floor vibration is modeled using neural networks and full-scale wind tunnel test data for low speed level flight conditions. Neural network connections between the wind tunnel test data and the tlxee flight test pilot vibration components (vertical, lateral, and longitudinal) are studied. Two full-scale UH-60A Black Hawk databases are used. The first database is the NASMArmy UH-60A Airloads Program flight test database. The second database is the UH-60A rotor-only wind tunnel database that was acquired in the NASA Ames SO- by 120- Foot Wind Tunnel with the Large Rotor Test Apparatus (LRTA). Using neural networks, the flight-test pilot vibration is modeled using the wind tunnel rotating system hub accelerations, and separately, using the hub loads. The results show that the wind tunnel rotating system hub accelerations and the operating parameters can represent the flight test pilot vibration. The six components of the wind tunnel N/rev balance-system hub loads and the operating parameters can also represent the flight test pilot vibration. The present neural network connections can significandy increase the value of wind tunnel testing.

UH1-Y - Benefits and Deficiencies

DTIC Science & Technology

2009-02-20

Report, NA 01 HCG -1 (hereinafter Test and Evaluation Report). 2 author’s experience. 3 Test and Evaluation Report. 4 Test and Evaluation Report...Critical Intelligence. Aug 14, 24(33). - - - 2008. DOD Approves Full Production for UH-1Y Despite Major Deficiency. Oct 2, 24(40). NA 01-11- HCG -2-1...2008. Operational Test and Evaluation Report, NA 01 HCG -1. Parmalee, Patricia, ed. 2005. Test Time. Aviation Week & Space Technology. Jun 20, 162

Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

PubMed

Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

2016-08-05

Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment. Copyright © 2016, American Association for the Advancement of Science.

Laser engineering of microbial systems

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Rapid Prototyping of Microbial Cell Factories via Genome-scale Engineering

PubMed Central

Si, Tong; Xiao, Han; Zhao, Huimin

2014-01-01

Advances in reading, writing and editing genetic materials have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome. Such capacity has greatly accelerated the cycles of design, build and test to engineer microbes for efficient synthesis of fuels, chemicals and drugs. In this review, we summarize the emerging technologies that have been applied, or are potentially useful for genome-scale engineering in microbial systems. We will focus on the development of high-throughput methodologies, which may accelerate the prototyping of microbial cell factories. PMID:25450192

Microbial chemical factories: recent advances in pathway engineering for synthesis of value added chemicals.

PubMed

Dhamankar, Himanshu; Prather, Kristala L J

2011-08-01

The dwindling nature of petroleum and other fossil reserves has provided impetus towards microbial synthesis of fuels and value added chemicals from biomass-derived sugars as a renewable resource. Microbes have naturally evolved enzymes and pathways that can convert biomass into hundreds of unique chemical structures, a property that can be effectively exploited for their engineering into Microbial Chemical Factories (MCFs). De novo pathway engineering facilitates expansion of the repertoire of microbially synthesized compounds beyond natural products. In this review, we visit some recent successes in such novel pathway engineering and optimization, with particular emphasis on the selection and engineering of pathway enzymes and balancing of their accessory cofactors. Copyright © 2011 Elsevier Ltd. All rights reserved.

Adaptive Neuro-Fuzzy Modeling of UH-60A Pilot Vibration

NASA Technical Reports Server (NTRS)

Kottapalli, Sesi; Malki, Heidar A.; Langari, Reza

2003-01-01

Adaptive neuro-fuzzy relationships have been developed to model the UH-60A Black Hawk pilot floor vertical vibration. A 200 point database that approximates the entire UH-60A helicopter flight envelope is used for training and testing purposes. The NASA/Army Airloads Program flight test database was the source of the 200 point database. The present study is conducted in two parts. The first part involves level flight conditions and the second part involves the entire (200 point) database including maneuver conditions. The results show that a neuro-fuzzy model can successfully predict the pilot vibration. Also, it is found that the training phase of this neuro-fuzzy model takes only two or three iterations to converge for most cases. Thus, the proposed approach produces a potentially viable model for real-time implementation.

Engineering Robustness of Microbial Cell Factories.

PubMed

Gong, Zhiwei; Nielsen, Jens; Zhou, Yongjin J

2017-10-01

Metabolic engineering and synthetic biology offer great prospects in developing microbial cell factories capable of converting renewable feedstocks into fuels, chemicals, food ingredients, and pharmaceuticals. However, prohibitively low production rate and mass concentration remain the major hurdles in industrial processes even though the biosynthetic pathways are comprehensively optimized. These limitations are caused by a variety of factors unamenable for host cell survival, such as harsh industrial conditions, fermentation inhibitors from biomass hydrolysates, and toxic compounds including metabolic intermediates and valuable target products. Therefore, engineered microbes with robust phenotypes is essential for achieving higher yield and productivity. In this review, the recent advances in engineering robustness and tolerance of cell factories is described to cope with these issues and briefly introduce novel strategies with great potential to enhance the robustness of cell factories, including metabolic pathway balancing, transporter engineering, and adaptive laboratory evolution. This review also highlights the integration of advanced systems and synthetic biology principles toward engineering the harmony of overall cell function, more than the specific pathways or enzymes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CRISPR-enabled tools for engineering microbial genomes and phenotypes.

PubMed

Tarasava, Katia; Oh, Eun Joong; Eckert, Carrie A; Gill, Ryan T

2018-06-19

In recent years CRISPR-Cas technologies have revolutionized microbial engineering approaches. Genome editing and non-editing applications of various CRISPR-Cas systems have expanded the throughput and scale of engineering efforts, as well as opened up new avenues for manipulating genomes of non-model organisms. As we expand the range of organisms used for biotechnological applications, we need to develop better, more versatile tools for manipulation of these systems. Here we summarize the current advances in microbial gene editing using CRISPR-Cas based tools, and highlight state-of-the-art methods for high-throughput, efficient genome-scale engineering in model organisms Escherichia coli and Saccharomyces cerevisiae. We also review non-editing CRISPR-Cas applications available for gene expression manipulation, epigenetic remodeling, RNA editing, labeling and synthetic gene circuit design. Finally, we point out the areas of research that need further development in order to expand the range of applications and increase the utility of these new methods. This article is protected by copyright. All rights reserved.

Prospects of microbial cell factories developed through systems metabolic engineering.

PubMed

Gustavsson, Martin; Lee, Sang Yup

2016-09-01

While academic-level studies on metabolic engineering of microorganisms for production of chemicals and fuels are ever growing, a significantly lower number of such production processes have reached commercial-scale. In this work, we review the challenges associated with moving from laboratory-scale demonstration of microbial chemical or fuel production to actual commercialization, focusing on key requirements on the production organism that need to be considered during the metabolic engineering process. Metabolic engineering strategies should take into account techno-economic factors such as the choice of feedstock, the product yield, productivity and titre, and the cost effectiveness of midstream and downstream processes. Also, it is important to develop an industrial strain through metabolic engineering for pathway construction and flux optimization together with increasing tolerance to products and inhibitors present in the feedstock, and ensuring genetic stability and strain robustness under actual fermentation conditions. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Investigation of Rotor Performance and Loads of a UH-60A Individual Blade Control System

NASA Technical Reports Server (NTRS)

Yeo, Hyeonsoo; Romander, Ethan A.; Norman, Thomas R.

2010-01-01

A full-scale wind tunnel test was recently conducted (March 2009) in the National Full-Scale Aerodynamics Complex (NFAC) 40- by 80-FootWind Tunnel to evaluate the potential of an individual blade control (IBC) system to improve rotor performance and reduce vibrations, loads, and noise for a UH-60A rotor system [1]. This test was the culmination of a long-termcollaborative effort between NASA, U.S. Army, Sikorsky Aircraft Corporation, and ZF Luftfahrttechnik GmbH (ZFL) to demonstrate the benefits of IBC for a UH-60Arotor. Figure 1 shows the UH-60Arotor and IBC system mounted on the NFAC Large Rotor Test Apparatus (LRTA). The IBC concept used in the current study utilizes actuators placed in the rotating frame, one per blade. In particular, the pitch link of the rotor blade was replacedwith an actuator, so that the blade root pitch can be changed independently. This concept, designed for a full-scale UH-60A rotor, was previously tested in the NFAC 80- by 120-FootWind Tunnel in September 2001 at speeds up to 85 knots [2]. For the current test, the same UH-60A rotor and IBC system were tested in the 40- by 80-FootWind Tunnel at speeds up to 170 knots. Figure 2 shows the servo-hydraulic IBC actuator installed between the swashplate and the blade pitch horn. Although previous wind tunnel experiments [3, 4] and analytical studies on IBC [5, 6] have shown the promise to improve the rotor s performance, in-depth correlation studies have not been performed. Thus, the current test provides a unique resource that can be used to assess the accuracy and reliability of prediction methods and refine theoretical models, with the ultimate goal of providing the technology for timely and cost-effective design and development of new rotors. In this paper, rotor performance and loads calculations are carried out using the analyses CAMRAD II and coupled OVERFLOW-2/CAMRAD II and the results are compared with these UH-60A/IBC wind tunnel test data.

Rapid prototyping of microbial cell factories via genome-scale engineering.

PubMed

Si, Tong; Xiao, Han; Zhao, Huimin

2015-11-15

Advances in reading, writing and editing genetic materials have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome. Such capacity has greatly accelerated the cycles of design, build and test to engineer microbes for efficient synthesis of fuels, chemicals and drugs. In this review, we summarize the emerging technologies that have been applied, or are potentially useful for genome-scale engineering in microbial systems. We will focus on the development of high-throughput methodologies, which may accelerate the prototyping of microbial cell factories. Copyright © 2014 Elsevier Inc. All rights reserved.

SCAT Classifications of 5 Supernovae with the UH88/SNIFS

NASA Astrophysics Data System (ADS)

Tucker, Michael A.; Huber, Mark; Shappee, Benjamin J.; Dong, Subo; Bose, S.; Chen, Ping

2018-03-01

We present the first classifications from the newly formed Spectral Classification of Astronomical Transients (SCAT) survey. SCAT is a transient identification survey utilizing the SuperNova Integral Field Spectrograph (SNIFS) on the University of Hawaii (UH) 88-inch telescope.

Simulated Guide Stars: Adapting the Robo-AO Telescope Simulator to UH 88”

NASA Astrophysics Data System (ADS)

Ashcraft, Jaren; Baranec, Christoph

2018-01-01

Robo-AO is an autonomous adaptive optics system that is in development for the UH 88” Telescope on the Mauna Kea Observatory. This system is capable of achieving near diffraction limited imaging for astronomical telescopes, and has seen successful deployment and use at the Palomar and Kitt Peak Observatories previously. A key component of this system, the telescope simulator, will be adapted from the Palomar Observatory design to fit the UH 88” Telescope. The telescope simulator will simulate the exit pupil of the UH 88” telescope so that the greater Robo-AO system can be calibrated before observing runs. The system was designed in Code V, and then further improved upon in Zemax for later development. Alternate design forms were explored for the potential of adapting the telescope simulator to the NASA Infrared Telescope Facility, where simulating the exit pupil of the telescope proved to be more problematic. A proposed design composed of solely catalog optics was successfully produced for both telescopes, and they await assembly as time comes to construct the new Robo-AO system.

A Model-based Health Monitoring and Diagnostic System for the UH-60 Helicopter. Appendix D

NASA Technical Reports Server (NTRS)

Patterson-Hine, Ann; Hindson, William; Sanderfer, Dwight; Deb, Somnath; Domagala, Chuck

2001-01-01

Model-based reasoning techniques hold much promise in providing comprehensive monitoring and diagnostics capabilities for complex systems. We are exploring the use of one of these techniques, which utilizes multi-signal modeling and the TEAMS-RT real-time diagnostic engine, on the UH-60 Rotorcraft Aircrew Systems Concepts Airborne Laboratory (RASCAL) flight research aircraft. We focus on the engine and transmission systems, and acquire sensor data across the 1553 bus as well as by direct analog-to-digital conversion from sensors to the QHuMS (Qualtech health and usage monitoring system) computer. The QHuMS computer uses commercially available components and is rack-mounted in the RASCAL facility. A multi-signal model of the transmission and engine subsystems enables studies of system testability and analysis of the degree of fault isolation available with various instrumentation suites. The model and examples of these analyses will be described and the data architectures enumerated. Flight tests of this system will validate the data architecture and provide real-time flight profiles to be further analyzed in the laboratory.

Engineering Microbial Metabolite Dynamics and Heterogeneity.

PubMed

Schmitz, Alexander C; Hartline, Christopher J; Zhang, Fuzhong

2017-10-01

As yields for biological chemical production in microorganisms approach their theoretical maximum, metabolic engineering requires new tools, and approaches for improvements beyond what traditional strategies can achieve. Engineering metabolite dynamics and metabolite heterogeneity is necessary to achieve further improvements in product titers, productivities, and yields. Metabolite dynamics, the ensemble change in metabolite concentration over time, arise from the need for microbes to adapt their metabolism in response to the extracellular environment and are important for controlling growth and productivity in industrial fermentations. Metabolite heterogeneity, the cell-to-cell variation in a metabolite concentration in an isoclonal population, has a significant impact on ensemble productivity. Recent advances in single cell analysis enable a more complete understanding of the processes driving metabolite heterogeneity and reveal metabolic engineering targets. The authors present an overview of the mechanistic origins of metabolite dynamics and heterogeneity, why they are important, their potential effects in chemical production processes, and tools and strategies for engineering metabolite dynamics and heterogeneity. The authors emphasize that the ability to control metabolite dynamics and heterogeneity will bring new avenues of engineering to increase productivity of microbial strains. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates.

PubMed

Aldor, Ilana S; Keasling, Jay D

2003-10-01

Implementing several metabolic engineering strategies, either individually or in combination, it is possible to construct microbial plastic factories to produce a variety of polyhydroxyalkanoate (PHA) biopolymers with desirable structures and material properties. Approaches include external substrate manipulation, inhibitor addition, recombinant gene expression, host cell genome manipulation and, most recently, protein engineering of PHA biosynthetic enzymes. In addition, mathematical models and molecular methods can be used to elucidate metabolically engineered systems and to identify targets for performance improvement.

Experimental observations of nonlinearly enhanced 2omega-UH electromagnetic radiation excited by steady-state colliding electron beams

NASA Technical Reports Server (NTRS)

Intrator, T.; Hershkowitz, N.; Chan, C.

1984-01-01

Counterstreaming large-diameter electron beams in a steady-state laboratory experiment are observed to generate transverse radiation at twice the upper-hybrid frequency (2omega-UH) with a quadrupole radiation pattern. The electromagnetic wave power density is nonlinearly enhanced over the power density obtained from a single beam-plasma system. Electromagnetic power density scales exponentially with beam energy and increases with ion mass. Weak turbulence theory can predict similar (but weaker) beam energy scaling but not the high power density, or the predominance of the 2omega-UH radiation peak over the omega-UH peak. Significant noise near the upper-hybrid and ion plasma frequencies is also measured, with normalized electrostatic wave energy density W(ES)/n(e)T(e) approximately 0.01.

UNBROKEN: UH 1N AIRCREW CONTINUE OPS DESPITE WEAK HEARING PROTECTION

DTIC Science & Technology

2016-02-29

AU/ACSC/2016 AIR COMMAND AND STAFF COLLEGE AIR UNIVERSITY UNBROKEN: UH-1N AIRCREW CONTINUE OPS DESPITE WEAK HEARING... student training. The final one at Fairchild AFB, Washington, is focused on search and rescue operations and supports the Survival, Evasion

Modeling of UH-60A Hub Accelerations with Neural Networks

NASA Technical Reports Server (NTRS)

Kottapalli, Sesi

2002-01-01

Neural network relationships between the full-scale, flight test hub accelerations and the corresponding three N/rev pilot floor vibration components (vertical, lateral, and longitudinal) are studied. The present quantitative effort on the UH-60A Black Hawk hub accelerations considers the lateral and longitudinal vibrations. An earlier study had considered the vertical vibration. The NASA/Army UH-60A Airloads Program flight test database is used. A physics based "maneuver-effect-factor (MEF)", derived using the roll-angle and the pitch-rate, is used. Fundamentally, the lateral vibration data show high vibration levels (up to 0.3 g's) at low airspeeds (for example, during landing flares) and at high airspeeds (for example, during turns). The results show that the advance ratio and the gross weight together can predict the vertical and the longitudinal vibration. However, the advance ratio and the gross weight together cannot predict the lateral vibration. The hub accelerations and the advance ratio can be used to satisfactorily predict the vertical, lateral, and longitudinal vibration. The present study shows that neural network based representations of all three UH-60A pilot floor vibration components (vertical, lateral, and longitudinal) can be obtained using the hub accelerations along with the gross weight and the advance ratio. The hub accelerations are clearly a factor in determining the pilot vibration. The present conclusions potentially allow for the identification of neural network relationships between the experimental hub accelerations obtained from wind tunnel testing and the experimental pilot vibration data obtained from flight testing. A successful establishment of the above neural network based link between the wind tunnel hub accelerations and the flight test vibration data can increase the value of wind tunnel testing.

Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems

PubMed Central

Bernstein, Hans C; Carlson, Ross P

2012-01-01

This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery. PMID:24688677

Implementing the UH Asynchronous Learning Network: Practices, Issues and Challenges

ERIC Educational Resources Information Center

Odin, Jaishree K.

2002-01-01

In spite of ten campuses spread over four islands, access to higher education at the University of Hawai'i (UH) is unevenly distributed across the state. In an effort to address the problem of access, the Alfred P. Sloan Foundation has funded the University of Hawai'i to develop online courses and programs. In this article, the author describes…

Millstone: software for multiplex microbial genome analysis and engineering

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

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.; ...

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Improving microbial biogasoline production in Escherichia coli using tolerance engineering.

PubMed

Foo, Jee Loon; Jensen, Heather M; Dahl, Robert H; George, Kevin; Keasling, Jay D; Lee, Taek Soon; Leong, Susanna; Mukhopadhyay, Aindrila

2014-11-04

Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerance phenotypes belonged to diverse functional groups, such as oxidative stress response (soxS, fpr, and nrdH), general stress response (metR, yqhD, and gidB), heat shock-related response (ibpA), and transport (mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production. The use of microbial host platforms for the production of bulk commodities, such as chemicals and fuels, is now a focus of many biotechnology efforts. Many of these compounds are inherently toxic to the host microbe, which in turn places a limit on production despite efforts to optimize the bioconversion pathways. In order to achieve economically

Improving microbial biogasoline production in Escherichia coli using tolerance engineering

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

Foo, Jee Loon; Jensen, Heather M.; Dahl, Robert H.

Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerancemore » phenotypes belonged to diverse functional groups, such as oxidative stress response ( soxS, fpr, and nrdH), general stress response ( metR, yqhD, and gidB), heat shock-related response ( ibpA), and transport ( mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production.The use of microbial host platforms for the production of bulk commodities, such as chemicals and fuels, is now a focus of many biotechnology efforts. Many of these compounds are inherently toxic to the host microbe, which in turn places a limit on production despite efforts to optimize the bioconversion pathways. In order to achieve

Improving microbial biogasoline production in Escherichia coli using tolerance engineering

DOE PAGES

Foo, Jee Loon; Jensen, Heather M.; Dahl, Robert H.; ...

2014-11-04

Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerancemore » phenotypes belonged to diverse functional groups, such as oxidative stress response ( soxS, fpr, and nrdH), general stress response ( metR, yqhD, and gidB), heat shock-related response ( ibpA), and transport ( mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production.The use of microbial host platforms for the production of bulk commodities, such as chemicals and fuels, is now a focus of many biotechnology efforts. Many of these compounds are inherently toxic to the host microbe, which in turn places a limit on production despite efforts to optimize the bioconversion pathways. In order to achieve

Genetically engineered microbial biosensors for in situ monitoring of environmental pollution.

PubMed

Shin, Hae Ja

2011-02-01

Microbial biosensors are compact, portable, cost effective, and simple to use, making them seem eminently suitable for the in situ monitoring of environmental pollution. One promising approach for such applications is the fusion of reporter genes with regulatory genes that are dose-dependently responsive to the target chemicals or physiological signals. Their biosensor capabilities, such as target range and sensitivity, could be improved by modification of regulatory genes. Recent uses of such genetically engineered microbial biosensors include the development of portable biosensor kits and high-throughput cell arrays on chips, optic fibers, or other platforms for on-site and on-line monitoring of environmental pollution. This mini-review discusses recent advances in microbial biosensors and their future prospects, with a focus on the development and application of genetically modified microbial biosensors for in situ environmental monitoring.

Survivability on the Island of Spice: The Development of the UH-60 Blackhawk and Its Baptism of Fire in Operation Urgent Fury

DTIC Science & Technology

2015-06-12

SURVIVABILITY ON THE ISLAND OF SPICE : THE DEVELOPMENT OF THE UH-60 BLACKHAWK AND ITS BAPTISM OF FIRE IN OPERATION URGENT FURY......THESIS APPROVAL PAGE Name of Candidate: Major Matthew G. Easley Thesis Title: Survivability on the Island of Spice : The Development of the UH

Piloted Evaluation of a UH-60 Mixer Equivalent Turbulence Simulation Model

NASA Technical Reports Server (NTRS)

Lusardi, Jeff A.; Blanken, Chris L.; Tischeler, Mark B.

2002-01-01

A simulation study of a recently developed hover/low speed Mixer Equivalent Turbulence Simulation (METS) model for the UH-60 Black Hawk helicopter was conducted in the NASA Ames Research Center Vertical Motion Simulator (VMS). The experiment was a continuation of previous work to develop a simple, but validated, turbulence model for hovering rotorcraft. To validate the METS model, two experienced test pilots replicated precision hover tasks that had been conducted in an instrumented UH-60 helicopter in turbulence. Objective simulation data were collected for comparison with flight test data, and subjective data were collected that included handling qualities ratings and pilot comments for increasing levels of turbulence. Analyses of the simulation results show good analytic agreement between the METS model and flight test data, with favorable pilot perception of the simulated turbulence. Precision hover tasks were also repeated using the more complex rotating-frame SORBET (Simulation Of Rotor Blade Element Turbulence) model to generate turbulence. Comparisons of the empirically derived METS model with the theoretical SORBET model show good agreement providing validation of the more complex blade element method of simulating turbulence.

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

PubMed Central

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

2016-01-01

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

Testing of UH-60A helicopter transmission in NASA Lewis 2240-kW (3000-hp) facility

NASA Technical Reports Server (NTRS)

Mitchell, A. M.; Oswald, F. B.; Coe, H. H.

1986-01-01

The U.S. Army's UH-60A Black Hawk 2240-kW (3000-hp) class, twin-engine helicopter transmission was tested at the NASA Lewis Research Center. The vibration and efficiency test results will be used to enhance the data base for similar-class helicopters. Most of the data were obtained for a matrix of test conditions of 50 to 100 percent of rated rotor speed and 20 to 100 percent of rated input power. The transmission's mechanical efficiency at 100 percent of rated power was 97.3 and 97.5 percent with its inlet oil maintained at 355 and 372 K (180 and 210 F), respectively. The highest vibration reading was 72 g's rms at the upper housing side wall. Other vibration levels measured near the gear meshes are reported.

Blade Deflection Measurements of a Full-Scale UH-60A Rotor System

NASA Technical Reports Server (NTRS)

Olson, Lawrence E.; Abrego, Anita; Barrows, Danny A.; Burner, Alpheus W.

2010-01-01

Blade deflection (BD) measurements using stereo photogrammetry have been made during the individual blade control (IBC) testing of a UH-60A 4-bladed rotor system in the 40 by 80-foot test section of the National Full-Scale Aerodynamic Complex (NFAC). Measurements were made in quadrants one and two, encompassing advance ratios from 0.15 to 0.40, thrust coefficient/solidities from 0.05 to 0.12 and rotor-system drive shaft angles from 0.0 to -9.6 deg. The experiment represents a significant step toward providing benchmark databases to be utilized by theoreticians in the development and validation of rotorcraft prediction techniques. In addition to describing the stereo measurement technique and reporting on preliminary measurements made to date, the intent of this paper is to encourage feedback from the rotorcraft community concerning continued analysis of acquired data and to solicit suggestions for improved test technique and areas of emphasis for measurements in the upcoming UH-60A Airloads test at the NFAC.

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

PubMed Central

Warren, Lesley A.; Kendra, Kathryn E.

2015-01-01

Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

NASTRAN Modeling of Flight Test Components for UH-60A Airloads Program Test Configuration

NASA Technical Reports Server (NTRS)

Idosor, Florentino R.; Seible, Frieder

1993-01-01

Based upon the recommendations of the UH-60A Airloads Program Review Committee, work towards a NASTRAN remodeling effort has been conducted. This effort modeled and added the necessary structural/mass components to the existing UH-60A baseline NASTRAN model to reflect the addition of flight test components currently in place on the UH-60A Airloads Program Test Configuration used in NASA-Ames Research Center's Modern Technology Rotor Airloads Program. These components include necessary flight hardware such as instrument booms, movable ballast cart, equipment mounting racks, etc. Recent modeling revisions have also been included in the analyses to reflect the inclusion of new and updated primary and secondary structural components (i.e., tail rotor shaft service cover, tail rotor pylon) and improvements to the existing finite element mesh (i.e., revisions of material property estimates). Mode frequency and shape results have shown that components such as the Trimmable Ballast System baseplate and its respective payload ballast have caused a significant frequency change in a limited number of modes while only small percent changes in mode frequency are brought about with the addition of the other MTRAP flight components. With the addition of the MTRAP flight components, update of the primary and secondary structural model, and imposition of the final MTRAP weight distribution, modal results are computed representative of the 'best' model presently available.

Application of genetically engineered microbial whole-cell biosensors for combined chemosensing.

PubMed

He, Wei; Yuan, Sheng; Zhong, Wen-Hui; Siddikee, Md Ashaduzzaman; Dai, Chuan-Chao

2016-02-01

The progress of genetically engineered microbial whole-cell biosensors for chemosensing and monitoring has been developed in the last 20 years. Those biosensors respond to target chemicals and produce output signals, which offer a simple and alternative way of assessment approaches. As actual pollution caused by human activities usually contains a combination of different chemical substances, how to employ those biosensors to accurately detect real contaminant samples and evaluate biological effects of the combined chemicals has become a realistic object of environmental researches. In this review, we outlined different types of the recent method of genetically engineered microbial whole-cell biosensors for combined chemical evaluation, epitomized their detection performance, threshold, specificity, and application progress that have been achieved up to now. We also discussed the applicability and limitations of this biosensor technology and analyzed the optimum conditions for their environmental assessment in a combined way.

Helicopter noise definition report: UH-60A, S-76, A-109, 206-L

DOT National Transportation Integrated Search

1981-12-31

This document presents noise data for the Sikorsky UH-60A Blackhawk, the Sikorsky S-76 Spirit, the Agusta A-109 and the Bell 206-L. The acoustical data are accompanied by phototheodolite tracking data, cockpit instrument panel photo data, and meteoro...

Engineering a microbial platform for de novo biosynthesis of diverse methylxanthines

PubMed Central

McKeague, Maureen; Wang, Yen-Hsiang; Cravens, Aaron; Win, Maung Nyan; Smolke, Christina D.

2016-01-01

Engineered microbial biosynthesis of plant natural products can support manufacturing of complex bioactive molecules and enable discovery of non-naturally occurring derivatives. Purine alkaloids, including caffeine (coffee), theophylline (antiasthma drug), theobromine (chocolate), and other methylxanthines, play a significant role in pharmacology and food chemistry. Here, we engineered the eukaryotic microbial host Saccharomyces cerevisiae for the de novo biosynthesis of methylxanthines. We constructed a xanthine-to-xanthosine conversion pathway in native yeast central metabolism to increase endogenous purine flux for the production of 7-methylxanthine, a key intermediate in caffeine biosynthesis. Yeast strains were further engineered to produce caffeine through expression of several enzymes from the coffee plant. By expressing combinations of different N-methyltransferases, we were able to demonstrate re-direction of flux to an alternate pathway and develop strains that support the production of diverse methylxanthines. We achieved production of 270 μg/L, 61 μg/L, and 3700 μg/L of caffeine, theophylline, and 3-methylxanthine, respectively, in 0.3-L bench-scale batch fermentations. The constructed strains provide an early platform for de novo production of methylxanthines and with further development will advance the discovery and synthesis of xanthine derivatives. PMID:27519552

Navier-Stokes Simulation of UH-60A Rotor/Wake Interaction Using Adaptive Mesh Refinement

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

2017-01-01

High-resolution simulations of rotor/vortex-wake interaction for a UH60-A rotor under BVI and dynamic stallconditions were carried out with the OVERFLOW Navier-Stokes code.a. The normal force and pitching moment variation with azimuth angle were in good overall agreementwith flight-test data, similar to other CFD results reported in the literature.b. The wake-grid resolution did not have a significant effect on the rotor-blade airloads. This surprisingresult indicates that a wake grid spacing of (Delta)S=10% ctip is sufficient for engineering airloads predictionfor hover and forward flight. This assumes high-resolution body grids, high-order spatial accuracy, anda hybrid RANS/DDES turbulence model.c. Three-dimensional dynamic stall was found to occur due the presence of blade-tip vortices passing overa rotor blade on the retreating side. This changed the local airfoil angle of attack, causing stall, unlikethe 2D perspective of pure pitch oscillation of the local airfoil section.

Human Factors Assessment of the UH-60M Common Avionics Architecture System (CAAS) Crew Station During the Limited User Evaluation (LEUE)

DTIC Science & Technology

2005-12-01

weapon system evaluation as a high-level architecture and distributed interactive simulation 6 compliant, human-in-the-loop, virtual environment...Directorate to participate in the Limited Early User Evaluation (LEUE) of the Common Avionics Architecture System (CAAS) cockpit. ARL conducted a human...CAAS, the UH-60M PO conducted a limited early user evaluation (LEUE) to evaluate the integration of the CAAS in the UH-60M crew station. The

Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments.

PubMed

Tepper, Naama; Shlomi, Tomer

2011-01-21

Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools).

Using Fly-By-Wire Technology in Future Models of the UH-60 and Other Rotary Wing Aircraft

NASA Technical Reports Server (NTRS)

Solem, Courtney K.

2011-01-01

Several fixed-winged airplanes have successfully used fly-by-wire (FBW) technology for the last 40 years. This technology is now beginning to be incorporated into rotary wing aircraft. By using FBW technology, manufacturers are expecting to improve upon the weight, maintenance time and costs, handling and reliability of the aircraft. Before mass production of this new system begins in new models such as the UH-60MU, testing must be conducted to insure the safety of this technology as well as to reassure others it will be worth the time and money to make such a dramatic change to a perfectly functional machine. The RASCAL JUH-60A has been modified for these purposes. This Black Hawk helicopter has already been equipped with the FBW technology and can be configured as a near perfect representation of the UH-60MU. Because both machines have very similar qualities, the data collected from the RASCAL can be used to make future decisions about the UH-60MU. The U.S. Army AFDD Flight Project Office oversees all the design modifications for every hardware system used in the RASCAL aircraft. This project deals with specific designs and analyses of unique RASCAL aircraft subsystems and their modifications to conduct flight mechanics research.

[Engineering issues of microbial ecology in space agriculture].

PubMed

Yamashita, Masamichi; Ishikawa, Yoji; Oshima, Tairo

2005-03-01

how to conduct preventive maintenance for keeping cultivating soil healthy and productive. 3) Does microbial ecology contribute to building sustainable and expandable human habitation by utilizing the on site extraterrestrial resources? We are assessing technical feasibility of converting regolith to farming soil and structural materials for space agriculture. In the case of Mars habitation, carbon dioxide and a trace amount of nitrogen in atmosphere, and potassium and phosphor in minerals are the sources we consider. Excess oxygen can be accumulated by woods cultivation and their use for lumber. 4) Is the operation of space agriculture robust and safe, if it adopts hyper-thermophilic aerobic microbial ecology? Any ecological system is complex and non-linear, and shows latency and memory effects in its response. It is highly important to understand those features to design and operate space agriculture without falling into the fatal failure. Assessment should be made on the microbial safety and preparation of the preventive measures to eliminate negative elements that would either retard agricultural production or harm the healthy environment. It is worth to mention that such space agriculture would be an effective engineering testbed to solve the global problem on energy and environment. Mars and Moon exploration itself is a good advocate of healthy curiosity expressed by the sustainable civilization of our humankind. We propose to work together towards Mars and Moon with microbial ecology to assure pleasant habitation there.

Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production.

PubMed

Liu, Xiaonan; Ding, Wentao; Jiang, Huifeng

2017-07-19

Plant natural products (PNPs) are widely used as pharmaceuticals, nutraceuticals, seasonings, pigments, etc., with a huge commercial value on the global market. However, most of these PNPs are still being extracted from plants. A resource-conserving and environment-friendly synthesis route for PNPs that utilizes microbial cell factories has attracted increasing attention since the 1940s. However, at the present only a handful of PNPs are being produced by microbial cell factories at an industrial scale, and there are still many challenges in their large-scale application. One of the challenges is that most biosynthetic pathways of PNPs are still unknown, which largely limits the number of candidate PNPs for heterologous microbial production. Another challenge is that the metabolic fluxes toward the target products in microbial hosts are often hindered by poor precursor supply, low catalytic activity of enzymes and obstructed product transport. Consequently, despite intensive studies on the metabolic engineering of microbial hosts, the fermentation costs of most heterologously produced PNPs are still too high for industrial-scale production. In this paper, we review several aspects of PNP production in microbial cell factories, including important design principles and recent progress in pathway mining and metabolic engineering. In addition, implemented cases of industrial-scale production of PNPs in microbial cell factories are also highlighted.

Airworthiness and Flight Characteristics Evaluation, UH-60A (Black Hawk) Helicopter

DTIC Science & Technology

1981-09-01

ACTIVITY EDWARDS AIR FORCE BASE, CALIFORNIA 93523 8..30 83 09 0 1 n 04 DISCLoAIMER NOTICE The findings of this report are not to be constrned as an...EDWARDS AIR FORCE BASE, CALIFORNJA 68-0-BH031.-01-68 II. CONTROLLING OFFICE NAME AND ADORESS 1I. REPORT OATS US ARMY AVN RESEARCH & DEVELOPMENT COMMAND...34| conipliance with the applicable paragraphs of the Prime Item Development Specification The UH-60A was tested at Edwards Air Force Base. California

Comparison of NASTRAN analysis with ground vibration results of UH-60A NASA/AEFA test configuration

NASA Technical Reports Server (NTRS)

Idosor, Florentino; Seible, Frieder

1990-01-01

Preceding program flight tests, a ground vibration test and modal test analysis of a UH-60A Black Hawk helicopter was conducted by Sikorsky Aircraft to complement the UH-60A test plan and NASA/ARMY Modern Technology Rotor Airloads Program. The 'NASA/AEFA' shake test configuration was tested for modal frequencies and shapes and compared with its NASTRAN finite element model counterpart to give correlative results. Based upon previous findings, significant differences in modal data existed and were attributed to assumptions regarding the influence of secondary structure contributions in the preliminary NASTRAN modeling. An analysis of an updated finite element model including several secondary structural additions has confirmed that the inclusion of specific secondary components produces a significant effect on modal frequency and free-response shapes and improves correlations at lower frequencies with shake test data.

Design, engineering, and construction of photosynthetic microbial cell factories for renewable solar fuel production.

PubMed

Lindblad, Peter; Lindberg, Pia; Oliveira, Paulo; Stensjö, Karin; Heidorn, Thorsten

2012-01-01

There is an urgent need to develop sustainable solutions to convert solar energy into energy carriers used in the society. In addition to solar cells generating electricity, there are several options to generate solar fuels. This paper outlines and discusses the design and engineering of photosynthetic microbial systems for the generation of renewable solar fuels, with a focus on cyanobacteria. Cyanobacteria are prokaryotic microorganisms with the same type of photosynthesis as higher plants. Native and engineered cyanobacteria have been used by us and others as model systems to examine, demonstrate, and develop photobiological H(2) production. More recently, the production of carbon-containing solar fuels like ethanol, butanol, and isoprene have been demonstrated. We are using a synthetic biology approach to develop efficient photosynthetic microbial cell factories for direct generation of biofuels from solar energy. Present progress and advances in the design, engineering, and construction of such cyanobacterial cells for the generation of a portfolio of solar fuels, e.g., hydrogen, alcohols, and isoprene, are presented and discussed. Possibilities and challenges when introducing and using synthetic biology are highlighted.

Gear tooth stress measurements on the UH-60A helicopter transmission

NASA Technical Reports Server (NTRS)

Oswald, Fred B.

1987-01-01

The U.S. Army UH-60A (Black Hawk) 2200-kW (3000-hp) class twin-engine helicopter transmission was tested at the NASA Lewis Research Center. Results from these experimental (strain-gage) stress tests will enhance the data base for gear stress levels in transmissions of a similar power level. Strain-gage measurements were performed on the transmission's spiral-bevel combining pinions, the planetary Sun gear, and ring gear. Tests were performed at rated speed and at torque levels 25 to 100 percent that of rated. One measurement series was also taken at a 90 percent speed level. The largest stress found was 760 MPa (110 ksi) on the combining pinion fillet. This is 230 percent greater than the AGMA index stress. Corresponding mean and alternating stresses were 300 and 430 MPa (48 and 62 ksi). These values are within the range of successful test experience reported for other transmissions. On the fillet of the ring gear, the largest stress found was 410 MPa (59 ksi). The ring-gear peak stress was found to be 11 percent less than an analytical (computer simulation) value and it is 24 percent greater than the AGMA index stress. A peak compressive stress of 650 MPa (94 ksi) was found at the center of the Sun gear tooth root.

Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation - A chance for metabolic engineering.

PubMed

Kracke, Frauke; Lai, Bin; Yu, Shiqin; Krömer, Jens O

2018-01-01

More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimizing microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes. Metabolic engineering offers many opportunities to optimize these processes, for instance by genetic engineering of pathways for electron transfer on the one hand and target product synthesis on the other hand. With this review, we summarize the status quo of knowledge and engineering attempts around chemical production in bio-electrochemical systems from a microbe perspective. Challenges associated with the introduction or enhancement of extracellular electron transfer capabilities into production hosts versus the engineering of target compound synthesis pathways in natural exoelectrogens are discussed. Recent advances of the research community in both directions are examined critically. Further, systems biology approaches, for instance using metabolic modelling, are examined for their potential to provide insight into fundamental processes and to identify targets for metabolic engineering. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Engineering microbial fuels cells: recent patents and new directions.

PubMed

Biffinger, Justin C; Ringeisen, Bradley R

2008-01-01

Fundamental research into how microbes generate electricity within microbial fuel cells (MFCs) has far outweighed the practical application and large scale development of microbial energy harvesting devices. MFCs are considered alternatives to standard commercial polymer electrolyte membrane (PEM) fuel cell technology because the fuel supply does not need to be purified, ambient operating temperatures are maintained with biologically compatible materials, and the biological catalyst is self-regenerating. The generation of electricity during wastewater treatment using MFCs may profoundly affect the approach to anaerobic treatment technologies used in wastewater treatment as a result of developing this energy harvesting technology. However, the materials and engineering designs for MFCs were identical to commercial fuel cells until 2003. Compared to commercial fuel cells, MFCs will remain underdeveloped as long as low power densities are generated from the best systems. The variety of designs for MFCs has expanded rapidly in the last five years in the literature, but the patent protection has lagged behind. This review will cover recent and important patents relating to MFC designs and progress.

Analysis of propulsion system dynamics in the validation of a high-order state space model of the UH-60

NASA Technical Reports Server (NTRS)

Kim, Frederick D.

1992-01-01

Frequency responses generated from a high-order linear model of the UH-60 Black Hawk have shown that the propulsion system influences significantly the vertical and yaw dynamics of the aircraft at frequencies important to high-bandwidth control law designs. The inclusion of the propulsion system comprises the latest step in the development of a high-order linear model of the UH-60 that models additionally the dynamics of the fuselage, rotor, and inflow. A complete validation study of the linear model is presented in the frequency domain for both on-axis and off-axis coupled responses in the hoverflight condition, and on-axis responses for forward speeds of 80 and 120 knots.

[Advances in metabolic engineering for the microbial production of naturally occurring terpenes-limonene and bisabolene: a mini review].

PubMed

Pang, Yaru; Hu, Zhihui; Xiao, Dongguang; Yu, Aiqun

2018-01-25

Limonene (C₁₀H₁₆) and bisabolene (C₁₅H₂₄) are both naturally occurring terpenes in plants. Depending on the number of C₅ units, limonene and bisabolene are recognized as representative monoterpenes and sesquiterpenes, respectively. Limonene and bisabolene are important pharmaceutical and nutraceutical products used in the prevention and treatment of cancer and many other diseases. In addition, they can be used as starting materials to produce a range of commercially valuable products, such as pharmaceuticals, nutraceuticals, cosmetics, and biofuels. The low abundance or yield of limonene and bisabolene in plants renders their isolation from plant sources non-economically viable. Isolation of limonene and bisabolene from plants also suffers from low efficiency and often requires harsh reaction conditions, prolonged reaction times, and expensive equipment cost. Recently, the rapid developments in metabolic engineering of microbes provide a promising alternative route for producing these plant natural products. Therefore, producing limonene and bisabolene by engineering microbial cells into microbial factories is becoming an attractive alternative approach that can overcome the bottlenecks, making it more sustainable, environmentally friendly and economically competitive. Here, we reviewed the status of metabolic engineering of microbes that produce limonene and bisabolene including microbial hosts, key enzymes, metabolic pathways and engineering of limonene/bisabolene biosynthesis. Furthermore, key challenges and future perspectives were discussed.

Microbial isoprenoid production: an example of green chemistry through metabolic engineering.

PubMed

Maury, Jérôme; Asadollahi, Mohammad A; Møller, Kasper; Clark, Anthony; Nielsen, Jens

2005-01-01

Saving energy, cost efficiency, producing less waste, improving the biodegradability of products, potential for producing novel and complex molecules with improved properties, and reducing the dependency on fossil fuels as raw materials are the main advantages of using biotechnological processes to produce chemicals. Such processes are often referred to as green chemistry or white biotechnology. Metabolic engineering, which permits the rational design of cell factories using directed genetic modifications, is an indispensable strategy for expanding green chemistry. In this chapter, the benefits of using metabolic engineering approaches for the development of green chemistry are illustrated by the recent advances in microbial production of isoprenoids, a diverse and important group of natural compounds with numerous existing and potential commercial applications. Accumulated knowledge on the metabolic pathways leading to the synthesis of the principal precursors of isoprenoids is reviewed, and recent investigations into isoprenoid production using engineered cell factories are described.

Comparison of Computed and Measured Vortex Evolution for a UH-60A Rotor in Forward Flight

NASA Technical Reports Server (NTRS)

Ahmad, Jasim Uddin; Yamauchi, Gloria K.; Kao, David L.

2013-01-01

A Computational Fluid Dynamics (CFD) simulation using the Navier-Stokes equations was performed to determine the evolutionary and dynamical characteristics of the vortex flowfield for a highly flexible aeroelastic UH-60A rotor in forward flight. The experimental wake data were acquired using Particle Image Velocimetry (PIV) during a test of the fullscale UH-60A rotor in the National Full-Scale Aerodynamics Complex 40- by 80-Foot Wind Tunnel. The PIV measurements were made in a stationary cross-flow plane at 90 deg rotor azimuth. The CFD simulation was performed using the OVERFLOW CFD solver loosely coupled with the rotorcraft comprehensive code CAMRAD II. Characteristics of vortices captured in the PIV plane from different blades are compared with CFD calculations. The blade airloads were calculated using two different turbulence models. A limited spatial, temporal, and CFD/comprehensive-code coupling sensitivity analysis was performed in order to verify the unsteady helicopter simulations with a moving rotor grid system.

V/STOL AND digital avionics system for UH-1H

NASA Technical Reports Server (NTRS)

Liden, S.

1978-01-01

A hardware and software system for the Bell UH-1H helicopter was developed that provides sophisticated navigation, guidance, control, display, and data acquisition capabilities for performing terminal area navigation, guidance and control research. Two Sperry 1819B general purpose digital computers were used. One contains the development software that performs all the specified system flight computations. The second computer is available to NASA for experimental programs that run simultaneously with the other computer programs and which may, at the push of a button, replace selected computer computations. Other features that provide research flexibility include keyboard selectable gains and parameters and software generated alphanumeric and CRT displays.

Pathway engineering strategies for production of beneficial carotenoids in microbial hosts.

PubMed

Ye, Victor M; Bhatia, Sujata K

2012-08-01

Carotenoids, such as lycopene, β-carotene, zeaxanthin, canthaxanthin and astaxanthin have many benefits for human health. In addition to the functional role of carotenoids as vitamin A precursors, adequate consumption of carotenoids prevents the development of a variety of serious diseases. Biosynthesis of carotenoids is a complex process and it starts with the common isoprene precursors. Condensation of these precursors and subsequent modifications, by introducing hydroxyl- and keto-groups, leads to the generation of diversified carotenoid structures. To improve carotenoid production, metabolic engineering has been explored in bacteria, yeast, and algae. The success of the pathway engineering effort depends on the host metabolism, specific enzymes used, the enzyme expression levels, and the strategies employed. Despite the difficulty of pathway engineering for carotenoid production, great progress has been made over the past decade. We review metabolic engineering approaches used in a variety of microbial hosts for carotenoid biosynthesis. These advances will greatly expedite our efforts to bring the health benefits of carotenoids and other nutritional compounds to our diet.

Engineering microbial chemical factories to produce renewable "biomonomers".

PubMed

Adkins, Jake; Pugh, Shawn; McKenna, Rebekah; Nielsen, David R

2012-01-01

By applying metabolic engineering tools and strategies to engineer synthetic enzyme pathways, the number and diversity of commodity and specialty chemicals that can be derived directly from renewable feedstocks is rapidly and continually expanding. This of course includes a number of monomer building-block chemicals that can be used to produce replacements to many conventional plastic materials. This review aims to highlight numerous recent and important advancements in the microbial production of these so-called "biomonomers." Relative to naturally-occurring renewable bioplastics, biomonomers offer several important advantages, including improved control over the final polymer structure and purity, the ability to synthesize non-natural copolymers, and allowing products to be excreted from cells which ultimately streamlines downstream recovery and purification. To highlight these features, a handful of biomonomers have been selected as illustrative examples of recent works, including polyamide monomers, styrenic vinyls, hydroxyacids, and diols. Where appropriate, examples of their industrial penetration to date and end-product uses are also highlighted. Novel biomonomers such as these are ultimately paving the way toward new classes of renewable bioplastics that possess a broader diversity of properties than ever before possible.

A model structure for identification of linear models of the UH-60 helicopter in hover and forward flight

DOT National Transportation Integrated Search

1995-08-01

A linear model structure applicable to identification of the UH-60 flight : dynamics in hover and forward flight without rotor-state data is developed. The : structure of the model is determined through consideration of the important : dynamic modes ...

Computation of UH-60A Airloads Using CFD/CSD Coupling on Unstructured Meshes

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Lee-Rausch, Elizabeth M.

2011-01-01

An unsteady Reynolds-averaged Navier-Stokes solver for unstructured grids is used to compute the rotor airloads on the UH-60A helicopter at high-speed and high thrust conditions. The flow solver is coupled to a rotorcraft comprehensive code in order to account for trim and aeroelastic deflections. Simulations are performed both with and without the fuselage, and the effects of grid resolution, temporal resolution and turbulence model are examined. Computed airloads are compared to flight data.

An engineered microbial platform for direct biofuel production from brown macroalgae.

PubMed

Wargacki, Adam J; Leonard, Effendi; Win, Maung Nyan; Regitsky, Drew D; Santos, Christine Nicole S; Kim, Peter B; Cooper, Susan R; Raisner, Ryan M; Herman, Asael; Sivitz, Alicia B; Lakshmanaswamy, Arun; Kashiyama, Yuki; Baker, David; Yoshikuni, Yasuo

2012-01-20

Prospecting macroalgae (seaweeds) as feedstocks for bioconversion into biofuels and commodity chemical compounds is limited primarily by the availability of tractable microorganisms that can metabolize alginate polysaccharides. Here, we present the discovery of a 36-kilo-base pair DNA fragment from Vibrio splendidus encoding enzymes for alginate transport and metabolism. The genomic integration of this ensemble, together with an engineered system for extracellular alginate depolymerization, generated a microbial platform that can simultaneously degrade, uptake, and metabolize alginate. When further engineered for ethanol synthesis, this platform enables bioethanol production directly from macroalgae via a consolidated process, achieving a titer of 4.7% volume/volume and a yield of 0.281 weight ethanol/weight dry macroalgae (equivalent to ~80% of the maximum theoretical yield from the sugar composition in macroalgae).

UH-1 Helicopter Mechanic (MOS 67N20) Job Description Survey: Performance of Specific Maintenance Tasks.

ERIC Educational Resources Information Center

Schulz, Russel E.; And Others

The report is the second of two describing the results of a world-wide survey of the maintenance activities of UH-1 helicopter mechanics for the purpose of studying the relationships among job requirements, training, and manpower considerations for aviation maintenance. A summary of the results of the first report is included. The survey…

UH-1 Helicopter Mechanic (MOS 67N20) Job Description Survey: Background, Training, and General Maintenance Activities.

ERIC Educational Resources Information Center

Schulz, Russel E.; And Others

The report, the first of two documents examining the relationship among job requirements, training, and manpower considerations for Army aviation maintenance Personnel, discusses the development of task data gathering techniques and procedures for incorporating this data into training programs for the UH-1 helicopter mechanic sPecialty (MOS…

Fidelity assessment of a UH-60A simulation on the NASA Ames vertical motion simulator

NASA Technical Reports Server (NTRS)

Atencio, Adolph, Jr.

1993-01-01

Helicopter handling qualities research requires that a ground-based simulation be a high-fidelity representation of the actual helicopter, especially over the frequency range of the investigation. This experiment was performed to assess the current capability to simulate the UH-60A Black Hawk helicopter on the Vertical Motion Simulator (VMS) at NASA Ames, to develop a methodology for assessing the fidelity of a simulation, and to find the causes for lack of fidelity. The approach used was to compare the simulation to the flight vehicle for a series of tasks performed in flight and in the simulator. The results show that subjective handling qualities ratings from flight to simulator overlap, and the mathematical model matches the UH-60A helicopter very well over the range of frequencies critical to handling qualities evaluation. Pilot comments, however, indicate a need for improvement in the perceptual fidelity of the simulation in the areas of motion and visual cuing. The methodology used to make the fidelity assessment proved useful in showing differences in pilot work load and strategy, but additional work is needed to refine objective methods for determining causes of lack of fidelity.

Modular co-culture engineering, a new approach for metabolic engineering.

PubMed

Zhang, Haoran; Wang, Xiaonan

2016-09-01

With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

ET-26 hydrochloride (ET-26 HCl) has similar hemodynamic stability to that of etomidate in normal and uncontrolled hemorrhagic shock (UHS) rats.

PubMed

Wang, Bin; Chen, Shouming; Yang, Jun; Yang, Linghui; Liu, Jin; Zhang, Wensheng

2017-01-01

ET-26 HCl is a promising sedative-hypnotic anesthetic with virtually no effect on adrenocortical steroid synthesis. However, whether or not ET-26 HCl also has a sufficiently wide safety margin and hemodynamic stability similar to that of etomidate and related compounds remains unknown. In this study, the effects of ET-26 HCl, etomidate and propofol on therapeutic index, heart rate (HR), mean arterial pressure (MAP), maximal rate for left ventricular pressure rise (Dmax/t), and maximal rate for left ventricular pressure decline (Dmin/t) were investigated in healthy rats and a rat model of uncontrolled hemorrhagic shock (UHS). 50% effective dose (ED50) and 50% lethal dose (LD50) were determined after single bolus doses of propofol, etomidate, or ET-26 HCl using the Bliss method and the up and down method, respectively. All rats were divided into either the normal group and received either etomidate, ET-26 HCl or propofol, (n = 6 per group) or the UHS group and received either etomidate, ET-26 HCl or propofol, (n = 6 per group). In the normal group, after preparation for hemodynamic and heart-function monitoring, rats were administered a dose of one of the test agents twofold-higher than the established ED50, followed by hemodynamic and heart-function monitoring. Rats in the UHS group underwent experimentally induced UHS with a target arterial pressure of 40 mmHg for 1 hour, followed by administration of an ED50 dose of one of the experimental agents. Blood-gas analysis was conducted on samples obtained during equilibration with the experimental setup and at the end of the experiment. In the normal group, no significant differences in HR, MAP, Dmax/t and Dmin/t (all P > 0.05) were observed at any time point between the etomidate and ET-26 HCl groups, whereas HR, MAP and Dmax/t decreased briefly and Dmin/t increased following propofol administration. In the UHS group, no significant differences in HR, MAP, Dmax/t and Dmin/t were observed before and after administration

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient.

PubMed

Eldridge, David J; Delgado-Baquerizo, Manuel; Woodhouse, Jason N; Neilan, Brett A

2016-11-01

The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative

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

PubMed

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

2018-05-15

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

Evaluation of Wind Tunnel and Scaling Effects with the UH-60A Airloads Rotor

DTIC Science & Technology

2011-05-01

V! free-stream velocity, ft/s x chordwise distance from leading edge, ft #c, #s corrected/geometric shaft angles, deg $1c, $1s cos/sin components...attached to spindles that were retained by elastomeric bearings to a one-piece titanium hub. These bearings permitted blade flap, lead-lag, and...Figure 3. UH-60A small-scale rotor installed in DNW. Main rotor dampers were installed between each of the main rotor spindles and the hub to

"Uh," "Um," and Autism: Filler Disfluencies as Pragmatic Markers in Adolescents with Optimal Outcomes from Autism Spectrum Disorder

ERIC Educational Resources Information Center

Irvine, Christina A.; Eigsti, Inge-Marie; Fein, Deborah A.

2016-01-01

Filler disfluencies--"uh" and "um"--are thought to serve distinct discourse functions. We examined fillers in spontaneous speech by youth with autism spectrum disorder (ASD), who struggle with pragmatic language, and by youth with ASD who have achieved an "optimal outcome" (OO), as well as in peers with typical…

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

PubMed

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

2012-05-01

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

Accelerated Testing of UH-60 Viscous Bearings for Degraded Grease Fault

NASA Technical Reports Server (NTRS)

Dykas, Brian; Hood, Adrian; Krantz, Timothy; Klemmer, Marko

2015-01-01

An accelerated aging investigation of critical aviation bearings lubricated with MIL-PRF- 81322 grease was conducted to derive an understanding of the mechanisms of grease degradation and loss of lubrication over time. The current study focuses on UH-60 Black Hawk viscous damper bearings supporting the tail rotor driveshaft, which were subjected to more than 5800 hours of testing in a heated environment to accelerate the deterioration of the grease. The mechanism of grease degradation is a reduction in the oil/thickener ratio rather than the expected chemical degradation of grease constituents. Over the course of testing, vibration and temperature monitoring of bearings was conducted and trends for failing bearings are presented.

Metabolic engineering for microbial production and applications of copolyesters consisting of 3-hydroxybutyrate and medium-chain-length 3-hydroxyalkanoates.

PubMed

Zou, Xiang Hui; Chen, Guo-Qiang

2007-02-12

Poly(hydroxyalkanoate)s (PHAs) are a class of microbially synthesized polyesters that combine biological properties, such as biocompatibility and biodegradability, and non-bioproperties such as thermoprocessability, piezoelectricity, and nonlinear optical activity. PHA monomer structures and their contents strongly affect the PHA properties. Using metabolic engineering approaches, PHA structures and contents can be manipulated to achieve controllable monomer and PHA cellular contents. This paper focuses on metabolic engineering methods to produce PHA consisting of 3-hydroxybutyrate (3HB) and medium-chain-length 3-hydroxyalkanoates (3HA) in recombinant microbial systems. This type of copolyester has mechanical and thermal properties similar to conventional plastics such as poly(propylene) and poly(ethylene terephthalate) (PET). In addition, pathways containing engineered PHA synthases have proven to be useful for enhanced PHA production with adjustable PHA monomers and contents. The applications of PHA as implant biomaterials are briefly discussed here. In the very near term, metabolic engineering will help solve many problems in promoting PHA as a new type of plastic material for many applications.

Microbial desalination cell for enhanced biodegradation of waste engine oil using a novel bacterial strain Bacillus subtilis moh3.

PubMed

Sabina, K; Fayidh, Mohammed A; Archana, G; Sivarajan, M; Babuskin, S; Babu, P Azhagu Saravana; Radha, K Krishnan; Sukumar, M

2014-01-01

Microbial desalination cell (MDC) is a bioelectrochemical system developed recently from microbial fuel cells (MFCs), for producing green energy from organic wastes along with desalination of saltwater. MDC is proved to be a better performer than MFC in terms of power output and chemical oxygen demand removal, with desalination as an additional feature. This study investigates the application potential of MDC for integrated biodegradation of waste engine oil. This study showed, for the first time, that waste engine oil could be used as an organic substrate in MDC, achieving biodegradation of engine oil along with considerable desalination and power production. Utilization of these wastes in MDC can protect the environment from waste engine oil contamination. Indigenous oil-degrading bacteria were isolated and identified from engine oil contaminated sludge. Degradation of waste engine oil by these novel isolates was studied in batch cultures and optimized the growth conditions. The same cultures when used in MDC, gave enhanced biodegradation (70.1 +/- 0.5%) along with desalination (68.3 +/- 0.6%) and power production (3.1 +/- 0.3 mW/m2). Fourier transform-infrared spectroscopy and gas chromatography-mass spectrometry analyses were performed to characterize the degradation metabolites in the anolyte of MDC which clearly indicated the biodegradation of long chain, branched and cyclic hydrocarbons present in waste engine oil.

Engineering Ecosystems and Synthetic Ecologies#

PubMed Central

Mee, Michael T; Wang, Harris H

2012-01-01

Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here, we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. We highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of microbial ecosystem engineering. We argue that simply engineering individual microbes will lead to fragile homogenous populations that are difficult to sustain, especially in highly heterogeneous and unpredictable environments. Instead, engineered microbial ecosystems are likely to be more robust and able to achieve complex tasks at the spatial and temporal resolution needed for truly programmable biology. PMID:22722235

Application of Neural Networks to Predict UH-60L Electrical Generator Condition using (IMD-HUMS) Data

DTIC Science & Technology

2006-12-01

Data transfer unit ( DTU ) • Remote data concentrator (RDC) • Main processor unit (MPU) • 2 junction boxes (JB1/JB2) • 20 drive train and...NETWORKS TO PREDICT UH-60L ELECTRICAL GENERATOR CONDITION USING (IMD-HUMS) DATA by Evangelos Tourvalis December 2006 Thesis Advisor...including the time for reviewing instruction, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the

If You Say Thee Uh You Are Describing Something Hard: The On-Line Attribution of Disfluency during Reference Comprehension

ERIC Educational Resources Information Center

Arnold, Jennifer E.; Kam, Carla L. Hudson; Tanenhaus, Michael K.

2007-01-01

Eye-tracking and gating experiments examined reference comprehension with fluent (Click on the red. . .) and disfluent (Click on [pause] thee uh red . . .) instructions while listeners viewed displays with 2 familiar (e.g., ice cream cones) and 2 unfamiliar objects (e.g., squiggly shapes). Disfluent instructions made unfamiliar objects more…

A failure effects simulation of a low authority flight control augmentation system on a UH-1H helicopter

NASA Technical Reports Server (NTRS)

Corliss, L. D.; Talbot, P. D.

1977-01-01

A two-pilot moving base simulator experiment was conducted to assess the effects of servo failures of a flight control system on the transient dynamics of a Bell UH-1H helicopter. The flight control hardware considered was part of the V/STOLAND system built with control authorities of from 20-40%. Servo hardover and oscillatory failures were simulated in each control axis. Measurements were made to determine the adequacy of the failure monitoring system time delay and the servo center and lock time constant, the pilot reaction times, and the altitude and attitude excursions of the helicopter at hover and 60 knots. Safe recoveries were made from all failures under VFR conditions. Pilot reaction times were from 0.5 to 0.75 sec. Reduction of monitor delay times below these values resulted in significantly reduced excursion envelopes. A subsequent flight test was conducted on a UH-1H helicopter with the V/STOLAND system installed. Series servo hardovers were introduced in hover and at 60 knots straight and level. Data from these tests are included for comparison.

A high fidelity real-time simulation of a small turboshaft engine

NASA Technical Reports Server (NTRS)

Ballin, Mark G.

1988-01-01

A high-fidelity component-type model and real-time digital simulation of the General Electric T700-GE-700 turboshaft engine were developed for use with current generation real-time blade-element rotor helicopter simulations. A control system model based on the specification fuel control system used in the UH-60A Black Hawk helicopter is also presented. The modeling assumptions and real-time digital implementation methods particular to the simulation of small turboshaft engines are described. The validity of the simulation is demonstrated by comparison with analysis-oriented simulations developed by the manufacturer, available test data, and flight-test time histories.

Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology.

PubMed

Pandey, Ramesh Prasad; Parajuli, Prakash; Koffas, Mattheos A G; Sohng, Jae Kyung

2016-01-01

In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. Copyright © 2016 Elsevier Inc. All rights reserved.

V/STOLAND avionics system flight-test data on a UH-1H helicopter

NASA Technical Reports Server (NTRS)

Baker, F. A.; Jaynes, D. N.; Corliss, L. D.; Liden, S.; Merrick, R. B.; Dugan, D. C.

1980-01-01

The flight-acceptance test results obtained during the acceptance tests of the V/STOLAND (versatile simplex digital avionics system) digital avionics system on a Bell UH-1H helicopter in 1977 at Ames Research Center are presented. The system provides navigation, guidance, control, and display functions for NASA terminal area VTOL research programs and for the Army handling qualities research programs at Ames Research Center. The acceptance test verified system performance and contractual acceptability. The V/STOLAND hardware navigation, guidance, and control laws resident in the digital computers are described. Typical flight-test data are shown and discussed as documentation of the system performance at acceptance from the contractor.

Engineering Shewanella oneidensis enables xylose-fed microbial fuel cell.

PubMed

Li, Feng; Li, Yuanxiu; Sun, Liming; Li, Xiaofei; Yin, Changji; An, Xingjuan; Chen, Xiaoli; Tian, Yao; Song, Hao

2017-01-01

The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications. Herein, to enable S. oneidensis to directly utilize xylose as the sole carbon source for bioelectricity production in MFCs, we used synthetic biology strategies to successfully construct four genetically engineered S. oneidensis (namely XE, GE, XS, and GS) by assembling one of the xylose transporters (from Candida intermedia and Clostridium acetobutylicum ) with one of intracellular xylose metabolic pathways (the isomerase pathway from Escherichia coli and the oxidoreductase pathway from Scheffersomyces stipites ), respectively. We found that among these engineered S. oneidensis strains, the strain GS (i.e. harbouring Gxf1 gene encoding the xylose facilitator from C. intermedi , and XYL1 , XYL2 , and XKS1 genes encoding the xylose oxidoreductase pathway from S. stipites ) was able to generate the highest power density, enabling a maximum electricity power density of 2.1 ± 0.1 mW/m 2 . To the best of our knowledge, this was the first report on the rationally designed Shewanella that could use xylose as the sole carbon source and electron donor to produce electricity. The synthetic biology strategies developed in this study could be further extended to rationally engineer other exoelectrogens for lignocellulosic biomass utilization to generate electricity power.

Microbial synthesis of propane by engineering valine pathway and aldehyde-deformylating oxygenase.

PubMed

Zhang, Lei; Liang, Yajing; Wu, Wei; Tan, Xiaoming; Lu, Xuefeng

2016-01-01

Propane, a major component of liquid petroleum gas (LPG) derived from fossil fuels, has widespread applications in vehicles, cooking, and ambient heating. Given the concerns about fossil fuel depletion and carbon emission, exploiting alternative and renewable source of propane have become attractive. In this study, we report the construction of a novel propane biosynthetic pathway in Escherichia coli. We constructed an aldehyde reductases (ALR)-deprived E. coli strain BW25113(DE3) Δ13 via genetic engineering, which produced sufficient isobutyraldehyde precursors and finally achieved de novo synthesis of propane (91 μg/L) by assembling the engineered valine pathway and cyanobacterial aldehyde-deformylating oxygenase (ADO). Additionally, after extensive screening of ADO mutants generated by engineering the active center to accommodate branched-chain isobutyraldehyde, we identified two ADO mutants (I127G, I127G/A48G) which exhibited higher catalytic activity for isobutyraldehyde and improved propane productivity by three times (267 μg/L). The propane biosynthetic pathway constructed here through the engineered valine pathway can produce abundant isobutyraldehyde for ADO and overcome the low availability of precursors in propane production. Furthermore, the rational design aiming at the ADO active center illustrates the plasticity and catalytic potential of ADO. These results together highlight the potential for developing a microbial biomanufacturing platform for propane.

Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation.

PubMed

Luo, Hongzhen; Yang, Rongling; Zhao, Yuping; Wang, Zhaoyu; Liu, Zheng; Huang, Mengyu; Zeng, Qingwei

2018-04-01

Butyric acid is an important platform chemical, which is widely used in the fields of food, pharmaceutical, energy, etc. Microbial fermentation as an alternative approach for butyric acid production is attracting great attention as it is an environmentally friendly bioprocessing. However, traditional fermentative butyric acid production is still not economically competitive compared to chemical synthesis route, due to the low titer, low productivity, and high production cost. Therefore, reduction of butyric acid production cost by utilization of alternative inexpensive feedstock, and improvement of butyric acid production and productivity has become an important target. Recently, several advanced strategies have been developed for enhanced butyric acid production, including bioprocess techniques and metabolic engineering methods. This review provides an overview of advances and strategies in process and strain engineering for butyric acid production by microbial fermentation. Additionally, future perspectives on improvement of butyric acid production are also proposed. Copyright © 2018 Elsevier Ltd. All rights reserved.

In silico characterization of microbial electrosynthesis for metabolic engineering of biochemicals

PubMed Central

2011-01-01

Background A critical concern in metabolic engineering is the need to balance the demand and supply of redox intermediates such as NADH. Bioelectrochemical techniques offer a novel and promising method to alleviate redox imbalances during the synthesis of biochemicals and biofuels. Broadly, these techniques reduce intracellular NAD+ to NADH and therefore manipulate the cell's redox balance. The cellular response to such redox changes and the additional reducing power available to the cell can be harnessed to produce desired metabolites. In the context of microbial fermentation, these bioelectrochemical techniques can be used to improve product yields and/or productivity. Results We have developed a method to characterize the role of bioelectrosynthesis in chemical production using the genome-scale metabolic model of E. coli. The results in this paper elucidate the role of bioelectrosynthesis and its impact on biomass growth, cellular ATP yields and biochemical production. The results also suggest that strain design strategies can change for fermentation processes that employ microbial electrosynthesis and suggest that dynamic operating strategies lead to maximizing productivity. Conclusions The results in this paper provide a systematic understanding of the benefits and limitations of bioelectrochemical techniques for biochemical production and highlight how electrical enhancement can impact cellular metabolism and biochemical production. PMID:21967745

Employing metabolic engineered lipolytic microbial platform for 1-alkene one-step conversion.

PubMed

Wang, Juli; Yu, Haiying; Zhu, Kun

2018-05-01

1-Alkenes are traditionally used as basic chemicals with great importance. Biosynthetic 1-alkenes also have the potential to serve as biofuels. In this study, we engineered a Pseudomonas lipolytic microbial platform for 1-alkene production using hydrophobic substrate as sole carbon source. Fatty acid decarboxylase UndA and UndB were cloned and expressed, which successfully produced 1-alkenes. Optimal culturing temperature and the interruption of competitive pathway were proven to be beneficial to 1-alkene synthesis. Chromosomal integration of UndB conferred 177.8 mg/L 1-alkenes (mainly 1-undecene) in lauric acid medium and 128.9 mg/L 1-alkenes (mainly 1-pentadecene) in palm oil medium. Thioesterase expression, adjustments of fatty acid degradation pathway and a second copy of UndB improved 1-alkene titer to 1102.6 mg/L using lauric acid and 778.4 mg/L using palm oil. All in all, this study offers the first demonstration of lipolytic microbial 1-alkene producing platform with highest reported 1-alkene product titer up to date. Copyright © 2018 Elsevier Ltd. All rights reserved.

Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering

PubMed Central

Foo, Jee Loon; Jensen, Heather M.; Dahl, Robert H.; George, Kevin; Keasling, Jay D.; Lee, Taek Soon; Leong, Susanna

2014-01-01

ABSTRACT Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerance phenotypes belonged to diverse functional groups, such as oxidative stress response (soxS, fpr, and nrdH), general stress response (metR, yqhD, and gidB), heat shock-related response (ibpA), and transport (mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production. PMID:25370492

Flight Test Identification and Simulation of a UH-60A Helicopter and Slung Load

NASA Technical Reports Server (NTRS)

Cicolani, Luigi S.; Sahai, Ranjana; Tucker, George E.; McCoy, Allen H.; Tyson, Peter H.; Tischler, Mark B.; Rosen, Aviv

2001-01-01

Helicopter slung-load operations are common in both military and civil contexts. Helicopters and loads are often qualified for these operations by means of flight tests, which can be expensive and time consuming. There is significant potential to reduce such costs both through revisions in flight-test methods and by using validated simulation models. To these ends, flight tests were conducted at Moffett Field to demonstrate the identification of key dynamic parameters during flight tests (aircraft stability margins and handling-qualities parameters, and load pendulum stability), and to accumulate a data base for simulation development and validation. The test aircraft was a UH-60A Black Hawk, and the primary test load was an instrumented 8- by 6- by 6-ft cargo container. Tests were focused on the lateral and longitudinal axes, which are the axes most affected by the load pendulum modes in the frequency range of interest for handling qualities; tests were conducted at airspeeds from hover to 80 knots. Using telemetered data, the dynamic parameters were evaluated in near real time after each test airspeed and before clearing the aircraft to the next test point. These computations were completed in under 1 min. A simulation model was implemented by integrating an advanced model of the UH-60A aerodynamics, dynamic equations for the two-body slung-load system, and load static aerodynamics obtained from wind-tunnel measurements. Comparisons with flight data for the helicopter alone and with a slung load showed good overall agreement for all parameters and test points; however, unmodeled secondary dynamic losses around 2 Hz were found in the helicopter model and they resulted in conservative stability margin estimates.

Guiding bioprocess design by microbial ecology.

PubMed

Volmer, Jan; Schmid, Andreas; Bühler, Bruno

2015-06-01

Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application of Freeze-Dried Powders of Genetically Engineered Microbial Strains as Adsorbents for Rare Earth Metal Ions.

PubMed

Moriwaki, Hiroshi; Masuda, Reiko; Yamazaki, Yuki; Horiuchi, Kaoru; Miyashita, Mari; Kasahara, Jun; Tanaka, Tatsuhito; Yamamoto, Hiroki

2016-10-12

The adsorption behaviors of the rare earth metal ions onto freeze-dried powders of genetically engineered microbial strains were compared. Cell powders obtained from four kinds of strains, Bacillus subtilis 168 wild type (WT), lipoteichoic acid-defective (ΔLTA), wall teichoic acid-defective (ΔWTA), and cell wall hydrolases-defective (EFKYOJLp) strains, were used as an adsorbent of the rare earth metal ions at pH 3. The adsorption ability of the rare earth metal ions was in the order of EFKYOJLp > WT > ΔLTA > ΔWTA. The order was the same as the order of the phosphorus quantity of the strains. This result indicates that the main adsorption sites for the ions are the phosphate groups and the teichoic acids, LTA and WTA, that contribute to the adsorption of the rare earth metal ions onto the cell walls. The contribution of WTA was clearly greater than that of LTA. Each microbial powder was added to a solution containing 16 kinds of rare earth metal ions, and the removals (%) of each rare earth metal ion were obtained. The scandium ion showed the highest removal (%), while that of the lanthanum ion was the lowest for all the microbial powders. Differences in the distribution coefficients between the kinds of lanthanide ions by the EFKYOJLp and ΔWTA powders were greater than those of the other strains. Therefore, the EFKYOJLp and ΔWTA powders could be applicable for the selective extraction of the lanthanide ions. The ΔLTA powder coagulated by mixing with a rare earth metal ion, although no sedimentation of the WT or ΔWTA powder with a rare earth metal ion was observed under the same conditions. The EFKYOJLp powder was also coagulated, but its flocculating activity was lower than that of ΔLTA. The ΔLTA and EFKYOJLp powders have a long shape compared to those of the WT or ΔWTA strain. The shapes of the cells will play an important role in the sedimentation of the microbial powders with rare earth metal ions. As the results, three kinds of the genetically

Leveraging knowledge engineering and machine learning for microbial bio-manufacturing.

PubMed

Oyetunde, Tolutola; Bao, Forrest Sheng; Chen, Jiung-Wen; Martin, Hector Garcia; Tang, Yinjie J

2018-05-03

Genome scale modeling (GSM) predicts the performance of microbial workhorses and helps identify beneficial gene targets. GSM integrated with intracellular flux dynamics, omics, and thermodynamics have shown remarkable progress in both elucidating complex cellular phenomena and computational strain design (CSD). Nonetheless, these models still show high uncertainty due to a poor understanding of innate pathway regulations, metabolic burdens, and other factors (such as stress tolerance and metabolite channeling). Besides, the engineered hosts may have genetic mutations or non-genetic variations in bioreactor conditions and thus CSD rarely foresees fermentation rate and titer. Metabolic models play important role in design-build-test-learn cycles for strain improvement, and machine learning (ML) may provide a viable complementary approach for driving strain design and deciphering cellular processes. In order to develop quality ML models, knowledge engineering leverages and standardizes the wealth of information in literature (e.g., genomic/phenomic data, synthetic biology strategies, and bioprocess variables). Data driven frameworks can offer new constraints for mechanistic models to describe cellular regulations, to design pathways, to search gene targets, and to estimate fermentation titer/rate/yield under specified growth conditions (e.g., mixing, nutrients, and O 2 ). This review highlights the scope of information collections, database constructions, and machine learning techniques (such as deep learning and transfer learning), which may facilitate "Learn and Design" for strain development. Copyright © 2018. Published by Elsevier Inc.

Microbially derived biosensors for diagnosis, monitoring and epidemiology.

PubMed

Chang, Hung-Ju; Voyvodic, Peter L; Zúñiga, Ana; Bonnet, Jérôme

2017-09-01

Living cells have evolved to detect and process various signals and can self-replicate, presenting an attractive platform for engineering scalable and affordable biosensing devices. Microbes are perfect candidates: they are inexpensive and easy to manipulate and store. Recent advances in synthetic biology promise to streamline the engineering of microbial biosensors with unprecedented capabilities. Here we review the applications of microbially-derived biosensors with a focus on environmental monitoring and healthcare applications. We also identify critical challenges that need to be addressed in order to translate the potential of synthetic microbial biosensors into large-scale, real-world applications. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

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

PubMed

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

2018-01-01

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

In-Drift Microbial Communities

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

D. Jolley

2000-11-09

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999).more » This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.« less

Helicopter Noise Definition Report UH-60A, S-76, A-109, 206-L

DTIC Science & Technology

1981-12-01

ALL THE WORLDS AIRCRAF~ 25 -.. H., . . . I - I’I Fi.I 2.3. Sikrsk UH .0A "Bla *khaw -" | r a’ Fig. 2.3.2 Sikoraky S-76, "Spirit" -. q A,~ ~ j A. "I...1305 1:2 -04830 8545 82+9 75*1 O1,6 87,b Sete 11,5 10s5 1#2 -1*0 31 85.7 83,3 75,1 80.0 86#6 67,7 16#5 150 1#1 -0#7 32 83.7 81.2 73.5 79.3 85,6 8669...RIO. TIMITIKE PNLTP WAR REOORDED RAOD TIMiTIME PNLTM WAS RADIATED R/OlAIORAFT RPATE OLI•ND OR DS6ENT O’D-ANGtOL•IM OR DESCENT ANGE.E G*6GROUND SPEED

Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

PubMed

Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

2016-04-01

Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.

Center of Microbial Oceanography Research and Education (C-MORE) Initiatives Toward Promoting Diversity in the Ocean Sciences

NASA Astrophysics Data System (ADS)

Bruno, B. C.

2007-05-01

The ocean sciences suffer from a lack of diversity, particularly among indigenous peoples, despite the fact that indigenous peoples often have deep, cultural knowledge about the marine environment. Nowhere is this inequity more glaring than in Hawaii. Traditional knowledge in marine science enabled Native Hawaiians and Pacific Islanders (NHPI) to become world leaders in transpacific canoe voyaging, aquaculture, and fisheries. Yet today, NHPI are severely underrepresented in the ocean sciences (and in STEM fields in general) at all levels of education and employment. When compared to other ethnic and racial groups in Hawaii, NHPI students as a group have among the poorest educational performance, indicated in part by underrepresentation in college enrolment and pre-college gifted and talented programs, as well as overrepresentation in eligibility for special education and free and reduced lunch programs. The Center of Microbial Oceanography Research and Education (C-MORE), a NSF-funded, multi-institutional Science and Technology Center based at the University of Hawai (UH), is determined to address this inequity. C- MORE is committed to increasing diversity in the ocean sciences, particularly among NHPI, at all levels of education and research. Our approach is to work with existing programs with a track record of increasing diversity among NHPI. We are currently developing culturally relevant materials including educational games for K-12 students, mentorships for high school and community college students, and laboratory and shipboard experiences for teachers and undergraduates in partnership with minority-serving organizations. Some of our main partners are EPSCoR (Experimental Program to Stimulate Competitive Research), Ka `Imi `Ike (an NSF- funded program to recruit and retain NHPI undergraduates in geosciences), Upward Bound (an enrichment program for economically disadvantaged high school students which includes intensive summer courses), the UH Center on

Blade Displacement Measurements of the Full-Scale UH-60A Airloads Rotor

NASA Technical Reports Server (NTRS)

Barrows, Danny A.; Burner, Alpheus W.; Abrego, Anita I.; Olson, Lawrence E.

2011-01-01

Blade displacement measurements were acquired during a wind tunnel test of the full-scale UH-60A Airloads rotor. The test was conducted in the 40- by 80-Foot Wind Tunnel of the National Full-Scale Aerodynamics Complex at NASA Ames Research Center. Multi-camera photogrammetry was used to measure the blade displacements of the four-bladed rotor. These measurements encompass a range of test conditions that include advance ratios from 0.15 to unique slowed-rotor simulations as high as 1.0, thrust coefficient to rotor solidity ratios from 0.01 to 0.13, and rotor shaft angles from -10.0 to 8.0 degrees. The objective of these measurements is to provide a benchmark blade displacement database to be utilized in the development and validation of rotorcraft computational tools. The methodology, system development, measurement techniques, and preliminary sample blade displacement measurements are presented.

Uh and um in Children With Autism Spectrum Disorders or Language Impairment

PubMed Central

Gorman, Kyle; Olson, Lindsay; Presmanes Hill, Alison; Lunsford, Rebecca; Heeman, Peter A.; van Santen, Jan P. H.

2016-01-01

Atypical pragmatic language is often present in individuals with autism spectrum disorders (ASD), along with delays or deficits in structural language. This study investigated the use of the “fillers” uh and um by children ages 4–8 during the autism diagnostic observation schedule. Fillers reflect speakers’ difficulties with planning and delivering speech, but they also serve communicative purposes, such as negotiating control of the floor or conveying uncertainty. We hypothesized that children with ASD would use different patterns of fillers compared to peers with typical development or with specific language impairment (SLI), reflecting differences in social ability and communicative intent. Regression analyses revealed that children in the ASD group were much less likely to use um than children in the other two groups. Filler use is an easy-to-quantify feature of behavior that, in concert with other observations, may help to distinguish ASD from SLI. PMID:26800246

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production.

PubMed

George, Kevin W; Chen, Amy; Jain, Aakriti; Batth, Tanveer S; Baidoo, Edward E K; Wang, George; Adams, Paul D; Petzold, Christopher J; Keasling, Jay D; Lee, Taek Soon

2014-08-01

The ability to rapidly assess and optimize heterologous pathway function is critical for effective metabolic engineering. Here, we develop a systematic approach to pathway analysis based on correlations between targeted proteins and metabolites and apply it to the microbial production of isopentenol, a promising biofuel. Starting with a seven-gene pathway, we performed a correlation analysis to reduce pathway complexity and identified two pathway proteins as the primary determinants of efficient isopentenol production. Aided by the targeted quantification of relevant pathway intermediates, we constructed and subsequently validated a conceptual model of isopentenol pathway function. Informed by our analysis, we assembled a strain which produced isopentenol at a titer 1.5 g/L, or 46% of theoretical yield. Our engineering approach allowed us to accurately identify bottlenecks and determine appropriate pathway balance. Paired with high-throughput cloning techniques and analytics, this strategy should prove useful for the analysis and optimization of increasingly complex heterologous pathways. © 2014 Wiley Periodicals, Inc.

Metabolic Network Modeling of Microbial Communities

PubMed Central

Biggs, Matthew B.; Medlock, Gregory L.; Kolling, Glynis L.

2015-01-01

Genome-scale metabolic network reconstructions and constraint-based analysis are powerful methods that have the potential to make functional predictions about microbial communities. Current use of genome-scale metabolic networks to characterize the metabolic functions of microbial communities includes species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the “enzyme-soup” approach, multi-scale modeling, and others. There are many challenges inherent to the field, including a need for tools that accurately assign high-level omics signals to individual community members, new automated reconstruction methods that rival manual curation, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be proportional advances in the fields of ecology, health science, and microbial community engineering. PMID:26109480

An Examination of Unsteady Airloads on a UH-60A Rotor: Computation Versus Measurement

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Lee-Rausch, Elizabeth

2012-01-01

An unsteady Reynolds-averaged Navier-Stokes solver for unstructured grids is used to simulate the flow over a UH-60A rotor. Traditionally, the computed pressure and shear stresses are integrated on the computational mesh at selected radial stations and compared to measured airloads. However, the corresponding integration of experimental data uses only the pressure contribution, and the set of integration points (pressure taps) is modest compared to the computational mesh resolution. This paper examines the difference between the traditional integration of computed airloads and an integration consistent with that used for the experimental data. In addition, a comparison of chordwise pressure distributions between computation and measurement is made. Examination of this unsteady pressure data provides new opportunities to understand differences between computation and flight measurement.

Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

PubMed

Yu, Ping; Chen, Xingge; Li, Peng

2017-09-01

Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

System Engineering and Management,

DTIC Science & Technology

1994-08-11

UJ H os UH Z Z * CO CD O ZO 1 cc CO CO o u. UJ a. z < u. < a 3 os a H < 3 S Z UJ OH CL „ • . LU...OS H Q CJ Z UH Z —.__J Q ’O * CO CO I-H CO HH UJ 3 I-H CO Z Z UJ tt...SHvnoa -- isoD Nomsmtov urn 60 oo OO UJ O oc oo oo >- I <c a: <t c/) >■ z <t a. UJ Q 0) o (O (_3 * >- o _JO et 2: r

Blade Displacement Predictions for the Full-Scale UH-60A Airloads Rotor

NASA Technical Reports Server (NTRS)

Bledron, Robert T.; Lee-Rausch, Elizabeth M.

2014-01-01

An unsteady Reynolds-Averaged Navier-Stokes solver for unstructured grids is loosely coupled to a rotorcraft comprehensive code and used to simulate two different test conditions from a wind-tunnel test of a full-scale UH-60A rotor. Performance data and sectional airloads from the simulation are compared with corresponding tunnel data to assess the level of fidelity of the aerodynamic aspects of the simulation. The focus then turns to a comparison of the blade displacements, both rigid (blade root) and elastic. Comparisons of computed root motions are made with data from three independent measurement systems. Finally, comparisons are made between computed elastic bending and elastic twist, and the corresponding measurements obtained from a photogrammetry system. Overall the correlation between computed and measured displacements was good, especially for the root pitch and lag motions and the elastic bending deformation. The correlation of root lead-lag motion and elastic twist deformation was less favorable.

Ground shake test of the UH-60A helicopter airframe and comparison with NASTRAN finite element model predictions

NASA Technical Reports Server (NTRS)

Howland, G. R.; Durno, J. A.; Twomey, W. J.

1990-01-01

Sikorsky Aircraft, together with the other major helicopter airframe manufacturers, is engaged in a study to improve the use of finite element analysis to predict the dynamic behavior of helicopter airframes, under a rotorcraft structural dynamics program called DAMVIBS (Design Analysis Methods for VIBrationS), sponsored by the NASA-Langley. The test plan and test results are presented for a shake test of the UH-60A BLACK HAWK helicopter. A comparison is also presented of test results with results obtained from analysis using a NASTRAN finite element model.

Biofuel alternatives to ethanol: pumping the microbial well

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

Fortman, J. L.; Chhabra, Swapnil; Mukhopadhyay, Aindrila

Engineered microorganisms are currently used for the production of food products, pharmaceuticals, ethanol fuel and more. Even so, the enormous potential of this technology has yet to be fully exploited. The need for sustainable sources of transportation fuels has gener-ated a tremendous interest in technologies that enable biofuel production. Decades of work have produced a considerable knowledge-base for the physiology and pathway engineering of microbes, making microbial engineering an ideal strategy for producing biofuel. Although ethanol currently dominates the biofuel mar-ket, some of its inherent physical properties make it a less than ideal product. To highlight additional options, we reviewmore » advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways.« less

Biofuel alternatives to ethanol: pumping the microbial well

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

Fortman, J.L.; Chhabra, Swapnil; Mukhopadhyay, Aindrila

2009-08-19

Engineered microorganisms are currently used for the production of food products, pharmaceuticals, ethanol fuel and more. Even so, the enormous potential of this technology has yet to be fully exploited. The need for sustainable sources of transportation fuels has generated a tremendous interest in technologies that enable biofuel production. Decades of work have produced a considerable knowledge-base for the physiology and pathway engineering of microbes, making microbial engineering an ideal strategy for producing biofuel. Although ethanol currently dominates the biofuel market, some of its inherent physical properties make it a less than ideal product. To highlight additional options, we reviewmore » advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways.« less

Biochemical Engineering Fundamentals

ERIC Educational Resources Information Center

Bailey, J. E.; Ollis, D. F.

1976-01-01

Discusses a biochemical engineering course that is offered as part of a chemical engineering curriculum and includes topics that influence the behavior of man-made or natural microbial or enzyme reactors. (MLH)

Strategies for enhancing microbial tolerance to inhibitors for biofuel production: A review.

PubMed

Wang, Shizeng; Sun, Xinxiao; Yuan, Qipeng

2018-06-01

Using lignocellulosic biomass for the production of renewable biofuel provides a sustainable and promising solution to the crisis of energy and environment. However, the processes of biomass pretreatment and biofuel fermentation bring a variety of inhibitors to microbial strains. These inhibitors repress microbial growth, decrease biofuel yields and increase fermentation costs. The production of biofuels from renewable lignocellulosic biomass relies on the development of tolerant and robust microbial strains. In recent years, the advancement of tolerance engineering and evolutionary engineering provides powerful platform for obtaining host strains with desired tolerance for further metabolic engineering of biofuel pathways. In this review, we summarized the inhibitors derived from biomass pretreatment and biofuel fermentation, the mechanisms of inhibitor toxicity, and the strategies for enhancing microbial tolerance. Copyright © 2018 Elsevier Ltd. All rights reserved.

UH-60A Black Hawk engineering simulation program. Volume 1: Mathematical model

NASA Technical Reports Server (NTRS)

Howlett, J. J.

1981-01-01

A nonlinear mathematical model of the UR-60A Black Hawk helicopter was developed. This mathematical model, which was based on the Sikorsky General Helicopter (Gen Hel) Flight Dynamics Simulation, provides NASA with an engineering simulation for performance and handling qualities evaluations. This mathematical model is total systems definition of the Black Hawk helicopter represented at a uniform level of sophistication considered necessary for handling qualities evaluations. The model is a total force, large angle representation in six rigid body degrees of freedom. Rotor blade flapping, lagging, and hub rotational degrees of freedom are also represented. In addition to the basic helicopter modules, supportive modules were defined for the landing interface, power unit, ground effects, and gust penetration. Information defining the cockpit environment relevant to pilot in the loop simulation is presented.

Detached Eddy Simulation of the UH-60 Rotor Wake Using Adaptive Mesh Refinement

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.; Ahmad, Jasim U.

2012-01-01

Time-dependent Navier-Stokes flow simulations have been carried out for a UH-60 rotor with simplified hub in forward flight and hover flight conditions. Flexible rotor blades and flight trim conditions are modeled and established by loosely coupling the OVERFLOW Computational Fluid Dynamics (CFD) code with the CAMRAD II helicopter comprehensive code. High order spatial differences, Adaptive Mesh Refinement (AMR), and Detached Eddy Simulation (DES) are used to obtain highly resolved vortex wakes, where the largest turbulent structures are captured. Special attention is directed towards ensuring the dual time accuracy is within the asymptotic range, and verifying the loose coupling convergence process using AMR. The AMR/DES simulation produced vortical worms for forward flight and hover conditions, similar to previous results obtained for the TRAM rotor in hover. AMR proved to be an efficient means to capture a rotor wake without a priori knowledge of the wake shape.

An Economic Framework of Microbial Trade

PubMed Central

Mee, Michael T.

2015-01-01

A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET) from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET) model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a necessary condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular exchange. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments that put greater pressure on group selection versus individual selection will promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results match the predictions of the model. This framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century. PMID:26222307

Water Microbiology Kit/Microbial Capture Devices (WMK MCD)

NASA Image and Video Library

2009-08-04

ISS020-E-027318 (4 Aug. 2009) --- Canadian Space Agency astronaut Robert Thirsk, Expedition 20 flight engineer, performs a subsequent in-flight analysis with a Water Microbiology Kit/Microbial Capture Devices (WMK MCD) for microbial traces in the Destiny laboratory of the International Space Station.

[Synthetic biology toward microbial secondary metabolites and pharmaceuticals].

PubMed

Wu, Lin-Zhuan; Hong, Bin

2013-02-01

Microbial secondary metabolites are one of the major sources of anti-bacterial, anti-fungal, antitumor, anti-virus and immunosuppressive agents for clinical use. Present challenges in microbial pharmaceutical development are the discovery of novel secondary metabolites with significant biological activities, improving the fermentation titers of industrial microbial strains, and production of natural product drugs by re-establishing their biosynthetic pathways in suitable microbial hosts. Synthetic biology, which is developed from systematic biology and metabolic engineering, provides a significant driving force for microbial pharmaceutical development. The review describes the major applications of synthetic biology in novel microbial secondary metabolite discovery, improved production of known secondary metabolites and the production of some natural drugs in genetically modified or reconstructed model microorganisms.

[Fermentation production of microbial catalase and its application in textile industry].

PubMed

Zhang, Dongxu; Du, Guocheng; Chen, Jian

2010-11-01

Microbial catalase is an important industrial enzyme that catalyzes the decomposition of hydrogen peroxide to water and oxygen. This enzyme has great potential of application in food, textile and pharmaceutical industries. The production of microbial catalase has been significantly improved thanks to advances in bioprocess engineering and genetic engineering. In this paper, we review the progresses in fermentation production of microbial catalase and its application in textile industry. Among these progresses, we will highlight strain isolation, substrate and environment optimization, enzyme induction, construction of engineering strains and application process optimization. Meanwhile, we also address future research trends for microbial catalase production and its application in textile industry. Molecular modification (site-directed mutagenesis and directed revolution) will endue catalase with high pH and temperature stabilities. Improvement of catalase production, based on the understanding of induction mechanism and the process control of recombinant stain fermentation, will further accelerate the application of catalase in textile industry.

Management of Electronic Test Equipment. Volume 3. Organizations, Policies, and Procedures.

DTIC Science & Technology

1986-07-01

is not guaranteed. The best example, probably, is the UH - 60 Black Hawk program, where the specific tools used by organizational maintainers were nailed...tools. This innovative and highly effective approach was large!i, Successful. even though it became obvious once the UH - 60 was fielded, that a special...test set was necessary to cope with the electronic control unit assembly of the turbine engine. The UH - 60 example, however, does illustrate that support

Flight-Time Identification of a UH-60A Helicopter and Slung Load

NASA Technical Reports Server (NTRS)

Cicolani, Luigi S.; McCoy, Allen H.; Tischler, Mark B.; Tucker, George E.; Gatenio, Pinhas; Marmar, Dani

1998-01-01

This paper describes a flight test demonstration of a system for identification of the stability and handling qualities parameters of a helicopter-slung load configuration simultaneously with flight testing, and the results obtained.Tests were conducted with a UH-60A Black Hawk at speeds from hover to 80 kts. The principal test load was an instrumented 8 x 6 x 6 ft cargo container. The identification used frequency domain analysis in the frequency range to 2 Hz, and focussed on the longitudinal and lateral control axes since these are the axes most affected by the load pendulum modes in the frequency range of interest for handling qualities. Results were computed for stability margins, handling qualities parameters and load pendulum stability. The computations took an average of 4 minutes before clearing the aircraft to the next test point. Important reductions in handling qualities were computed in some cases, depending, on control axis and load-slung combination. A database, including load dynamics measurements, was accumulated for subsequent simulation development and validation.

UH cosmic rays and solar system material - The elements just beyond iron

NASA Technical Reports Server (NTRS)

Wefel, J. P.; Schramm, D. N.; Blake, J. B.

1977-01-01

The nucleosynthesis of cosmic-ray elements between the iron peak and the rare-earth region is examined, and compositional changes introduced by propagation in interstellar space are calculated. Theories on the origin of elements heavier than iron are reviewed, a supernova model of explosive nucleosynthesis is adopted for the ultraheavy (UH) cosmic rays, and computational results for different source distributions are compared with experimental data. It is shown that both the cosmic-ray data and the nucleosynthesis calculations are not yet of sufficient precision to pinpoint the processes occurring in cosmic-ray source regions, that the available data do provide boundary conditions for cosmic-ray nucleosynthesis, and that these limits may apply to the origin of elements in the solar system. Specifically, it is concluded that solar-system abundances appear to be consistent with a superposition of the massive-star core-helium-burning s-process plus explosive-carbon-burning synthesis for the elements from Cu to As and are explained adequately by the s- and r-processes for heavier elements.

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.

Microbial production of value-added nutraceuticals.

PubMed

Wang, Jian; Guleria, Sanjay; Koffas, Mattheos Ag; Yan, Yajun

2016-02-01

Nutraceuticals are important natural bioactive compounds that confer health-promoting and medical benefits to humans. Globally growing demands for value-added nutraceuticals for prevention and treatment of human diseases have rendered nutraceuticals a multi-billion dollar market. However, supply limitations and extraction difficulties from natural sources such as plants, animals or fungi, restrict the large-scale use of nutraceuticals. Metabolic engineering via microbial production platforms has been advanced as an eco-friendly alternative approach for production of value-added nutraceuticals from simple carbon sources. Microbial platforms like the most widely used Escherichia coli and Saccharomyces cerevisiae have been engineered as versatile cell factories for production of diverse and complex value-added chemicals such as phytochemicals, prebiotics, polysaccaharides and poly amino acids. This review highlights the recent progresses in biological production of value-added nutraceuticals via metabolic engineering approaches. Copyright © 2015 Elsevier Ltd. All rights reserved.

Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities

DTIC Science & Technology

2004-09-01

Science 190 and Engineering DOCTORAL DISSERTATION Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj...Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj Massachusetts Institute of Technology Cambridge, Massachusetts 02139 and Woods Hole...Phylogenetic Structure of Two Complex Marine Microbial Communities. Ph.D. Thesis. MIT/WHOI, 2004-11. Approved for publication; distribution unlimited

Army Aircraft Safety Performance Review, FY 87-FY 91. UH-60, OH-58D, AH-64, MH/CH-47D

DTIC Science & Technology

1992-12-01

is $10,000 or more, but less than $200,000; a nonfatal injury that causes any loss of time from work beyond the day or shift on which it occurred; or...a nonfatal illness or disability that causes loss of time from work or disability at any time (lost-time case). Class D accident The resulting...flex horoscope so that a complete inspection of the drive shaft can be made. Wire strike While on approach to land at the scene of a UH-60 wire

Microbial load monitor

NASA Technical Reports Server (NTRS)

Caplin, R. S.; Royer, E. R.

1977-01-01

Design analysis of a microbial load monitor system flight engineering model was presented. Checkout of the card taper and media pump system was fabricated as well as the final two incubating reading heads, the sample receiving and card loading device assembly, related sterility testing, and software. Progress in these areas was summarized.

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.

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.

Recent advances in systems metabolic engineering tools and strategies.

PubMed

Chae, Tong Un; Choi, So Young; Kim, Je Woong; Ko, Yoo-Sung; Lee, Sang Yup

2017-10-01

Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic and metabolic engineering for microbial production of poly-γ-glutamic acid.

PubMed

Cao, Mingfeng; Feng, Jun; Sirisansaneeyakul, Sarote; Song, Cunjiang; Chisti, Yusuf

2018-05-28

Poly-γ-glutamic acid (γ-PGA) is a natural biopolymer of glutamic acid. The repeating units of γ-PGA may be derived exclusively from d-glutamic acid, or l-glutamic acid, or both. The monomer units are linked by amide bonds between the α-amino group and the γ-carboxylic acid group. γ-PGA is biodegradable, edible and water-soluble. It has numerous existing and emerging applications in processing of foods, medicines and cosmetics. This review focuses on microbial production of γ-PGA via genetically and metabolically engineered recombinant bacteria. Strategies for improving production of γ-PGA include modification of its biosynthesis pathway, enhancing the production of its precursor (glutamic acid), and preventing loss of the precursor to competing byproducts. These and other strategies are discussed. Heterologous synthesis of γ-PGA in industrial bacterial hosts that do not naturally produce γ-PGA is discussed. Emerging trends and the challenges affecting the production of γ-PGA are reviewed. Copyright © 2018. Published by Elsevier Inc.

What is microbial community ecology?

PubMed

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Effects of Microclimate Cooling on Physiology and Performance While Flying the UH-60 Helicopter Simulator in NBC Conditions in a Controlled Heat Environment

DTIC Science & Technology

1992-08-01

including instrumenting and dressing the subjects, monitoring the physiological parameters in the simulator, and collecting and processing data. They...also was decided to extend the recruiting process to include all helicopter aviators, even if not UH-60 qualified. There is little in the flight profile...parameter channels, and the data were processed to produce a single root mean square (RMS) error value for each channel appropriate to each of the 9

Navier-Stokes Simulation of UH-60A Rotor/Wake Interaction Using Adaptive Mesh Refinement

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

2017-01-01

Time-dependent Navier-Stokes simulations have been carried out for a flexible UH-60A rotor in forward flight, where the rotor wake interacts with the rotor blades. These flow conditions involved blade vortex interaction and dynamic stall, two common conditions that occur as modern helicopter designs strive to achieve greater flight speeds and payload capacity. These numerical simulations utilized high-order spatial accuracy and delayed detached eddy simulation. Emphasis was placed on understanding how improved rotor wake resolution affects the prediction of the normal force, pitching moment, and chord force of the rotor. Adaptive mesh refinement was used to highly resolve the turbulent rotor wake in a computationally efficient manner. Moreover, blade vortex interaction was found to trigger dynamic stall. Time-dependent flow visualization was utilized to provide an improved understanding of the numerical and physical mechanisms involved with three-dimensional dynamic stall.

Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis.

PubMed

Pirie, Christopher M; De Mey, Marjan; Jones Prather, Kristala L; Ajikumar, Parayil Kumaran

2013-04-19

Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.

Automated Power Assessment for Helicopter Turboshaft Engines

NASA Technical Reports Server (NTRS)

Simon, Donald L.; Litt, Jonathan S.

2008-01-01

An accurate indication of available power is required for helicopter mission planning purposes. Available power is currently estimated on U.S. Army Blackhawk helicopters by performing a Maximum Power Check (MPC), a manual procedure performed by maintenance pilots on a periodic basis. The MPC establishes Engine Torque Factor (ETF), an indication of available power. It is desirable to replace the current manual MPC procedure with an automated approach that will enable continuous real-time assessment of available power utilizing normal mission data. This report presents an automated power assessment approach which processes data currently collected within helicopter Health and Usage Monitoring System (HUMS) units. The overall approach consists of: 1) a steady-state data filter which identifies and extracts steady-state operating points within HUMS data sets; 2) engine performance curve trend monitoring and updating; and 3) automated ETF calculation. The algorithm is coded in MATLAB (The MathWorks, Inc.) and currently runs on a PC. Results from the application of this technique to HUMS mission data collected from UH-60L aircraft equipped with T700-GE-701C engines are presented and compared to manually calculated ETF values. Potential future enhancements are discussed.

Research progress of microbial corrosion of reinforced concrete structure

NASA Astrophysics Data System (ADS)

Li, Shengli; Li, Dawang; Jiang, Nan; Wang, Dongwei

2011-04-01

Microbial corrosion of reinforce concrete structure is a new branch of learning. This branch deals with civil engineering , environment engineering, biology, chemistry, materials science and so on and is a interdisciplinary area. Research progress of the causes, research methods and contents of microbial corrosion of reinforced concrete structure is described. The research in the field is just beginning and concerted effort is needed to go further into the mechanism of reinforce concrete structure and assess the security and natural life of reinforce concrete structure under the special condition and put forward the protective methods.

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

PubMed

Jagmann, Nina; Philipp, Bodo

2014-12-20

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

Identification and microbial production of a terpene-based advanced biofuel

PubMed Central

Peralta-Yahya, Pamela P.; Ouellet, Mario; Chan, Rossana; Mukhopadhyay, Aindrila; Keasling, Jay D.; Lee, Taek Soon

2011-01-01

Rising petroleum costs, trade imbalances and environmental concerns have stimulated efforts to advance the microbial production of fuels from lignocellulosic biomass. Here we identify a novel biosynthetic alternative to D2 diesel fuel, bisabolane, and engineer microbial platforms for the production of its immediate precursor, bisabolene. First, we identify bisabolane as an alternative to D2 diesel by measuring the fuel properties of chemically hydrogenated commercial bisabolene. Then, via a combination of enzyme screening and metabolic engineering, we obtain a more than tenfold increase in bisabolene titers in Escherichia coli to >900 mg l−1. We produce bisabolene in Saccharomyces cerevisiae (>900 mg l−1), a widely used platform for the production of ethanol. Finally, we chemically hydrogenate biosynthetic bisabolene into bisabolane. This work presents a framework for the identification of novel terpene-based advanced biofuels and the rapid engineering of microbial farnesyl diphosphate-overproducing platforms for the production of biofuels. PMID:21952217

Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels.

PubMed

Srirangan, Kajan; Bruder, Mark; Akawi, Lamees; Miscevic, Dragan; Kilpatrick, Shane; Moo-Young, Murray; Chou, C Perry

2017-09-01

Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].

Energy, ecology and the distribution of microbial life.

PubMed

Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

2013-07-19

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

Energy, ecology and the distribution of microbial life

PubMed Central

Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

2013-01-01

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

Evolutionary engineering of industrial microorganisms-strategies and applications.

PubMed

Zhu, Zhengming; Zhang, Juan; Ji, Xiaomei; Fang, Zhen; Wu, Zhimeng; Chen, Jian; Du, Guocheng

2018-06-01

Microbial cells have been widely used in the industry to obtain various biochemical products, and evolutionary engineering is a common method in biological research to improve their traits, such as high environmental tolerance and improvement of product yield. To obtain better integrate functions of microbial cells, evolutionary engineering combined with other biotechnologies have attracted more attention in recent years. Classical laboratory evolution has been proven effective to letting more beneficial mutations occur in different genes but also has some inherent limitations such as a long evolutionary period and uncontrolled mutation frequencies. However, recent studies showed that some new strategies may gradually overcome these limitations. In this review, we summarize the evolutionary strategies commonly used in industrial microorganisms and discuss the combination of evolutionary engineering with other biotechnologies such as systems biology and inverse metabolic engineering. Finally, we prospect the importance and application prospect of evolutionary engineering as a powerful tool especially in optimization of industrial microbial cell factories.

[Synthetic biology and rearrangements of microbial genetic material].

PubMed

Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

2011-10-01

As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.

Methodological approaches for studying the microbial ecology of drinking water distribution systems.

PubMed

Douterelo, Isabel; Boxall, Joby B; Deines, Peter; Sekar, Raju; Fish, Katherine E; Biggs, Catherine A

2014-11-15

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Closed nutrient recycling via microbial catabolism in an eco-engineered self regenerating mixed anaerobic microbiome for hydrogenotrophic methanogenesis.

PubMed

Savvas, Savvas; Donnelly, Joanne; Patterson, Tim P; Dinsdale, Richard; Esteves, Sandra R

2017-03-01

A novel eco-engineered mixed anaerobic culture was successfully demonstrated for the first time to be capable of continuous regeneration in nutrient limiting conditions. Microbial catabolism has been found to support a closed system of nutrients able to enrich a culture of lithotrophic methanogens and provide microbial cell recycling. After enrichment, the hydrogenotrophic species was the dominating methanogens while a bacterial substratum was responsible for the redistribution of nutrients. q-PCR results indicated that 7% of the total population was responsible for the direct conversion of the gases. The efficiency of H 2 /CO 2 conversion to CH 4 reached 100% at a gassing rate of above 60v/v/d. The pH of the culture media was effectively sustained at optimal levels (pH 7-8) through a buffering system created by the dissolved CO 2 . The novel approach can reduce the process nutrient/metal requirement and enhance the environmental and financial performance of hydrogenotrophic methanogenesis for renewable energy storage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches.

PubMed

Jang, Yu-Sin; Park, Jong Myoung; Choi, Sol; Choi, Yong Jun; Seung, Do Young; Cho, Jung Hee; Lee, Sang Yup

2012-01-01

The increasing oil price and environmental concerns caused by the use of fossil fuel have renewed our interest in utilizing biomass as a sustainable resource for the production of biofuel. It is however essential to develop high performance microbes that are capable of producing biofuels with very high efficiency in order to compete with the fossil fuel. Recently, the strategies for developing microbial strains by systems metabolic engineering, which can be considered as metabolic engineering integrated with systems biology and synthetic biology, have been developed. Systems metabolic engineering allows successful development of microbes that are capable of producing several different biofuels including bioethanol, biobutanol, alkane, and biodiesel, and even hydrogen. In this review, the approaches employed to develop efficient biofuel producers by metabolic engineering and systems metabolic engineering approaches are reviewed with relevant example cases. It is expected that systems metabolic engineering will be employed as an essential strategy for the development of microbial strains for industrial applications. Copyright © 2011 Elsevier Inc. All rights reserved.

Engineered microbes and methods for microbial oil production

DOEpatents

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

2015-02-10

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

Installation of C-6533(XE-2)/ARC ICS in UH-1H helicopter

NASA Astrophysics Data System (ADS)

Hnat, J. A.

1980-07-01

This report documents the results of the installation of the C-6533(XE-2)/ARC ICS in UH-1H helicopter. Installation was performed at the AEL, Inc., Monmouth County Airport facility. Design of each installation was coordinated and approved by the Government. The mechanical and electrical installation drawings for the helicopter are attached as Appendix A of this report. The new ICS system consisted of new cabling, new intercoms and helmets rewired with new microphones. All four crew stations of the helicopter were reconfigured with the new system. Existing cabling for the standard ICS system remained in the aircraft but was securely stowed for later restoration of the aircraft. The helmets (4) were rewired using separate jacks for headphones and microphone lines. Transmit and receive cables were installed in the aircraft with a minimum separation of one inch between cables. A junction box was fabricated and installed on the aft end of the console to house the fan-out terminal strips. Transmit and receive lines' separation was maintained in the junction box. During the test phase the onboard radios were used with the new ICS system.

76 FR 8707 - Syngenta Seeds, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered To...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-15

... for Corn Genetically Engineered To Produce an Enzyme That Facilitates Ethanol Production AGENCY... event 3272, which has been genetically engineered to produce a microbial enzyme that facilitates ethanol... transformation event 3272, which has been genetically engineered to produce a microbial enzyme that facilitates...

Comparative genome analysis of a thermotolerant Escherichia coli obtained by Genome Replication Engineering Assisted Continuous Evolution (GREACE) and its parent strain provides new understanding of microbial heat tolerance.

PubMed

Luan, Guodong; Bao, Guanhui; Lin, Zhao; Li, Yang; Chen, Zugen; Li, Yin; Cai, Zhen

2015-12-25

Heat tolerance of microbes is of great importance for efficient biorefinery and bioconversion. However, engineering and understanding of microbial heat tolerance are difficult and insufficient because it is a complex physiological trait which probably correlates with all gene functions, genetic regulations, and cellular metabolisms and activities. In this work, a novel strain engineering approach named Genome Replication Engineering Assisted Continuous Evolution (GREACE) was employed to improve the heat tolerance of Escherichia coli. When the E. coli strain carrying a mutator was cultivated under gradually increasing temperature, genome-wide mutations were continuously generated during genome replication and the mutated strains with improved thermotolerance were autonomously selected. A thermotolerant strain HR50 capable of growing at 50°C on LB agar plate was obtained within two months, demonstrating the efficiency of GREACE in improving such a complex physiological trait. To understand the improved heat tolerance, genomes of HR50 and its wildtype strain DH5α were sequenced. Evenly distributed 361 mutations covering all mutation types were found in HR50. Closed material transportations, loose genome conformation, and possibly altered cell wall structure and transcription pattern were the main differences of HR50 compared with DH5α, which were speculated to be responsible for the improved heat tolerance. This work not only expanding our understanding of microbial heat tolerance, but also emphasizing that the in vivo continuous genome mutagenesis method, GREACE, is efficient in improving microbial complex physiological trait. Copyright © 2015 Elsevier B.V. All rights reserved.

Engineered microbes and methods for microbial oil production

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

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis andmore » storage properties.« less

DEB modeling for nanotoxicology, microbial ecology, and environmental engineering. Comment on: ;Physics of metabolic organization; by Marko Jusup et al.

NASA Astrophysics Data System (ADS)

Holden, Patricia A.

2017-03-01

Jusup et al. [1] appeal to mathematical physicists, and to biologists, by providing the theoretical basis for dynamic energy budget (DEB) modeling of individual organisms and populations, while emphasizing model simplicity, universality, and applicability to real world problems. Comments herein regard the disciplinary tensions proposed by the authors and suggest that-in addition to important applications in eco- and specifically nano-toxicology-there are opportunities for DEB frameworks to inform relative complexity in microbial ecological process modeling. This commentary also suggests another audience for bridging DEB theory and application-engineers solving environmental problems.

The information science of microbial ecology.

PubMed

Hahn, Aria S; Konwar, Kishori M; Louca, Stilianos; Hanson, Niels W; Hallam, Steven J

2016-06-01

A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

[Promoting efficiency of microbial extracellular electron transfer by synthetic biology].

PubMed

Li, Feng; Song, Hao

2017-03-25

Electroactive bacteria, including electrigenic bacteria (exoelectrogens) and electroautotrophic bacteria, implement microbial bioelectrocatalysis processes via bi-directional exchange of electrons and energy with environments, enabling a wide array of applications in environmental and energy fields, including microbial fuel cells (MFC), microbial electrolysis cells (MEC), microbial electrosynthesis (MES) to produce electricity and bulk fine chemicals. However, the low efficiency in the extracellular electron transfer (EET) of exoelectrogens and electrotrophic microbes limited their industrial applications. Here, we reviewed synthetic biology approaches to engineer electroactive microorganisms to break the bottleneck of their EET pathways, to achieve higher efficiency of EET of a number of electroactive microorganisms. Such efforts will lead to a breakthrough in the applications of these electroactive microorganisms and microbial electrocatalysis systems.

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.

Experimental Investigation and Fundamental Understanding of a Slowed UH-60A Rotor at High Advance Ratios

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Yeo, Hyeonsoo; Norman, Thomas R.

2011-01-01

This paper describes and analyzes the measurements from a full-scale, slowed RPM, UH-60A rotor tested at the National Full-Scale Aerodynamics Complex 40- by 80- ft wind tunnel up to an advance ratio of 1.0. A comprehensive set of measurements, that includes performance, blade loads, hub loads and pressures/airloads makes this data set unique. The measurements reveal new and rich aeromechanical phenomena that are special to this exotic regime. These include reverse chord dynamic stall, retreating side impulse in pitch-link load, large inboard-outboard elastic twist differential, supersonic flow at low subsonic advancing tip Mach numbers, diminishing rotor forces yet dramatic build up of blade loads, and dramatic blade loads yet benign levels of vibratory hub loads. The objective of this research is the fundamental understanding of these unique aeromechanical phenomena. The intent is to provide useful knowledge for the design of high speed, high efficiency, slowed RPM rotors of the future and a challenging database for advanced analyses validation.

A NASTRAN investigation of simulated projectile damage effects on a UH-1B tail boom model

NASA Technical Reports Server (NTRS)

Futterer, A. T.

1980-01-01

A NASTRAN model of a UH-1B tail boom that had been designed for another project was used to investigate the effect on structural integrity of simulated projectile damage. Elements representing skin, and sections of stringers, longerons and bulkheads were systematically deleted to represent projectile damage. The structure was loaded in a manner to represent the flight loads that would be imposed on the tail boom at a 130 knot cruise. The deflection of four points on the rear of the tail boom relative to the position of these points for the unloaded, undamaged condition of the tail boom was used as a measure of the loss of structural rigidity. The same procedure was then used with the material properties of the aluminum alloys replaced with the material properties of T300/5208 high strength graphite/epoxy fibrous composite material, (0, + or - 45, 90)s for the skin and (0, + or - 45)s for the longerons, stringers, and bulk heads.

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces.

PubMed

Wang, Gang; Or, Dani

2014-10-24

The spatial context of microbial interactions common in natural systems is largely absent in traditional pure culture-based microbiology. The understanding of how interdependent microbial communities assemble and coexist in limited spatial domains remains sketchy. A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields. The emerging patterns were persistent irrespective of initial conditions and resilient to spatial and temporal perturbations. Surprisingly, the hydration conditions conducive for self-assembly are extremely narrow and last only while microbial cells remain motile within thin aqueous films. The resulting self-organized microbial consortia patterns could represent optimal ecological templates for the architecture that underlie sessile microbial colonies on natural surfaces. Understanding microbial spatial self-organization offers new insights into mechanisms that sustain small-scale soil microbial diversity; and may guide the engineering of functional artificial microbial consortia.

Loads Correlation of a Full-Scale UH-60A Airloads Rotor in a Wind Tunnel

NASA Technical Reports Server (NTRS)

Yeo, Hyeonsoo; Romander, Ethan A.

2012-01-01

Wind tunnel measurements of the rotor trim, blade airloads, and structural loads of a full-scale UH-60A Black Hawk main rotor are compared with calculations obtained using the comprehensive rotorcraft analysis CAMRAD II and a coupled CAMRAD II/OVERFLOW 2 analysis. A speed sweep at constant lift up to an advance ratio of 0.4 and a thrust sweep at constant speed into deep stall are investigated. The coupled analysis shows significant improvement over comprehensive analysis. Normal force phase is better captured and pitching moment magnitudes are better predicted including the magnitude and phase of the two stall events in the fourth quadrant at the deeply stalled condition. Structural loads are, in general, improved with the coupled analysis, but the magnitude of chord bending moment is still significantly underpredicted. As there are three modes around 4 and 5/rev frequencies, the structural responses to the 5/rev airloads due to dynamic stall are magnified and thus care must be taken in the analysis of the deeply stalled condition.

Summary of Full-Scale Blade Displacement Measurements of the UH- 60A Airloads Rotor

NASA Technical Reports Server (NTRS)

Abrego, Anita I.; Meyn, Larry; Burner, Alpheus W.; Barrows, Danny A.

2016-01-01

Blade displacement measurements using multi-camera photogrammetry techniques were acquired for a full-scale UH-60A rotor, tested in the National Full-Scale Aerodynamic Complex 40-Foot by 80-Foot Wind Tunnel. The measurements, acquired over the full rotor azimuth, encompass a range of test conditions that include advance ratios from 0.15 to 1.0, thrust coefficient to rotor solidity ratios from 0.01 to 0.13, and rotor shaft angles from -10.0 to 8.0 degrees. The objective was to measure the blade displacements and deformations of the four rotor blades and provide a benchmark blade displacement database to be utilized in the development and validation of rotorcraft prediction techniques. An overview of the blade displacement measurement methodology, system development, and data analysis techniques are presented. Sample results based on the final set of camera calibrations, data reduction procedures and estimated corrections that account for registration errors due to blade elasticity are shown. Differences in blade root pitch, flap and lag between the previously reported results and the current results are small. However, even small changes in estimated root flap and pitch can lead to significant differences in the blade elasticity values.

Design and development of synthetic microbial platform cells for bioenergy

PubMed Central

Lee, Sang Jun; Lee, Sang-Jae; Lee, Dong-Woo

2013-01-01

The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy. PMID:23626588

Engineering Pseudomonas stutzeri as a biogeochemical biosensor

NASA Astrophysics Data System (ADS)

Boynton, L.; Cheng, H. Y.; Del Valle, I.; Masiello, C. A.; Silberg, J. J.

2016-12-01

Biogeochemical cycles are being drastically altered as a result of anthropogenic activities, such as the burning of fossil fuels and the industrial production of ammonia. We know microbes play a major part in these cycles, but the extent of their biogeochemical roles remains largely uncharacterized due to inadequacies with culturing and measurement. While metagenomics and other -omics methods offer ways to reconstruct microbial communities, these approaches can only give an indication of the functional roles of microbes in a community. These -omics approaches are rapidly being expanded to the point of outpacing our knowledge of functional genes, which highlights an inherent need for analytical methods that non-invasively monitor Earth's processes in real time. Here we aim to exploit synthetic biology methods in order to engineer a ubiquitous denitrifying microbe, Pseudomonas stutzeri that can act as a biosensor in soil and marine environments. By using an easily cultivated microbe that is also common in many environments, we hope to develop a tool that allows us to zoom in on specific aspects of the nitrogen cycle. In order to monitor processes occurring at the genetic level in environments that cannot be resolved with fluorescence-based methods, such as soils, we have developed a system that instead relies on gas production by engineered microbial biosensors. P. stutzeri has been successfully engineered to release a gas, methyl bromide, which can continuously and non-invasively be measured by GC-MS. Similar to using Green Fluorescent Protein, GFP, in the biological sciences, the gene controlling gas production can be linked to those involved in denitrification, thereby creating a quantifiable gas signal that is correlated with microbial activity in the soil. Synthetically engineered microbial biosensors could reveal key aspects of metabolism in soil systems and offer a tool for characterizing the scope and degree of microbial impact on major biogeochemical cycles.

A Workflow to Model Microbial Loadings in Watersheds ...

EPA Pesticide Factsheets

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated with 1) land-applied manure on undeveloped areas from domestic animals; 2) direct shedding on undeveloped lands by domestic animals and wildlife; 3) urban or engineered areas; and 4) point sources that directly discharge to streams from septic systems and shedding by domestic animals. A microbial source module, which houses these formulations, is linked within a workflow containing eight models and a set of databases that form a loosely configured modeling infrastructure which supports watershed-scale microbial source-to-receptor modeling by focusing on animal-impacted catchments. A hypothetical example application – accessing, retrieving, and using real-world data – demonstrates the ability of the infrastructure to automate many of the manual steps associated with a standard watershed assessment, culminating with calibrated flow and microbial densities at the pour point of a watershed. Presented at 2016 Biennial Conference, International Environmental Modelling & Software Society.

Helicopter noise measurements data report. volume II. helicopter models: Bell 212 (UH-1N), Sikorsky S-61 (SH-3A), Sikorsky S-64 'Skycrane' (CH- 54B), Boeing Vertol 'Chinook' (CH-47C)

DOT National Transportation Integrated Search

1977-04-01

The helicopter models used in this test program were the Hughes 300C, Hughes 500C, Bell 47-G, Bell 206-L, Bell 212 (UH-1N), Sikorsky S-61 (SH-3A), Sikorsky S-64 'Skycrane' (CH-54B), and Boeing Vertol 'Chinook' CH-47C. Volume I contains the measured n...

Synthetic microbial ecosystems for biotechnology.

PubMed

Pandhal, Jagroop; Noirel, Josselin

2014-06-01

Most highly controlled and specific applications of microorganisms in biotechnology involve pure cultures. Maintaining single strain cultures is important for industry as contaminants can reduce productivity and lead to longer "down-times" during sterilisation. However, microbes working together provide distinct advantages over pure cultures. They can undertake more metabolically complex tasks, improve efficiency and even expand applications to open systems. By combining rapidly advancing technologies with ecological theory, the use of microbial ecosystems in biotechnology will inevitably increase. This review provides insight into the use of synthetic microbial communities in biotechnology by applying the engineering paradigm of measure, model, manipulate and manufacture, and illustrate the emerging wider potential of the synthetic ecology field. Systems to improve biofuel production using microalgae are also discussed.

Production of anthocyanins in metabolically engineered microorganisms: Current status and perspectives.

PubMed

Zha, Jian; Koffas, Mattheos A G

2017-12-01

Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes. Here, we review the recent progress on anthocyanin biosynthesis in engineered bacteria, with a special focus on the systematic engineering modifications such as selection and engineering of biosynthetic enzymes, engineering of transportation, regulation of UDP-glucose supply, as well as process optimization. These promising engineering strategies will facilitate successful microbial production of anthocyanins in industry in the near future.

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas.

PubMed

Humphreys, Christopher M; Minton, Nigel P

2018-04-01

The future sustainable production of chemicals and fuels from non-petrochemical sources, while at the same time reducing greenhouse gas (GHG) emissions, represent two of society's greatest challenges. Microbial chassis able to grow on waste carbon monoxide (CO) and carbon dioxide (CO 2 ) can provide solutions to both. Ranging from the anaerobic acetogens, through the aerobic chemoautotrophs to the photoautotrophic cyanobacteria, they are able to convert C1 gases into a range of chemicals and fuels which may be enhanced and extended through appropriate metabolic engineering. The necessary improvements will be facilitated by the increasingly sophisticated gene tools that are beginning to emerge as part of the Synthetic Biology revolution. These tools, in combination with more accurate metabolic and genome scale models, will enable C1 chassis to deliver their full potential. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

New Transposon Tools Tailored for Metabolic Engineering of Gram-Negative Microbial Cell Factories

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

Martínez-García, Esteban; Aparicio, Tomás; Lorenzo, Víctor de

Re-programming microorganisms to modify their existing functions and/or to bestow bacteria with entirely new-to-Nature tasks have largely relied so far on specialized molecular biology tools. Such endeavors are not only relevant in the burgeoning metabolic engineering arena but also instrumental to explore the functioning of complex regulatory networks from a fundamental point of view. À la carte modification of bacterial genomes thus calls for novel tools to make genetic manipulations easier. We propose the use of a series of new broad-host-range mini-Tn5-vectors, termed pBAMDs, for the delivery of gene(s) into the chromosome of Gram-negative bacteria and for generating saturated mutagenesismore » libraries in gene function studies. These delivery vectors endow the user with the possibility of easy cloning and subsequent insertion of functional cargoes with three different antibiotic-resistance markers (kanamycin, streptomycin, and gentamicin). After validating the pBAMD vectors in the environmental bacterium Pseudomonas putida KT2440, their use was also illustrated by inserting the entire poly(3-hydroxybutyrate) (PHB) synthesis pathway from Cupriavidus necator in the chromosome of a phosphotransacetylase mutant of Escherichia coli. PHB is a completely biodegradable polyester with a number of industrial applications that make it attractive as a potential replacement of oil-based plastics. The non-selective nature of chromosomal insertions of the biosynthetic genes was evidenced by a large landscape of PHB synthesis levels in independent clones. One clone was selected and further characterized as a microbial cell factory for PHB accumulation, and it achieved polymer accumulation levels comparable to those of a plasmid-bearing recombinant. Taken together, our results demonstrate that the new mini-Tn5-vectors can be used to confer interesting phenotypes in Gram-negative bacteria that would be very difficult to engineer through direct manipulation of the structural

Microbial production of nattokinase: current progress, challenge and prospect.

PubMed

Cai, Dongbo; Zhu, Chengjun; Chen, Shouwen

2017-05-01

Nattokinase (EC 3.4.21.62) is a profibrinolytic serine protease with a potent fibrin-degrading activity, and it has been produced by many host strains. Compared to other fibrinolytic enzymes (urokinase, t-PA and streprokinase), nattokinase shows the advantages of having no side effects, low cost and long life-time, and it has the potential to be used as a drug for treating cardiovascular disease and served as a functional food additive. In this review, we focused on screening of producing strains, genetic engineering, fermentation process optimization for microbial nattokinase production, and the extraction and purification of nattokinase were also discussed in this particular chapter. The selection of optimal nattokinase producing strain was the crucial starting element for improvement of nattokinase production. Genetic engineering, protein engineering, fermentation optimization and process control have been proved to be the effective strategies for enhancement of nattokinase production. Also, extraction and purification of nattokinase are critical for the quality evaluation of nattokinase. Finally, the prospect of microbial nattokinase production was also discussed regarding the recent progress, challenge, and trends in this field.

Correlating CFD Simulation with Wind Tunnel Test for the Full-Scale UH-60A Airloads Rotor

NASA Technical Reports Server (NTRS)

Romandr, Ethan; Norman, Thomas R.; Chang, I-Chung

2011-01-01

Data from the recent UH-60A Airloads Test in the National Full-Scale Aerodynamics Complex 40- by 80- Foot Wind Tunnel at NASA Ames Research Center are presented and compared to predictions computed by a loosely coupled Computational Fluid Dynamics (CFD)/Comprehensive analysis. Primary calculations model the rotor in free-air, but initial calculations are presented including a model of the tunnel test section. The conditions studied include a speed sweep at constant lift up to an advance ratio of 0.4 and a thrust sweep at constant speed into deep stall. Predictions show reasonable agreement with measurement for integrated performance indicators such as power and propulsive but occasionally deviate significantly. Detailed analysis of sectional airloads reveals good correlation in overall trends for normal force and pitching moment but pitching moment mean often differs. Chord force is frequently plagued by mean shifts and an overprediction of drag on the advancing side. Locations of significant aerodynamic phenomena are predicted accurately although the magnitude of individual events is often missed.

Airloads Correlation of the UH-60A Rotor Inside the 40- by 80-Foot Wind Tunnel

NASA Technical Reports Server (NTRS)

Chang, I-Chung; Norman, Thomas R.; Romander, Ethan A.

2013-01-01

The presented research validates the capability of a loosely-coupled computational fluid dynamics (CFD) and comprehensive rotorcraft analysis (CRA) code to calculate the flowfield around a rotor and test stand mounted inside a wind tunnel. The CFD/CRA predictions for the full-scale UH-60A Airloads Rotor inside the National Full-Scale Aerodynamics Complex (NFAC) 40- by 80-Foot Wind Tunnel at NASA Ames Research Center are compared with the latest measured airloads and performance data. The studied conditions include a speed sweep at constant lift up to an advance ratio of 0.4 and a thrust sweep at constant speed up to and including stall. For the speed sweep, wind tunnel modeling becomes important at advance ratios greater than 0.37 and test stand modeling becomes increasingly important as the advance ratio increases. For the thrust sweep, both the wind tunnel and test stand modeling become important as the rotor approaches stall. Despite the beneficial effects of modeling the wind tunnel and test stand, the new models do not completely resolve the current airload discrepancies between prediction and experiment.

An algorithm for designing minimal microbial communities with desired metabolic capacities

PubMed Central

Eng, Alexander; Borenstein, Elhanan

2016-01-01

Motivation: Recent efforts to manipulate various microbial communities, such as fecal microbiota transplant and bioreactor systems’ optimization, suggest a promising route for microbial community engineering with numerous medical, environmental and industrial applications. However, such applications are currently restricted in scale and often rely on mimicking or enhancing natural communities, calling for the development of tools for designing synthetic communities with specific, tailored, desired metabolic capacities. Results: Here, we present a first step toward this goal, introducing a novel algorithm for identifying minimal sets of microbial species that collectively provide the enzymatic capacity required to synthesize a set of desired target product metabolites from a predefined set of available substrates. Our method integrates a graph theoretic representation of network flow with the set cover problem in an integer linear programming (ILP) framework to simultaneously identify possible metabolic paths from substrates to products while minimizing the number of species required to catalyze these metabolic reactions. We apply our algorithm to successfully identify minimal communities both in a set of simple toy problems and in more complex, realistic settings, and to investigate metabolic capacities in the gut microbiome. Our framework adds to the growing toolset for supporting informed microbial community engineering and for ultimately realizing the full potential of such engineering efforts. Availability and implementation: The algorithm source code, compilation, usage instructions and examples are available under a non-commercial research use only license at https://github.com/borenstein-lab/CoMiDA. Contact: elbo@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153571

Using Dynamic Interface Modeling and Simulation to Develop a Launch and Recovery Flight Simulation for a UH-60A Blackhawk

NASA Technical Reports Server (NTRS)

Sweeney, Christopher; Bunnell, John; Chung, William; Giovannetti, Dean; Mikula, Julie; Nicholson, Bob; Roscoe, Mike

2001-01-01

Joint Shipboard Helicopter Integration Process (JSHIP) is a Joint Test and Evaluation (JT&E) program sponsored by the Office of the Secretary of Defense (OSD). Under the JSHDP program is a simulation effort referred to as the Dynamic Interface Modeling and Simulation System (DIMSS). The purpose of DIMSS is to develop and test the processes and mechanisms that facilitate ship-helicopter interface testing via man-in-the-loop ground-based flight simulators. Specifically, the DIMSS charter is to develop an accredited process for using a flight simulator to determine the wind-over-the-deck (WOD) launch and recovery flight envelope for the UH-60A ship/helicopter combination. DIMSS is a collaborative effort between the NASA Ames Research Center and OSD. OSD determines the T&E and warfighter training requirements, provides the programmatics and dynamic interface T&E experience, and conducts ship/aircraft interface tests for validating the simulation. NASA provides the research and development element, simulation facility, and simulation technical experience. This paper will highlight the benefits of the NASA/JSHIP collaboration and detail achievements of the project in terms of modeling and simulation. The Vertical Motion Simulator (VMS) at NASA Ames Research Center offers the capability to simulate a wide range of simulation cueing configurations, which include visual, aural, and body-force cueing devices. The system flexibility enables switching configurations io allow back-to-back evaluation and comparison of different levels of cueing fidelity in determining minimum training requirements. The investigation required development and integration of several major simulation system at the VMS. A new UH-60A BlackHawk interchangeable cab that provides an out-the-window (OTW) field-of-view (FOV) of 220 degrees in azimuth and 70 degrees in elevation was built. Modeling efforts involved integrating Computational Fluid Dynamics (CFD) generated data of an LHA ship airwake and

Investigation of Rotor Performance and Loads of a UH-60A Individual Blade Control System

NASA Technical Reports Server (NTRS)

Yeo, Hyeonsoo; Romander, Ethan A.; Norman, Thomas R.

2011-01-01

Wind tunnel measurements of performance, loads, and vibration of a full-scale UH-60A Black Hawk main rotor with an individual blade control (IBC) system are compared with calculations obtained using the comprehensive helicopter analysis CAMRAD II and a coupled CAMRAD II/OVERFLOW 2 analysis. Measured data show a 5.1% rotor power reduction (8.6% rotor lift to effective-drag ratio increase) using 2/rev IBC actuation with 2.0 amplitude at = 0.4. At the optimum IBC phase for rotor performance, IBC actuator force (pitch link force) decreased, and neither flap nor chord bending moments changed significantly. CAMRAD II predicts the rotor power variations with the IBC phase reasonably well at = 0.35. However, the correlation degrades at = 0.4. Coupled CAMRAD II/OVERFLOW 2 shows excellent correlation with the measured rotor power variations with the IBC phase at both = 0.35 and = 0.4. Maximum reduction of IBC actuator force is better predicted with CAMRAD II, but general trends are better captured with the coupled analysis. The correlation of vibratory hub loads is generally poor by both methods, although the coupled analysis somewhat captures general trends.

Performance and Loads Correlation of a UH-60A Slowed Rotor at High Advance Ratios

NASA Technical Reports Server (NTRS)

Kottapalli, Sesi B.

2012-01-01

Measured data from the slowed rotor part of the 2010 UH-60A Airloads Rotor test in the NASA Ames 40- by 80- Foot Wind Tunnel are compared with CAMRAD II calculations. The emphasis in this initial study is to correlate overall trends. This analytical effort considers advance ratios from 0.3 to 1.0, with the rotor rotational speed at 40%NR. The rotor performance parameters considered are the thrust coefficient, power coefficient, L/DE, torque, and H-force. The blade loads considered are the half peak-to-peak, mid-span and outboard torsion, flatwise, and chordwise moments, and the pitch link load. For advance ratios . 0.7, the overall trends for the performance and loads (excluding the pitch link load) could be captured, but with substantial overprediction or underprediction. The correlation gradually deteriorates as the advance ratio is increased and for advance ratios . 0.8 there is no correlation. The pitch link load correlation is not good. There is considerable scope for improvement in the prediction of the blade loads. Considering the modeling complexity associated with the unconventional operating condition under consideration, the current predictive ability to capture overall trends is encouraging.

Investigation of Rotor Performance and Loads of a UH-60A Individual Blade Control System

NASA Technical Reports Server (NTRS)

Yeo, Hyeonsoo; Romander, Ethan A.; Norman, Thomas R.

2011-01-01

Wind tunnel measurements of performance, loads, and vibration of a full-scale UH-60A Black Hawk main rotor with an individual blade control (IBC) system are compared with calculations obtained using the comprehensive helicopter analysis CAMRAD II and a coupled CAMRAD II/OVERFLOW 2 analysis. Measured data show a 5.1% rotor power reduction (8.6% rotor lift to effective-drag ratio increase) using 2/rev IBC actuation with 2.0. amplitude at u = 0.4. At the optimum IBC phase for rotor performance, IBC actuator force (pitch link force) decreased, and neither flap nor chord bending moments changed significantly. CAMRAD II predicts the rotor power variations with IBC phase reasonably well at u = 0.35. However, the correlation degrades at u = 0.4. Coupled CAMRAD II/OVERFLOW 2 shows excellent correlation with the measured rotor power variations with IBC phase at both u = 0.35 and u = 0.4. Maximum reduction of IBC actuator force is better predicted with CAMRAD II, but general trends are better captured with the coupled analysis. The correlation of vibratory hub loads is generally poor by both methods, although the coupled analysis somewhat captures general trends.

CRISPR/Cas9 advances engineering of microbial cell factories.

PubMed

Jakočiūnas, Tadas; Jensen, Michael K; Keasling, Jay D

2016-03-01

One of the key drivers for successful metabolic engineering in microbes is the efficacy by which genomes can be edited. As such there are many methods to choose from when aiming to modify genomes, especially those of model organisms like yeast and bacteria. In recent years, clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) have become the method of choice for precision genome engineering in many organisms due to their orthogonality, versatility and efficacy. Here we review the strategies adopted for implementation of RNA-guided CRISPR/Cas9 genome editing with special emphasis on their application for metabolic engineering of yeast and bacteria. Also, examples of how nuclease-deficient Cas9 has been applied for RNA-guided transcriptional regulation of target genes will be reviewed, as well as tools available for computer-aided design of guide-RNAs will be highlighted. Finally, this review will provide a perspective on the immediate challenges and opportunities foreseen by the use of CRISPR/Cas9 genome engineering and regulation in the context of metabolic engineering. Copyright © 2015 International Metabolic Engineering Society. All rights reserved.

A Workflow to Model Microbial Loadings in Watersheds ...

EPA Pesticide Factsheets

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated with 1) land-applied manure on undeveloped areas from domestic animals; 2) direct shedding on undeveloped lands by domestic animals and wildlife; 3) urban or engineered areas; and 4) point sources that directly discharge to streams from septic systems and shedding by domestic animals. A microbial source module, which houses these formulations, is linked within a workflow containing eight models and a set of databases that form a loosely configured modeling infrastructure which supports watershed-scale microbial source-to-receptor modeling by focusing on animal-impacted catchments. A hypothetical example application – accessing, retrieving, and using real-world data – demonstrates the ability of the infrastructure to automate many of the manual steps associated with a standard watershed assessment, culminating with calibrated flow and microbial densities at the pour point of a watershed. In the Proceedings of the International Environmental Modelling and Software Society (iEMSs), 8th International Congress on Environmental Modelling and Software, Toulouse, France

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Microbial Fuel Cell as an Education Tool

ERIC Educational Resources Information Center

Dewan, Alim; Van Wie, Bernard; Beyenal, Haluk; Lewandowski, Zbigniew

2010-01-01

Many chemical engineering programs offer courses from a variety of disciplines to teach their students multidisciplinary concepts, but often these courses lack appropriate tools for linking newly learned concepts to principles learned in the core courses. This paper describes our experience of incorporating a microbial fuel cell education module…

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

PubMed

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

2018-03-14

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

Microbial ecology of deep-water mid-Atlantic canyons

USGS Publications Warehouse

Kellogg, Christina A.

2011-01-01

The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.

Life Forecasting as a Logistics Technique.

DTIC Science & Technology

1982-01-01

Two examples of RCM applications were investigated directly by the MIT project team: the T53-L-13B engine for the UH -lH Helicopter and the M- 60 Tank...for RCM activities. The candidate systems and the respective 4 readiness commands were the UH -lH helicopter (TSARCOM), TOY Weapon System (MIRCOM), M...have capability for developing Failure Modes and Effects Analyses ( FMEA ). 5. Accurate and dependable field or test data are generally not available. 6

Engineering cell factories for producing building block chemicals for bio-polymer synthesis.

PubMed

Tsuge, Yota; Kawaguchi, Hideo; Sasaki, Kengo; Kondo, Akihiko

2016-01-21

Synthetic polymers are widely used in daily life. Due to increasing environmental concerns related to global warming and the depletion of oil reserves, the development of microbial-based fermentation processes for the production of polymer building block chemicals from renewable resources is desirable to replace current petroleum-based methods. To this end, strains that efficiently produce the target chemicals at high yields and productivity are needed. Recent advances in metabolic engineering have enabled the biosynthesis of polymer compounds at high yield and productivities by governing the carbon flux towards the target chemicals. Using these methods, microbial strains have been engineered to produce monomer chemicals for replacing traditional petroleum-derived aliphatic polymers. These developments also raise the possibility of microbial production of aromatic chemicals for synthesizing high-performance polymers with desirable properties, such as ultraviolet absorbance, high thermal resistance, and mechanical strength. In the present review, we summarize recent progress in metabolic engineering approaches to optimize microbial strains for producing building blocks to synthesize aliphatic and high-performance aromatic polymers.

SYNTHETIC BIOLOGY. Emergent genetic oscillations in a synthetic microbial consortium.

PubMed

Chen, Ye; Kim, Jae Kyoung; Hirning, Andrew J; Josić, Krešimir; Bennett, Matthew R

2015-08-28

A challenge of synthetic biology is the creation of cooperative microbial systems that exhibit population-level behaviors. Such systems use cellular signaling mechanisms to regulate gene expression across multiple cell types. We describe the construction of a synthetic microbial consortium consisting of two distinct cell types—an "activator" strain and a "repressor" strain. These strains produced two orthogonal cell-signaling molecules that regulate gene expression within a synthetic circuit spanning both strains. The two strains generated emergent, population-level oscillations only when cultured together. Certain network topologies of the two-strain circuit were better at maintaining robust oscillations than others. The ability to program population-level dynamics through the genetic engineering of multiple cooperative strains points the way toward engineering complex synthetic tissues and organs with multiple cell types. Copyright © 2015, American Association for the Advancement of Science.

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

Ecological perspectives on synthetic biology: insights from microbial population biology

PubMed Central

Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

2015-01-01

The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

Microbial anodic consortia fed with fermentable substrates in microbial electrolysis cells: Significance of microbial structures.

PubMed

Flayac, Clément; Trably, Eric; Bernet, Nicolas

2018-05-28

Microbial community structure of anodic biofilms plays a key role in bioelectrochemical systems (BESs). When ecosystems are used as inocula, many bacterial species having interconnected ecological interactions are present. The aim of the present study was to identify these interactions for the conversion of single substrates into electrical current. Dual-chamber reactors were inoculated with activated sludge and fed in batch mode with acetate, lactate, butyrate and propionate at 80 mMe - equivalents in quadruplicate. Analyses of biofilms and planktonic microbial communities showed that the anodic biofilms were mainly dominated by the Geobacter genus (62.4% of the total sequences). At the species level, Geobacter sulfurreducens was dominant in presence of lactate and acetate, while Geobacter toluenoxydans and Geobacter pelophilus were dominant with butyrate and propionate as substrates. These results indicate for the first time a specificity within the Geobacter genus towards the electron donor, suggesting a competitive process for electrode colonization and the implementations of syntrophic interactions for complete oxidation of substrates such as propionate and butyrate. All together, these results provide a new insight into the ecological relationships within electroactive biofilms and suggest eco-engineering perspectives to improve the performances of BESs. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial Impact on Success of Human Exploration Missions

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Groves, T. O.; Paloski, W. H. (Technical Monitor)

2000-01-01

The purpose of this study is to identify microbiological risks associated with space exploration and identify potential countermeasures available. Identification of microbial risks associated with space habitation requires knowledge of the sources and expected types of microbial agents. Crew data along with environmental data from water, surfaces, air, and free condensate are utilized in risk examination. Data from terrestrial models are also used. Microbial risks to crew health include bacteria, fungi, protozoa, and viruses. Adverse effects of microbes include: infections, allergic reactions, toxin production, release of volatiles, food spoilage, plant disease, material degradation, and environmental contamination. Risk is difficult to assess because of unknown potential changes in microbes (e.g., mutation) and the human host (e.g., immune changes). Prevention of adverse microbial impacts is preferred over remediation. Preventative measures include engineering measures (e.g., air filtration), crew microbial screening, acceptability standards, and active verification by onboard monitoring. Microbiological agents are important risks to human health and performance during space flight and risks increase with mission duration. Acceptable risk level must be defined. Prevention must be given high priority. Careful screening of crewmembers and payloads is an important element of any risk mitigation plan. Improved quantitation of microbiological risks is a high priority.

Final Scientific/Technical Report for project “Increasing the Rate and Extent of Microbial Coal to Methane Conversion through Optimization of Microbial Activity, Thermodynamics, and Reactive Transport”

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

Fields, Matthew

Currently, coal bed methane (CBM) wells have a limited lifetime since the rate of methane removal via the installed wells is much faster than the in situ methane production rates. Along with water issues created by large amounts of CBM production water, the short life span of CBM wells is a huge deterrent to the environmental and economic feasibility of CBM production. The process of biogenic methanogenesis can be enhanced via the stimulation of the associated microbial communities that can convert the organic fractions of coal to methane. This process is termed Microbially-Enhanced Coal Bed Methane (MECBM). However, the ratesmore » of methane production are still limited and long incubation times are necessary. We hypothesized that the elucidation of chemical and biological parameters that limited MECBM together with thermodynamic considerations would inform strategies to optimize the process under flow conditions. We incorporated microbiological, physicochemical, and engineering processes to develop a more sustainable CBM production scheme with native coal and native microorganisms. The proposed combination of microbial ecology and physiology as well as optimized engineering principles minimized key constraints that impact microbial coal conversion to methane under environmentally relevant conditions. The combined approach for bench-scale tests resulted in more effective and less environmentally burdensome coal-dependent methane production with the potential for H 2O and CO 2 management.« less

Miniprimer PCR, a New Lens for Viewing the Microbial World▿ †

PubMed Central

Isenbarger, Thomas A.; Finney, Michael; Ríos-Velázquez, Carlos; Handelsman, Jo; Ruvkun, Gary

2008-01-01

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide “miniprimers” expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity. PMID:18083877

Aircraft engine and auxiliary power unit emissions from combusting JP-8 fuel

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

Kimm, L.T.; Sylvia, D.A.; Gerstle, T.C.

1997-12-31

Due to safety considerations and in an effort to standardize Department of Defense fuels, the US Air Force (USAF) replaced the naptha-based JP-4, MIL-T-5624, with the kerosene-based JP-8, MIL-T-83133, as the standard turbine fuel. Although engine emissions from combustion of JP-4 are well documented for criteria pollutants, little information exists for criteria and hazardous air pollutants from combustion of JP-8 fuel. Due to intrinsic differences between these two raw fuels, their combustion products were expected to differ. As part of a broader engine testing program, the Air Force, through the Human Systems Center at Brooks AFB, TX, has contracted tomore » have the emissions characterized from aircraft engines and auxiliary power units (APUs). Criteria pollutant and targeted HAP emissions of selected USAF aircraft engines were quantified during the test program. Emission test results will be used to develop emission factors for the tested aircraft engines and APUs. The Air Force intends to develop a mathematical relationship, using the data collected during this series of tests and from previous tests, to extrapolate existing JP-4 emission factors to representative JP-8 emission factors for other engines. This paper reports sampling methodologies for the following aircraft engine emissions tests: F110-GE-100, F101-GE-102, TF33-P-102, F108-CF-100, T56-A-15, and T39-GE-1A/C. The UH-60A helicopter engine, T700-GE-700, and the C-5A/B and C-130H auxiliary power units (GTCP165-1 and GTCP85-180, respectively) were also tested. Testing was performed at various engine settings to determine emissions of particulate matter, carbon monoxide, nitrogen oxides, sulfur oxides, total hydrocarbon, and selected hazardous air pollutants. Ambient monitoring was conducted concurrently to establish background pollutant concentrations for data correction.« less

Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions

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

Song, Hyun-Seob; Nelson, William C.; Lee, Joon-Yong

Interest in applying microbial communities to biotechnology continues to increase. Successful engineering of microbial communities requires a fundamental shift in focus from enhancing metabolic capabilities in individual organisms to promoting synergistic interspecies interactions. This goal necessitates in silico tools that provide a predictive understanding of how microorganisms interact with each other and their environments. In this regard, we highlight a need for a new concept that we have termed biological computer-aided design of interactions (BioCADi). We ground this discussion within the context of metabolic network modeling.

Microbial engineering for the production of advanced biofuels.

PubMed

Peralta-Yahya, Pamela P; Zhang, Fuzhong; del Cardayre, Stephen B; Keasling, Jay D

2012-08-16

Advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure. However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism. Such engineering is not based on just one specific feedstock or host organism. Data-driven and synthetic-biology approaches can be used to optimize both the host and pathways to maximize fuel production. Despite some success, challenges still need to be met to move advanced biofuels towards commercialization, and to compete with more conventional fuels.

Synthetic biology for microbial production of lipid-based biofuels

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

d’Espaux, Leo; Mendez-Perez, Daniel; Li, Rachel

The risks of maintaining current CO 2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO 2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here in this paper we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. Lastly, we further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential ofmore » synthetic biology for sustainable manufacturing.« less

Synthetic biology for microbial production of lipid-based biofuels.

PubMed

d'Espaux, Leo; Mendez-Perez, Daniel; Li, Rachel; Keasling, Jay D

2015-12-01

The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing. Published by Elsevier Ltd.

Microbial growth under a high-pressure CO2 environment

NASA Astrophysics Data System (ADS)

Thompson, J. R.; Hernandez, H. H.

2009-12-01

Carbon capture and storage (CCS) of CO2 has the potential to significantly reduce the emission of greenhouse gasses associated with fossil fuel combustion. The largest potential for storing captured CO2 in the United Sates is in deep geologic saline formations. Currently, little is known about the effects of CO2 storage on biologically active microbial communities found in the deep earth biosphere. Therefore, to investigate how deep earth microbial communities will be affected by the storage of CO2, we have built a high-pressure microbial growth system in which microbial samples are subjected to a supercritical CO2 (scCO2) environment. Recently we have isolated a microbial consortium that is capable of growth and extracellular matrix production in nutrient media under a supercritical CO2 headspace. This consortium was cultivated from hydrocarbon residues associated with saline formation waters and includes members of the gram-positive Bacillus genus. The cultivation of actively growing cells in an environment containing scCO2 is unexpected based on previous experimental evidence of microbial sterilization attributed to the acidic, desiccating, and solvent-like properties of scCO2. Such microbial consortia have potential for development as (i) biofilm barriers for geological carbon-dioxide sequestration, and as (ii) agents of biocatalysis in environmentally-friendly supercritical (sc) CO2 solvent systems. The discovery that microbes can remain biologically active, and grow, in these environments opens new frontiers for the use of self-regenerating biological systems in engineering applications.

Fundamental CRISPR-Cas9 tools and current applications in microbial systems.

PubMed

Tian, Pingfang; Wang, Jia; Shen, Xiaolin; Rey, Justin Forrest; Yuan, Qipeng; Yan, Yajun

2017-09-01

Derived from the bacterial adaptive immune system, CRISPR technology has revolutionized conventional genetic engineering methods and unprecedentedly facilitated strain engineering. In this review, we outline the fundamental CRISPR tools that have been employed for strain optimization. These tools include CRISPR editing, CRISPR interference, CRISPR activation and protein imaging. To further characterize the CRISPR technology, we present current applications of these tools in microbial systems, including model- and non-model industrial microorganisms. Specially, we point out the major challenges of the CRISPR tools when utilized for multiplex genome editing and sophisticated expression regulation. To address these challenges, we came up with strategies that place emphasis on the amelioration of DNA repair efficiency through CRISPR-Cas9-assisted recombineering. Lastly, multiple promising research directions were proposed, mainly focusing on CRISPR-based construction of microbial ecosystems toward high production of desired chemicals.

Genetic engineering of microorganisms for biodiesel production

PubMed Central

Lin, Hui; Wang, Qun; Shen, Qi; Zhan, Jumei; Zhao, Yuhua

2013-01-01

Biodiesel, as one type of renewable energy, is an ideal substitute for petroleum-based diesel fuel and is usually made from triacylglycerides by transesterification with alcohols. Biodiesel production based on microbial fermentation aiming to establish more efficient, less-cost and sustainable biodiesel production strategies is under current investigation by various start-up biotechnology companies and research centers. Genetic engineering plays a key role in the transformation of microbes into the desired cell factories with high efficiency of biodiesel production. Here, we present an overview of principal microorganisms used in the microbial biodiesel production and recent advances in metabolic engineering for the modification required. Overexpression or deletion of the related enzymes for de novo synthesis of biodiesel is highlighted with relevant examples. PMID:23222170

Genetic engineering of microorganisms for biodiesel production.

PubMed

Lin, Hui; Wang, Qun; Shen, Qi; Zhan, Jumei; Zhao, Yuhua

2013-01-01

Biodiesel, as one type of renewable energy, is an ideal substitute for petroleum-based diesel fuel and is usually made from triacylglycerides by transesterification with alcohols. Biodiesel production based on microbial fermentation aiming to establish more efficient, less-cost and sustainable biodiesel production strategies is under current investigation by various start-up biotechnology companies and research centers. Genetic engineering plays a key role in the transformation of microbes into the desired cell factories with high efficiency of biodiesel production. Here, we present an overview of principal microorganisms used in the microbial biodiesel production and recent advances in metabolic engineering for the modification required. Overexpression or deletion of the related enzymes for de novo synthesis of biodiesel is highlighted with relevant examples.

Oxygen - Enemy or Friend for Microbial Fuel Cell Anode Performance?

USDA-ARS?s Scientific Manuscript database

Until recently, scientists and engineers have held a strong belief that oxygen intrusion into the anode chamber of a bioelectrochemical system (BES) is detrimental to microbial fuel cell (MFC) performance because oxygen acts as an alternate electron acceptor. This would, according to recent beliefs...

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Research and engineering assessment of biological solubilization of phosphate

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

Rogers, R.D.; McIlwain, M.E.; Losinski, S.J.

This research and engineering assessment examined a microbial phosphate solubilization process as a method of recovering phosphate from phosphorus containing ore compared to the existing wet acid and electric arc methods. A total of 860 microbial isolates, collected from a range of natural environments were tested for their ability to solubilize phosphate from rock phosphate. A bacterium (Pseudomonas cepacia) was selected for extensive characterization and evaluation of the mechanism of phosphate solubilization and of process engineering parameters necessary to recover phosphate from rock phosphate. These studies found that concentration of hydrogen ion and production of organic acids arising from oxidationmore » of the carbon source facilitated microbial solubilization of both pure chemical insoluble phosphate compounds and phosphate rock. Genetic studies found that phosphate solubilization was linked to an enzyme system (glucose dehydrogenase). Process-related studies found that a critical solids density of 1% by weight (ore to liquid) was necessary for optimal solubilization. An engineering analysis evaluated the cost and energy requirements for a 2 million ton per year sized plant, whose size was selected to be comparable to existing wet acid plants.« less

Compact Cell Settlers for Perfusion Cultures of Microbial (and Mammalian) Cells.

PubMed

Freeman, Cassandra A; Samuel, Premsingh S D; Kompala, Dhinakar S

2017-07-01

As microbial secretory expression systems have become well developed for microbial yeast cells, such as Saccharomyces cerevisiae and Pichia pastoris, it is advantageous to develop high cell density continuous perfusion cultures of microbial yeast cells to retain the live and productive yeast cells inside the perfusion bioreactor while removing the dead cells and cell debris along with the secreted product protein in the harvest stream. While the previously demonstrated inclined or lamellar settlers can be used for such perfusion bioreactors for microbial cells, the size and footprint requirements of such inefficiently scaled up devices can be quite large in comparison to the bioreactor size. Faced with this constraint, we have now developed novel, patent-pending compact cell settlers that can be used more efficiently with microbial perfusion bioreactors to achieve high cell densities and bioreactor productivities. Reproducible results from numerous month-long perfusion culture experiments using these devices attached to the 5 L perfusion bioreactor demonstrate very high cell densities due to substantial sedimentation of the larger live yeast cells which are returned to the bioreactor, while the harvest stream from the top of these cell settlers is a significantly clarified liquid, containing less than 30% and more typically less than 10% of the bioreactor cell concentration. Size of cells in the harvest is smaller than that of the cells in the bioreactor. Accumulated protein collected from the harvest and rate of protein accumulation is significantly (> 6x) higher than the protein produced in repeated fed-batch cultures over the same culture duration. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:913-922, 2017. © 2017 American Institute of Chemical Engineers.

Relating Anaerobic Digestion Microbial Community and Process Function.

PubMed

Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

2015-01-01

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

Microbial fuel cells - Applications for generation of electrical power and beyond.

PubMed

Mathuriya, Abhilasha Singh; Yakhmi, J V

2016-01-01

A Microbial Fuel Cell is a bioelectrochemical device that exploits metabolic activities of living microorganisms for generation of electric current. The usefulness and unique and exclusive architecture of this device has received wide attention recently of engineers and researchers of various disciplines such as microbiologists, chemical engineers, biotechnologists, environment engineers and mechanical engineers, and the subject of MFCs has thereby progressed as a well-developed technology. Sustained innovations and continuous development efforts have established the usefulness of MFCs towards many specialized and value-added applications beyond electricity generation, such as wastewater treatment and implantable body devices. This review is an attempt to provide an update on this rapidly growing technology.

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste.

PubMed

Shaw, Grace Tzun-Wen; Liu, An-Chi; Weng, Chieh-Yin; Chou, Chu-Yang; Wang, Daryi

2017-01-01

Anaerobic digestion (AnD) is a microbiological process that converts organic waste materials into biogas. Because of its high methane content, biogas is a combustible energy source and serves as an important environmental technology commonly used in the management of animal waste generated on large animal farms. Much work has been done on hardware design and process engineering for the generation of biogas. However, little is known about the complexity of the microbiology in this process. In particular, how microbes interact in the digester and eventually breakdown and convert organic matter into biogas is still regarded as a "black box." We used 16S rRNA sequencing as a tool to study the microbial community in laboratory hog waste digesters under tightly controlled conditions, and systematically unraveled the distinct interaction networks of two microbial communities from mesophilic (MAnD) and thermophilic anaerobic digestion (TAnD). Under thermophilic conditions, the well-known association between hydrogen-producing bacteria, e.g., Ruminococcaceae and Prevotellaceae, and hydrotrophic methanogens, Methanomicrobiaceae, was reverse engineered by their interactive topological niches. The inferred interaction network provides a sketch enabling the determination of microbial interactive relationships that conventional strategy of finding differential taxa was hard to achieve. This research is still in its infancy, but it can help to depict the dynamics of microbial ecosystems and to lay the groundwork for understanding how microorganisms cohabit in the anaerobic digester.

Versatile microbial surface-display for environmental remediation and biofuels production

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

Wu, Cindy H.; Mulchandani, Ashok; Chen, wilfred

2008-02-14

Surface display is a powerful technique that utilizes natural microbial functional components to express proteins or peptides on the cell exterior. Since the reporting of the first surface-display system in the mid-1980s, a variety of new systems have been reported for yeast, Gram-positive and Gram-negative bacteria. Non-conventional display methods are emerging, eliminating the generation of genetically modified microorganisms. Cells with surface display are used as biocatalysts, biosorbents and biostimulants. Microbial cell-surface display has proven to be extremely important for numerous applications ranging from combinatorial library screening and protein engineering to bioremediation and biofuels production.

Recent advances of microbial breeding via heavy-ion mutagenesis at IMP.

PubMed

Hu, W; Li, W; Chen, J

2017-10-01

Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future. © 2017 The Society for Applied Microbiology.

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

PubMed Central

2012-01-01

Background Metabolic engineering design methodology has evolved from using pathway-centric, random and empirical-based methods to using systems-wide, rational and integrated computational and experimental approaches. Persistent during these advances has been the desire to develop design strategies that address multiple simultaneous engineering goals, such as maximizing productivity, while minimizing raw material costs. Results Here, we use constraint-based modeling to systematically design multiple combinations of medium compositions and gene-deletion strains for three microorganisms (Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis) and six industrially important byproducts (acetate, D-lactate, hydrogen, ethanol, formate, and succinate). We evaluated over 435 million simulated conditions and 36 engineering metabolic traits, including product rates, costs, yields and purity. Conclusions The resulting metabolic phenotypes can be classified into dominant clusters (meta-phenotypes) for each organism. These meta-phenotypes illustrate global phenotypic variation and sensitivities, trade-offs associated with multiple engineering goals, and fundamental differences in organism-specific capabilities. Given the increasing number of sequenced genomes and corresponding stoichiometric models, we envisage that the proposed strategy could be extended to address a growing range of biological questions and engineering applications. PMID:23009214

Microbial ecology of denitrification in biological wastewater treatment.

PubMed

Lu, Huijie; Chandran, Kartik; Stensel, David

2014-11-01

Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Medium-Throughput Screen of Microbially Produced Serotonin via a G-Protein-Coupled Receptor-Based Sensor.

PubMed

Ehrenworth, Amy M; Claiborne, Tauris; Peralta-Yahya, Pamela

2017-10-17

Chemical biosensors, for which chemical detection triggers a fluorescent signal, have the potential to accelerate the screening of noncolorimetric chemicals produced by microbes, enabling the high-throughput engineering of enzymes and metabolic pathways. Here, we engineer a G-protein-coupled receptor (GPCR)-based sensor to detect serotonin produced by a producer microbe in the producer microbe's supernatant. Detecting a chemical in the producer microbe's supernatant is nontrivial because of the number of other metabolites and proteins present that could interfere with sensor performance. We validate the two-cell screening system for medium-throughput applications, opening the door to the rapid engineering of microbes for the increased production of serotonin. We focus on serotonin detection as serotonin levels limit the microbial production of hydroxystrictosidine, a modified alkaloid that could accelerate the semisynthesis of camptothecin-derived anticancer pharmaceuticals. This work shows the ease of generating GPCR-based chemical sensors and their ability to detect specific chemicals in complex aqueous solutions, such as microbial spent medium. In addition, this work sets the stage for the rapid engineering of serotonin-producing microbes.

Ensemble engineering and statistical modeling for parameter calibration towards optimal design of microbial fuel cells

NASA Astrophysics Data System (ADS)

Sun, Hongyue; Luo, Shuai; Jin, Ran; He, Zhen

2017-07-01

Mathematical modeling is an important tool to investigate the performance of microbial fuel cell (MFC) towards its optimized design. To overcome the shortcoming of traditional MFC models, an ensemble model is developed through integrating both engineering model and statistical analytics for the extrapolation scenarios in this study. Such an ensemble model can reduce laboring effort in parameter calibration and require fewer measurement data to achieve comparable accuracy to traditional statistical model under both the normal and extreme operation regions. Based on different weight between current generation and organic removal efficiency, the ensemble model can give recommended input factor settings to achieve the best current generation and organic removal efficiency. The model predicts a set of optimal design factors for the present tubular MFCs including the anode flow rate of 3.47 mL min-1, organic concentration of 0.71 g L-1, and catholyte pumping flow rate of 14.74 mL min-1 to achieve the peak current at 39.2 mA. To maintain 100% organic removal efficiency, the anode flow rate and organic concentration should be controlled lower than 1.04 mL min-1 and 0.22 g L-1, respectively. The developed ensemble model can be potentially modified to model other types of MFCs or bioelectrochemical systems.

Systems metabolic engineering design: Fatty acid production as an emerging case study

PubMed Central

Tee, Ting Wei; Chowdhury, Anupam; Maranas, Costas D; Shanks, Jacqueline V

2014-01-01

Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities. PMID:24481660

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste

PubMed Central

Shaw, Grace Tzun-Wen; Liu, An-Chi; Weng, Chieh-Yin; Chou, Chu-Yang

2017-01-01

Anaerobic digestion (AnD) is a microbiological process that converts organic waste materials into biogas. Because of its high methane content, biogas is a combustible energy source and serves as an important environmental technology commonly used in the management of animal waste generated on large animal farms. Much work has been done on hardware design and process engineering for the generation of biogas. However, little is known about the complexity of the microbiology in this process. In particular, how microbes interact in the digester and eventually breakdown and convert organic matter into biogas is still regarded as a “black box.” We used 16S rRNA sequencing as a tool to study the microbial community in laboratory hog waste digesters under tightly controlled conditions, and systematically unraveled the distinct interaction networks of two microbial communities from mesophilic (MAnD) and thermophilic anaerobic digestion (TAnD). Under thermophilic conditions, the well-known association between hydrogen-producing bacteria, e.g., Ruminococcaceae and Prevotellaceae, and hydrotrophic methanogens, Methanomicrobiaceae, was reverse engineered by their interactive topological niches. The inferred interaction network provides a sketch enabling the determination of microbial interactive relationships that conventional strategy of finding differential taxa was hard to achieve. This research is still in its infancy, but it can help to depict the dynamics of microbial ecosystems and to lay the groundwork for understanding how microorganisms cohabit in the anaerobic digester. PMID:28732056

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

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

Song, Hyun-Seob; Cannon, William R.; Beliaev, Alex S.

Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can bemore » potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.« less

Recent patents on microbial proteases for the dairy industry.

PubMed

Feijoo-Siota, Lucía; Blasco, Lucía; Rodríguez-Rama, José Luis; Barros-Velázquez, Jorge; Miguel, Trinidad de; Sánchez-Pérez, Angeles; Villa, Tomás G

2014-01-01

This paper reviews the general characteristics of exo and endopeptidases of microbial origin currently used in the milk industry. It also includes recent patents developed either to potentiate the enzymatic activity or to improve the resulting milk derivatives. The main application of these proteases is in the cheese-making industry. Although this industry preferentially uses animal rennets, and in particular genetically engineered chymosins, it also utilizes milk coagulants of microbial origin. Enzymes derived from Rhizomucor miehei, Rhizomucor pusillus and Cryphonectria parasitica are currently used to replace the conventional milk-clotting enzymes. In addition, the dairy industry uses microbial endo and exoproteases for relatively new applications, such as debittering and flavor generation in cheese, accelerated cheese ripening, manufacture of protein hydrolysates with improved functional properties, and production of enzyme-modified cheeses. Lactic acid bacteria play an essential role in these processes, hence these bacteria and the proteases they produce are currently being investigated by the dairy industry and are the subject of many of their patent applications.

Economical challenges to microbial producers of butanol: feedstock, butanol ratio and titer.

PubMed

Gu, Yang; Jiang, Yu; Wu, Hui; Liu, Xudong; Li, Zhilin; Li, Jian; Xiao, Han; Shen, Zhaobing; Dong, Hongjun; Yang, Yunliu; Li, Yin; Jiang, Weihong; Yang, Sheng

2011-11-01

Butanol is an important solvent and transport fuel additive, and can be produced by microbial fermentation. Attempts to generate a superior microbial producer of butanol have been made through different metabolic engineering strategies. However, to date, butanol bio-production is still not economically competitive compared to petrochemical-derived production because of its major drawbacks, such as, high cost of the feedstocks, low butanol concentration in the fermentation broth and the co-production of low-value by-products acetone and ethanol. Here we analyze the main bottlenecks in microbial butanol production and summarize relevant advances from recently reported studies. Further needs and directions for developing real industrially applicable strains in butanol production are also discussed. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineering biological systems using automated biofoundries.

PubMed

Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin

2017-07-01

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Strategies for microbial synthesis of high-value phytochemicals

NASA Astrophysics Data System (ADS)

Li, Sijin; Li, Yanran; Smolke, Christina D.

2018-03-01

Phytochemicals are of great pharmaceutical and agricultural importance, but often exhibit low abundance in nature. Recent demonstrations of industrial-scale production of phytochemicals in yeast have shown that microbial production of these high-value chemicals is a promising alternative to sourcing these molecules from native plant hosts. However, a number of challenges remain in the broader application of this approach, including the limited knowledge of plant secondary metabolism and the inefficient reconstitution of plant metabolic pathways in microbial hosts. In this Review, we discuss recent strategies to achieve microbial biosynthesis of complex phytochemicals, including strategies to: (1) reconstruct plant biosynthetic pathways that have not been fully elucidated by mining enzymes from native and non-native hosts or by enzyme engineering; (2) enhance plant enzyme activity, specifically cytochrome P450 activity, by improving efficiency, selectivity, expression or electron transfer; and (3) enhance overall reaction efficiency of multi-enzyme pathways by dynamic control, compartmentalization or optimization with the host's metabolism. We also highlight remaining challenges to — and future opportunities of — this approach.

Microbiome engineering: Current applications and its future.

PubMed

Foo, Jee Loon; Ling, Hua; Lee, Yung Seng; Chang, Matthew Wook

2017-03-01

Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineering biocatalysts for production of commodity chemicals.

PubMed

Shanmugam, K T; Ingram, L O

2008-01-01

Lignocellulosic biomass is an attractive alternate to petroleum for production of both fuels and commodity chemicals. This conversion of biomass would require a new generation of microbial biocatalysts that can convert all the sugars present in the biomass to the desired compounds. In this review, the critical factors that need to be considered in engineering such microbial biocatalysts for cost-effective fermentation of sugars are discussed with specific emphasis on commodity chemicals such as lactic acid, succinic acid and acetic acid. (c) 2008 S. Karger AG, Basel

The Genome-Based Metabolic Systems Engineering to Boost Levan Production in a Halophilic Bacterial Model.

PubMed

Aydin, Busra; Ozer, Tugba; Oner, Ebru Toksoy; Arga, Kazim Yalcin

2018-03-01

Metabolic systems engineering is being used to redirect microbial metabolism for the overproduction of chemicals of interest with the aim of transforming microbial hosts into cellular factories. In this study, a genome-based metabolic systems engineering approach was designed and performed to improve biopolymer biosynthesis capability of a moderately halophilic bacterium Halomonas smyrnensis AAD6 T producing levan, which is a fructose homopolymer with many potential uses in various industries and medicine. For this purpose, the genome-scale metabolic model for AAD6 T was used to characterize the metabolic resource allocation, specifically to design metabolic engineering strategies for engineered bacteria with enhanced levan production capability. Simulations were performed in silico to determine optimal gene knockout strategies to develop new strains with enhanced levan production capability. The majority of the gene knockout strategies emphasized the vital role of the fructose uptake mechanism, and pointed out the fructose-specific phosphotransferase system (PTS fru ) as the most promising target for further metabolic engineering studies. Therefore, the PTS fru of AAD6 T was restructured with insertional mutagenesis and triparental mating techniques to construct a novel, engineered H. smyrnensis strain, BMA14. Fermentation experiments were carried out to demonstrate the high efficiency of the mutant strain BMA14 in terms of final levan concentration, sucrose consumption rate, and sucrose conversion efficiency, when compared to the AAD6 T . The genome-based metabolic systems engineering approach presented in this study might be considered an efficient framework to redirect microbial metabolism for the overproduction of chemicals of interest, and the novel strain BMA14 might be considered a potential microbial cell factory for further studies aimed to design levan production processes with lower production costs.

Syntrophic exchange in synthetic microbial communities

PubMed Central

Mee, Michael T.; Collins, James J.; Church, George M.; Wang, Harris H.

2014-01-01

Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology. PMID:24778240

Aged-engineered nanoparticles effect on sludge anaerobic digestion performance and associated microbial communities.

PubMed

Eduok, Samuel; Ferguson, Robert; Jefferson, Bruce; Villa, Raffaella; Coulon, Frédéric

2017-12-31

To investigate the potential effect of aged engineered nanoparticles (a-ENPs) on sludge digestion performance, 150L pilot anaerobic digesters (AD) were fed with a blend of primary and waste activated sludge spiked either with a mixture of silver oxide, titanium dioxide and zinc oxide or a mixture of their equivalent bulk metal salts to achieve a target concentration of 250, 2000, and 2800mgkg -1 dry weight, respectively. Volatile fatty acids (VFA) were 1.2 times higher in the spiked digesters and significantly different (p=0.05) from the control conditions. Specifically, isovaleric acid concentration was 2 times lower in the control digester compared to the spiked digesters, whereas hydrogen sulfide was 2 times lower in the ENPs spiked digester indicating inhibitory effect on sulfate reducing microorganisms. Based on the ether-linked isoprenoids concentration, the total abundance of methanogens was 1.4 times lower in the ENPs spiked digester than in the control and metal salt spiked digesters. Pyrosequencing indicated 80% decrease in abundance and diversity of methanogens in ENPs spiked digester compared to the control digester. Methanosarcina acetivorans and Methanosarcina barkeri were identified as nano-tolerant as their relative abundance increased by a factor of 6 and 11, respectively, compared to the other digesters. The results further provide compelling evidence on the resilience of Fusobacteria, Actinobacteria and the Trojan horse-like effect of ENPs which offered a competitive advantage to some organisms while reducing microbial abundance and diversity. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

A Comparison of the Microbial Production and Combustion Characteristics of Three Alcohol Biofuels: Ethanol, 1-Butanol, and 1-Octanol.

PubMed

Kremer, Florian; Blank, Lars M; Jones, Patrik R; Akhtar, M Kalim

2015-01-01

Over the last decade, microbes have been engineered for the manufacture of a variety of biofuels. Saturated linear-chain alcohols have great potential as transport biofuels. Their hydrocarbon backbones, as well as oxygenated content, confer combustive properties that make it suitable for use in internal combustion engines. Herein, we compared the microbial production and combustion characteristics of ethanol, 1-butanol, and 1-octanol. In terms of productivity and efficiency, current microbial platforms favor the production of ethanol. From a combustion standpoint, the most suitable fuel for spark-ignition engines would be ethanol, while for compression-ignition engines it would be 1-octanol. However, any general conclusions drawn at this stage regarding the most superior biofuel would be premature, as there are still many areas that need to be addressed, such as large-scale purification and pipeline compatibility. So far, the difficulties in developing and optimizing microbial platforms for fuel production, particularly for newer fuel candidates, stem from our poor understanding of the myriad biological factors underpinning them. A great deal of attention therefore needs to be given to the fundamental mechanisms that govern biological processes. Additionally, research needs to be undertaken across a wide range of disciplines to overcome issues of sustainability and commercial viability.

A Comparison of the Microbial Production and Combustion Characteristics of Three Alcohol Biofuels: Ethanol, 1-Butanol, and 1-Octanol

PubMed Central

Kremer, Florian; Blank, Lars M.; Jones, Patrik R.; Akhtar, M. Kalim

2015-01-01

Over the last decade, microbes have been engineered for the manufacture of a variety of biofuels. Saturated linear-chain alcohols have great potential as transport biofuels. Their hydrocarbon backbones, as well as oxygenated content, confer combustive properties that make it suitable for use in internal combustion engines. Herein, we compared the microbial production and combustion characteristics of ethanol, 1-butanol, and 1-octanol. In terms of productivity and efficiency, current microbial platforms favor the production of ethanol. From a combustion standpoint, the most suitable fuel for spark-ignition engines would be ethanol, while for compression-ignition engines it would be 1-octanol. However, any general conclusions drawn at this stage regarding the most superior biofuel would be premature, as there are still many areas that need to be addressed, such as large-scale purification and pipeline compatibility. So far, the difficulties in developing and optimizing microbial platforms for fuel production, particularly for newer fuel candidates, stem from our poor understanding of the myriad biological factors underpinning them. A great deal of attention therefore needs to be given to the fundamental mechanisms that govern biological processes. Additionally, research needs to be undertaken across a wide range of disciplines to overcome issues of sustainability and commercial viability. PMID:26301219

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.

Microbial biogeochemistry of uranium mill tailings

USGS Publications Warehouse

Landa, Edward R.

2005-01-01

Uranium mill tailings (UMT) are the crushed ore residues from the extraction of uranium (U) from ores. Among the radioactive wastes associated with the nuclear fuel cycle, UMT are unique in terms of their volume and their limited isolation from the surficial environment. For this latter reason, their management and long-term fate has many interfaces with environmental microbial communities and processes. The interactions of microorganisms with UMT have been shown to be diverse and with significant consequences for radionuclide mobility and bioremediation. These radionuclides are associated with the U-decay series. The addition of organic carbon and phosphate is required to initiate the reduction of the U present in the groundwater down gradient of the mills. Investigations on sediment and water from the U-contaminated aquifer, indicates that the addition of a carbon source stimulates the rate of U removal by microbial reduction. Moreover, most attention with respect to passive or engineered removal of U from groundwaters focuses on iron-reducing and sulfate-reducing bacteria.

Engineering microbial biofuel tolerance and export using efflux pumps

PubMed Central

Dunlop, Mary J; Dossani, Zain Y; Szmidt, Heather L; Chu, Hou Cheng; Lee, Taek Soon; Keasling, Jay D; Hadi, Masood Z; Mukhopadhyay, Aindrila

2011-01-01

Many compounds being considered as candidates for advanced biofuels are toxic to microorganisms. This introduces an undesirable trade-off when engineering metabolic pathways for biofuel production because the engineered microbes must balance production against survival. Cellular export systems, such as efflux pumps, provide a direct mechanism for reducing biofuel toxicity. To identify novel biofuel pumps, we used bioinformatics to generate a list of all efflux pumps from sequenced bacterial genomes and prioritized a subset of targets for cloning. The resulting library of 43 pumps was heterologously expressed in Escherichia coli, where we tested it against seven representative biofuels. By using a competitive growth assay, we efficiently distinguished pumps that improved survival. For two of the fuels (n-butanol and isopentanol), none of the pumps improved tolerance. For all other fuels, we identified pumps that restored growth in the presence of biofuel. We then tested a beneficial pump directly in a production strain and demonstrated that it improved biofuel yields. Our findings introduce new tools for engineering production strains and utilize the increasingly large database of sequenced genomes. PMID:21556065

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

PubMed Central

Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

2012-01-01

Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface.

PubMed

Mouser, Paula J; Borton, Mikayla; Darrah, Thomas H; Hartsock, Angela; Wrighton, Kelly C

2016-11-01

Horizontal drilling and hydraulic fracturing are increasingly used for recovering energy resources in black shales across the globe. Although newly drilled wells are providing access to rocks and fluids from kilometer depths to study the deep biosphere, we have much to learn about microbial ecology of shales before and after 'fracking'. Recent studies provide a framework for considering how engineering activities alter this rock-hosted ecosystem. We first provide data on the geochemical environment and microbial habitability in pristine shales. Next, we summarize data showing the same pattern across fractured shales: diverse assemblages of microbes are introduced into the subsurface, eventually converging to a low diversity, halotolerant, bacterial and archaeal community. Data we synthesized show that the shale microbial community predictably shifts in response to temporal changes in geochemistry, favoring conservation of key microorganisms regardless of inputs, shale location or operators. We identified factors that constrain diversity in the shale and inhibit biodegradation at the surface, including salinity, biocides, substrates and redox. Continued research in this engineered ecosystem is required to assess additive biodegradability, quantify infrastructure biocorrosion, treat wastewaters that return to the surface and potentially enhance energy production through in situ methanogenesis. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial load monitor

NASA Technical Reports Server (NTRS)

Caplin, R. S.; Royer, E. R.

1978-01-01

Attempts are made to provide a total design of a Microbial Load Monitor (MLM) system flight engineering model. Activities include assembly and testing of Sample Receiving and Card Loading Devices (SRCLDs), operator related software, and testing of biological samples in the MLM. Progress was made in assembling SRCLDs with minimal leaks and which operate reliably in the Sample Loading System. Seven operator commands are used to control various aspects of the MLM such as calibrating and reading the incubating reading head, setting the clock and reading time, and status of Card. Testing of the instrument, both in hardware and biologically, was performed. Hardware testing concentrated on SRCLDs. Biological testing covered 66 clinical and seeded samples. Tentative thresholds were set and media performance listed.

Processes of carbonate precipitation in modern microbial mats

NASA Astrophysics Data System (ADS)

Dupraz, Christophe; Reid, R. Pamela; Braissant, Olivier; Decho, Alan W.; Norman, R. Sean; Visscher, Pieter T.

2009-10-01

Microbial mats are ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to > 3.4 Ga bp, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-µm) scales. The activity of the mat communities has changed Earth's redox conditions (i.e. oxidation state) through oxygen and hydrogen production. Interpretation of fossil microbial mats and their potential role in alteration of the Earth's geochemical environment is challenging because these mats are generally not well preserved. Preservation of microbial mats in the fossil record can be enhanced through carbonate precipitation, resulting in the formation of lithified mats, or microbialites. Several types of microbially-mediated mineralization can be distinguished, including biologically-induced and biologically influenced mineralization. Biologically-induced mineralization results from the interaction between biological activity and the environment. Biologically-influenced mineralization is defined as passive mineralization of organic matter (biogenic or abiogenic in origin), whose properties influence crystal morphology and composition. We propose to use the term organomineralization sensu lato as an umbrella term encompassing biologically influenced and biologically induced mineralization. Key components of organomineralization sensu lato are the "alkalinity" engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and an organic matrix comprised of extracellular polymeric substances (EPS), which may provide a template for carbonate nucleation. Here we review the specific role of microbes and the EPS matrix in various mineralization processes and discuss examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites.

Environmental risk assessment of a genetically-engineered microorganism: Erwinia carotovora

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

Orvos, D.R.

1989-01-01

Environmental use of genetically-engineered microorganisms (GEMs) has raised concerns over potential ecological impact. Development of microcosm systems useful in preliminary testing for risk assessment will provide useful information for predicting potential structural, functional, and genetic effects of GEM release. This study was executed to develop techniques that may be useful in risk assessment and microbial ecology, to ascertain which parameters are useful in determining risk and to predict risk from releasing an engineered strain of Erwinia carotovora. A terrestrial microcosm system for use in GEM risk assessment studies was developed for use in assessing alterations of microbial structure and functionmore » that may be caused by introducing the engineered strain of E. carotovora. This strain is being developed for use as a biological control agent for plant soft rot. Parameters that were monitored included survival and intraspecific competition of E. carotovora, structural effects upon both total bacterial populations and numbers of selected bacterial genera, effects upon activities of dehydrogenase and alkaline phosphatase, effects upon soil nutrients, and potential for gene transfer into or out of the engineered strain.« less

Systems metabolic engineering design: fatty acid production as an emerging case study.

PubMed

Tee, Ting Wei; Chowdhury, Anupam; Maranas, Costas D; Shanks, Jacqueline V

2014-05-01

Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities. © 2014 Wiley Periodicals, Inc.

Microbial enhancement of oil recovery: Recent advances

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

Premuzic, E.T.; Woodhead, A.D.; Vivirito, K.J.

1992-01-01

During recent years, systematic, scientific, and engineering effort by researchers in the United States and abroad, has established the scientific basis for Microbial Enhanced Oil Recovery (MEOR) technology. The successful application of MEOR technology as an oil recovery process is a goal of the Department of Energy (DOE). Research efforts involving aspects of MEOR in the microbiological, biochemical, and engineering fields led DOE to sponsor an International Conference at Brookhaven National Laboratory in 1992, to facilitate the exchange of information and a discussion of ideas for the future research emphasis. At this, the Fourth International MEOR Conference, where international attendeesmore » from 12 countries presented a total of 35 papers, participants saw an equal distribution between research'' and field applications.'' In addition, several modeling and state-of-the-art'' presentations summed up the present status of MEOR science and engineering. Individual papers in this proceedings have been process separately for inclusion in the Energy Science and Technology Database.« less

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research.

PubMed

Sato, Fumihiko; Kumagai, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

PubMed

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

2016-11-01

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

Development and Operation of an Automatic Rotor Trim Control System for the UH-60 Individual Blade Control Wind Tunnel Test

NASA Technical Reports Server (NTRS)

Theodore, Colin R.; Tischler, Mark B.

2010-01-01

An automatic rotor trim control system was developed and successfully used during a wind tunnel test of a full-scale UH-60 rotor system with Individual Blade Control (IBC) actuators. The trim control system allowed rotor trim to be set more quickly, precisely and repeatably than in previous wind tunnel tests. This control system also allowed the rotor trim state to be maintained during transients and drift in wind tunnel flow, and through changes in IBC actuation. The ability to maintain a consistent rotor trim state was key to quickly and accurately evaluating the effect of IBC on rotor performance, vibration, noise and loads. This paper presents details of the design and implementation of the trim control system including the rotor system hardware, trim control requirements, and trim control hardware and software implementation. Results are presented showing the effect of IBC on rotor trim and dynamic response, a validation of the rotor dynamic simulation used to calculate the initial control gains and tuning of the control system, and the overall performance of the trim control system during the wind tunnel test.

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

DOE PAGES

Jha, Ramesh K.; Kern, Theresa L.; Kim, Youngchang; ...

2016-08-30

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires an access to an expanded repertoire of TFs. Using ligand docked homology models for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10 7 variants of PobR, four were active when pNP was added as an inducer, with two mutants showingmore » a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production and detect hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show that the fluorescence of the cells correlated with the catalytic efficiency of PTE variants, each cell expressed. High selectivity for similar molecules (4HB vs pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo- structures of PobR scaffold with computational models are notable successes presented in this work.« less

Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp.

PubMed

He, Yi; Wang, Bin; Chen, Wanping; Cox, Russell J; He, Jingren; Chen, Fusheng

High throughput genome sequencing has revealed a multitude of potential secondary metabolites biosynthetic pathways that remain cryptic. Pathway reconstruction coupled with genetic engineering via heterologous expression enables discovery of novel compounds, elucidation of biosynthetic pathways, and optimization of product yields. Apart from Escherichia coli and yeast, fungi, especially Aspergillus spp., are well known and efficient heterologous hosts. This review summarizes recent advances in heterologous expression of microbial secondary metabolite biosynthesis in Aspergillus spp. We also discuss the technological challenges and successes in regard to heterologous host selection and DNA assembly behind the reconstruction of microbial secondary metabolite biosynthesis. Copyright © 2018 Elsevier Inc. All rights reserved.

Recent Advances in Microbial Production of Aromatic Chemicals and Derivatives.

PubMed

Noda, Shuhei; Kondo, Akihiko

2017-08-01

Along with the development of metabolic engineering and synthetic biology tools, various microbes are being used to produce aromatic chemicals. In microbes, aromatics are mainly produced via a common important precursor, chorismate, in the shikimate pathway. Natural or non-natural aromatics have been produced by engineering metabolic pathways involving chorismate. In the past decade, novel approaches have appeared to produce various aromatics or to increase their productivity, whereas previously, the targets were mainly aromatic amino acids and the strategy was deregulating feedback inhibition. In this review, we summarize recent studies of microbial production of aromatics based on metabolic engineering approaches. In addition, future perspectives and challenges in this research area are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering biological systems using automated biofoundries

PubMed Central

Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin

2017-01-01

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges. PMID:28602523

Stimulation of electro-fermentation in single-chamber microbial electrolysis cells driven by genetically engineered anode biofilms

NASA Astrophysics Data System (ADS)

Awate, Bhushan; Steidl, Rebecca J.; Hamlischer, Thilo; Reguera, Gemma

2017-07-01

Unwanted metabolites produced during fermentations reduce titers and productivity and increase the cost of downstream purification of the targeted product. As a result, the economic feasibility of otherwise attractive fermentations is low. Using ethanol fermentation by the consolidated bioprocessing cellulolytic bacterium Cellulomonas uda, we demonstrate the effectiveness of anodic electro-fermentations at maximizing titers and productivity in a single-chamber microbial electrolysis cell (SCMEC) without the need for metabolic engineering of the fermentative microbe. The performance of the SCMEC platform relied on the genetic improvements of anode biofilms of the exoelectrogen Geobacter sulfurreducens that prevented the oxidation of cathodic hydrogen and improved lactate oxidation. Furthermore, a hybrid bioanode was designed that maximized the removal of organic acids in the fermentation broth. The targeted approach increased cellobiose consumption rates and ethanol titers, yields, and productivity three-fold or more, prevented pH imbalances and reduced batch-to-batch variability. In addition, the sugar substrate was fully consumed and ethanol was enriched in the broth during the electro-fermentation, simplifying its downstream purification. Such improvements and the possibility of scaling up SCMEC configurations highlight the potential of anodic electro-fermentations to stimulate fermentative bacteria beyond their natural capacity and to levels required for industrial implementation.

Microbial Biosynthesis of Silver Nanoparticles in Different Culture Media.

PubMed

Luo, Ke; Jung, Samuel; Park, Kyu-Hwan; Kim, Young-Rok

2018-01-31

Microbial biosynthesis of metal nanoparticles has been extensively studied for the applications in biomedical sciences and engineering. However, the mechanism for their synthesis through microorganism is not completely understood. In this study, several culture media were investigated for their roles in the microbial biosynthesis of silver nanoparticles (AgNPs). The size and morphology of the synthesized AgNPs were analyzed by UV-vis spectroscopy, Fourier-transform-infrared (FT-IR), transmission electron microscopy (TEM), and dynamic light scattering (DLS). The results demonstrated that nutrient broth (NB) and Mueller-Hinton broth (MHB) among tested media effectively reduced silver ions to form AgNPs with different particle size and shape. Although the involved microorganism enhanced the reduction of silver ions, the size and shape of the particles were shown to mainly depend on the culture media. Our findings suggest that the growth media of bacterial culture play an important role in the synthesis of metallic nanoparticles with regard to their size and shape. We believe our findings would provide useful information for further exploration of microbial biosynthesis of AgNPs and their biomedical applications.

Measuring microbial metabolism in atypical environments: Bentonite in used nuclear fuel storage.

PubMed

Stone, Wendy; Kroukamp, Otini; Moes, Ana; McKelvie, Jennifer; Korber, Darren R; Wolfaardt, Gideon M

2016-01-01

Genomics enjoys overwhelming popularity in the study of microbial ecology. However, extreme or atypical environments often limit the use of such well-established tools and consequently demand a novel approach. The bentonite clay matrix proposed for use in Deep Geological Repositories for the long-term storage of used nuclear fuel is one such challenging microbial habitat. Simple, accessible tools were developed for the study of microbial ecology and metabolic processes that occur within this habitat, since the understanding of the microbiota-niche interaction is fundamental to describing microbial impacts on engineered systems such as compacted bentonite barriers. Even when genomic tools are useful for the study of community composition, techniques to describe such microbial impacts and niche interactions should complement these. Tools optimised for assessing localised microbial activity within bentonite included: (a) the qualitative use of the resazurin-resorufin indicator system for redox localisation, (b) the use of a CaCl2 buffer for the localisation of pH, and (c) fluorometry for the localisation of precipitated sulphide. The use of the Carbon Dioxide Evolution Monitoring System was also validated for measuring microbial activity in desiccated and saturated bentonite. Finally, the buffering of highly-basic bentonite at neutral pH improved the success of isolation of microbial populations, but not DNA, from the bentonite matrix. Thus, accessible techniques were optimised for exploring microbial metabolism in the atypical environments of clay matrices and desiccated conditions. These tools have application to the applied field of used nuclear fuel management, as well as for examining the fundamental biogeochemical cycles active in sedimentary and deep geological environments. Copyright © 2015 Elsevier B.V. All rights reserved.

Advances in engineered microorganisms for improving metabolic conversion via microgravity effects.

PubMed

Huangfu, Jie; Zhang, Genlin; Li, Jun; Li, Chun

2015-01-01

As an extreme and unique environment, microgravity has significant effects on microbial cellular processes, such as cell growth, gene expression, natural pathways and biotechnological products. Application of microgravity effects to identify the regulatory elements in reengineering microbial hosts will draw much more attention in further research. In this commentary, we discuss the microgravity effects in engineered microorganisms for improving metabolic conversion, including cell growth kinetics, antimicrobial susceptibility, resistance to stresses, secondary metabolites production, recombinant protein production and enzyme activity, as well as gene expression changes. Application of microgravity effects in engineered microorganisms could provide valuable platform for innovative approaches in bioprocessing technology to largely improve the metabolic conversion efficacy of biopharmaceutical products.

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research

PubMed Central

SATO, Fumihiko; KUMAGAI, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed. PMID:23666088

High-Throughput Screening To Identify Potent and Specific Inhibitors of Microbial Sulfate Reduction.

PubMed

Carlson, Hans K; Mullan, Mark R; Mosqueda, Lorraine A; Chen, Steven; Arkin, Michelle R; Coates, John D

2017-06-20

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive, and corrosive. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to identify potent and selective inhibitors of SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Zinc pyrithione is the most potent inhibitor of sulfidogenesis that we identified, and is several orders of magnitude more potent than commonly used industrial biocides. Both zinc and copper pyrithione are also moderately selective against SRM. The high-throughput (HT) approach we present can be readily adapted to target SRM in diverse environments and similar strategies could be used to quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant to efforts to engineer environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering.

PubMed

Sardi, Maria; Gasch, Audrey P

2017-08-01

Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Parts plus pipes: synthetic biology approaches to metabolic engineering

PubMed Central

Boyle, Patrick M.; Silver, Pamela A.

2011-01-01

Synthetic biologists combine modular biological “parts” to create higher-order devices. Metabolic engineers construct biological “pipes” by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design. PMID:22037345

Systems metabolic engineering strategies for the production of amino acids.

PubMed

Ma, Qian; Zhang, Quanwei; Xu, Qingyang; Zhang, Chenglin; Li, Yanjun; Fan, Xiaoguang; Xie, Xixian; Chen, Ning

2017-06-01

Systems metabolic engineering is a multidisciplinary area that integrates systems biology, synthetic biology and evolutionary engineering. It is an efficient approach for strain improvement and process optimization, and has been successfully applied in the microbial production of various chemicals including amino acids. In this review, systems metabolic engineering strategies including pathway-focused approaches, systems biology-based approaches, evolutionary approaches and their applications in two major amino acid producing microorganisms: Corynebacterium glutamicum and Escherichia coli, are summarized.

Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

PubMed

Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

2013-03-01

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands. © 2012 Blackwell Publishing Ltd.

Microbial xylanases: engineering, production and industrial applications.

PubMed

Juturu, Veeresh; Wu, Jin Chuan

2012-01-01

Enzymatic depolymerization of hemicellulose to monomer sugars needs the synergistic action of multiple enzymes, among them endo-xylanases (EC 3.2.1.8) and β-xylosidases (EC 3.2.1.37) (collectively xylanases) play a vital role in depolymerizing xylan, the major component of hemicellulose. Recent developments in recombinant protein engineering have paved the way for engineering and expressing xylanases in both heterologous and homologous hosts. Functional expression of endo-xylanases has been successful in many hosts including bacteria, yeasts, fungi and plants with yeasts being the most promising expression systems. Functional expression of β-xylosidases is more challenging possibly due to their more complicated structures. The structures of endo-xylanases of glycoside hydrolase families 10 and 11 have been well elucidated. Family F/10 endo-xylanases are composed of a cellulose-binding domain and a catalytic domain connected by a linker peptide with a (β/α)8 fold TIM barrel. Family G/11 endo-xylanases have a β-jelly roll structure and are thought to be able to pass through the pores of hemicellulose network owing to their smaller molecular sizes. The structure of a β-D-xylosidase belonging to family 39 glycoside hydrolase has been elucidated as a tetramer with each monomer being composed of three distinct regions: a catalytic domain of the canonical (β/α)8--TIM barrel fold, a β-sandwich domain and a small α-helical domain with the enzyme active site that binds to D-xylooligomers being present on the upper side of the barrel. Glycosylation is generally considered as one of the most important post-translational modifications of xylanases, but a few examples showed functional expression of eukaryotic xylanases in bacteria. The optimal ratio of these synergistic enzymes is very important in improving hydrolysis efficiency and reducing enzyme dosage but has hardly been addressed in literature. Xylanases have been used in traditional fields such as food, feed

Impacts of Sampling and Handling Procedures on DNA- and RNA-based Microbial Characterization and Quantification of Groundwater and Saturated Soil

DTIC Science & Technology

2012-07-01

use of molecular biological techniques (MBTs) has allowed microbial ecologists and environmental engineers to determine microbial community...metabolic genes). The most common approaches used in bioremediation research are those based on the polymerase chain reaction (PCR) amplification of... bioremediation . Because of its sensitivity compared to direct hybridization/probing, PCR is increasingly used to analyze groundwater samples and soil samples

Creating and maintaining a successful geoscience pathway from 2YC to 4YC for Native Hawaiian Students: First Steps

NASA Astrophysics Data System (ADS)

Guidry, M.; Eschenberg, A.; McCoy, F. W.; McManus, M. A.; Lee, K.; DeLay, J. K.; Taylor, S. V.; Dire, J.; Krupp, D.

2017-12-01

In the Fall of 2015, the two four year (4YC) institutions within the University of Hawaii (UH) system offering baccalaureate degrees in geosciences enrolled only six Native Hawaiian (NH) students out of a total of 194 students in geoscience degree programs. This percentage (3%) of NH students enrolled in geosciences is far lower than the percentage of NH students enrolled at any single institution in the UH system, which ranges from 14 to 42%. At the same time, only six (3%) of the 194 students enrolled in geoscience baccalaureate programs were transfer students from the UH community colleges. Of these six transfer students, three were NH. This reflects the need for increased transfer of NH in the geosciences from two year (2YC) to 4YC. In the Fall of 2015, UH Manoa's (UHM) School of Ocean and Earth Science and Technology (SOEST) accounted for only 0.14% of transfer students from UH community colleges. This compares to 5% in the UHM School of Engineering and 27% in the UHM College of Arts and Sciences. As part of the first year of a multi-institutional five-year NSF TCUP-PAGE (Tribal Colleges and Universities Program - PArtnerships for Geoscience Education) award, we review our first steps and strategies for building a successful and sustainable geoscience transfer pathway for Native Hawaiian and community college students into the three undergraduate geoscience programs (Atmospheric Sciences, Environmental Sciences, and Geology & Geophysics) within SOEST.

Molecular-based environmental risk assessment of three varieties of genetically engineered cows.

PubMed

Xu, Jianxiang; Zhao, Jie; Wang, Jianwu; Zhao, Yaofeng; Zhang, Lei; Chu, Mingxing; Li, Ning

2011-10-01

The development of animal biotechnology has led to an increase in attention to biosafety issues. Here we evaluated the impact of genetically engineered cows on the environment. The probability of horizontal gene transfer and the impact on the microbial communities in cow gut and soil were tested using three varieties of genetically engineered cows that were previously transformed with a human gene encoding lysozyme, lactoferrin, or human alpha lactalbumin. The results showed that the transgenes were not detectable by polymerase chain reaction (PCR) or quantitative real-time PCR in gut microbial DNA extracts of manure or microbial DNA extracts of topsoil. In addition, the transgenes had no impact on the microbial communities in cow gut or soil as assessed by PCR-denaturing gradient gel electrophoresis or 16S rDNA sequencing. Furthermore, phylogenetic analyses showed that the manure bacteria sampled during each of the four seasons belonged primarily to two groups, Firmicutes and Bacteroidetes, and the soil bacteria belonged to four groups, Firmicutes, Bacteroidetes, Actinobacteria, and α-proteobacteria. Other groups, such as β-proteobacteria, γ-proteobacteria, δ-proteobacteria, ε-proteobacteria, Spirochaetes, Acidobacteria, Chloroflexi, and Nitrospira, were not dominant in the manure or soil.

Burn Wound Healing and Tissue Engineering.

PubMed

Singer, Adam J; Boyce, Steven T

In 2016 the American Burn Association held a State of the Science conference to help identify burn research priorities for the next decade. The current paper summarizes the work of the sub-committee on Burn Wound Healing and Tissue Engineering. We first present the priorities in wound healing research over the next 10 years. We then summarize the current state of the science related to burn wound healing and tissue engineering including determination of burn depth, limiting burn injury progression, eschar removal, management of microbial contamination and wound infection, measuring wound closure, accelerating wound healing and durable wound closure, and skin substitutes and tissue engineering. Finally, a summary of the round table discussion is presented.

Microbials for the production of monoclonal antibodies and antibody fragments.

PubMed

Spadiut, Oliver; Capone, Simona; Krainer, Florian; Glieder, Anton; Herwig, Christoph

2014-01-01

Monoclonal antibodies (mAbs) and antibody fragments represent the most important biopharmaceutical products today. Because full length antibodies are glycosylated, mammalian cells, which allow human-like N-glycosylation, are currently used for their production. However, mammalian cells have several drawbacks when it comes to bioprocessing and scale-up, resulting in long processing times and elevated costs. By contrast, antibody fragments, that are not glycosylated but still exhibit antigen binding properties, can be produced in microbial organisms, which are easy to manipulate and cultivate. In this review, we summarize recent advances in the expression systems, strain engineering, and production processes for the three main microbials used in antibody and antibody fragment production, namely Saccharomyces cerevisiae, Pichia pastoris, and Escherichia coli. Copyright © 2013 Elsevier Ltd. All rights reserved.

Using Intact Iron Microbial Mats to Gain Insights Into Mat Ecology and Geochemical Niche at the Microbial Scale

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Chan, C. S. Y.; Mcallister, S.; Leavitt, A.; Emerson, D.

2015-12-01

Microbial mats are formed by microorganisms working in coordinated symbiosis, often benefitting the community by controlling the local geochemical or physical environment. Thus, the ecology of the mat depends on the individual roles of microbes organized into niches within a larger architecture. Chemolithotrophic Fe-oxidizing bacteria (FeOB) form distinctive Fe oxyhydroxide biominerals which constitute the building blocks of the mat. However, the majority of our progress has been in understanding the overall community structure. Understanding the physical mat structure on the microbial scale is important to unraveling FeOB evolution, the biogeochemistry and ecology of Fe-rich habitats, and ultimately interpreting FeOB biosignatures in the rock record. Mats in freshwater and marine environments contain strikingly similar biomineral morphologies, yet they are formed by phylogenetically distinct microorganisms. This suggests that the overall architecture and underlying genetics of freshwater and marine mats has evolved to serve particular roles specific to Fe oxidation. Thus, we conducted a comparative study of Fe seep freshwater mats and marine hydrothermal mats. We have developed a new approach to sampling Fe mats in order to preserve the delicate structure for analysis by confocal and scanning electron microscopy. Our analyses of these intact mats show that freshwater and marine mats are similarly initiated by a single type of structure-former. These ecosystem engineers form either a hollow sheath or a twisted stalk biomineral during mat formation, with a highly directional structure. These microbes appear to be the vanguard organisms that anchor the community within oxygen/Fe(II) gradients, further allowing for community succession in the mat interior as evidenced by other mineralized morphologies. Patterns in biomineral thickness and directionality were indicative of redox gradients and temporal changes in the geochemical environment. These observations show that

Microbial lipid extraction from Lipomyces starkeyi using irreversible electroporation.

PubMed

Karim, Ahasanul; Yousuf, Abu; Islam, M Amirul; Naif, Yasir H; Faizal, Che Ku Mohammad; Alam, Md Zahangir; Pirozzi, Domenico

2018-02-21

The aim of the study was to investigate the feasibility of using irreversible electroporation (EP) as a microbial cell disruption technique to extract intracellular lipid within short time and in an eco-friendly manner. An EP circuit was designed and fabricated to obtain 4 kV with frequency of 100 Hz of square waves. The yeast cells of Lipomyces starkeyi (L. starkeyi) were treated by EP for 2-10 min where the distance between electrodes was maintained at 2, 4, and 6 cm. Colony forming units (CFU) were counted to observe the cell viability under the high voltage electric field. The forces of the pulsing electric field caused significant damage to the cell wall of L. starkeyi and the disruption of microbial cells was visualized by field emission scanning electron microscopic (FESEM) image. After breaking the cell wall, lipid was extracted and measured to assess the efficiency of EP over other techniques. The extent of cell inactivation was up to 95% when the electrodes were placed at the distance of 2 cm, which provided high treatment intensity (36.7 kWh m -3 ). At this condition, maximum lipid (63 mg g -1 ) was extracted when the biomass was treated for 10 min. During the comparison, EP could extract 31.88% lipid while the amount was 11.89% for ultrasonic and 16.8% for Fenton's reagent. The results recommend that the EP is a promising technique for lowering the time and solvent usage for lipid extraction from microbial biomass. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Microbial Genetic Memory to Study Heterogeneous Soil Processes

NASA Astrophysics Data System (ADS)

Fulk, E. M.; Silberg, J. J.; Masiello, C. A.

2017-12-01

Microbes can be engineered to sense environmental conditions and produce a detectable output. These microbial biosensors have traditionally used visual outputs that are difficult to detect in soil. However, recently developed gas-producing biosensors can be used to noninvasively monitor complex soil processes such as horizontal gene transfer or cell-cell signaling. While these biosensors report on the fraction of a microbial population exposed to a process or chemical signal at the time of measurement, they do not record a "memory" of past exposure. Synthetic biologists have recently developed a suite of genetically encoded memory circuits capable of reporting on historical exposure to the signal rather than just the current state. We will provide an overview of the microbial memory systems that may prove useful to studying microbial decision-making in response to environmental conditions. Simple memory circuits can give a yes/no report of any past exposure to the signal (for example anaerobic conditions, osmotic stress, or high nitrate concentrations). More complicated systems can report on the order of exposure of a population to multiple signals or the experiences of spatially distinct populations, such as those in root vs. bulk soil. We will report on proof-of-concept experiments showing the function of a simple permanent memory system in soil-cultured microbes, and we will highlight additional applications. Finally, we will discuss challenges still to be addressed in applying these memory circuits for biogeochemical studies.

Engineering monolayer poration for rapid exfoliation of microbial membranes.

PubMed

Pyne, Alice; Pfeil, Marc-Philipp; Bennett, Isabel; Ravi, Jascindra; Iavicoli, Patrizia; Lamarre, Baptiste; Roethke, Anita; Ray, Santanu; Jiang, Haibo; Bella, Angelo; Reisinger, Bernd; Yin, Daniel; Little, Benjamin; Muñoz-García, Juan C; Cerasoli, Eleonora; Judge, Peter J; Faruqui, Nilofar; Calzolai, Luigi; Henrion, Andre; Martyna, Glenn J; Grovenor, Chris R M; Crain, Jason; Hoogenboom, Bart W; Watts, Anthony; Ryadnov, Maxim G

2017-02-01

The spread of bacterial resistance to traditional antibiotics continues to stimulate the search for alternative antimicrobial strategies. All forms of life, from bacteria to humans, are postulated to rely on a fundamental host defense mechanism, which exploits the formation of open pores in microbial phospholipid bilayers. Here we predict that transmembrane poration is not necessary for antimicrobial activity and reveal a distinct poration mechanism that targets the outer leaflet of phospholipid bilayers. Using a combination of molecular-scale and real-time imaging, spectroscopy and spectrometry approaches, we introduce a structural motif with a universal insertion mode in reconstituted membranes and live bacteria. We demonstrate that this motif rapidly assembles into monolayer pits that coalesce during progressive membrane exfoliation, leading to bacterial cell death within minutes. The findings offer a new physical basis for designing effective antibiotics.

Systems metabolic engineering of microorganisms to achieve large-scale production of flavonoid scaffolds.

PubMed

Wu, Junjun; Du, Guocheng; Zhou, Jingwen; Chen, Jian

2014-10-20

Flavonoids possess pharmaceutical potential due to their health-promoting activities. The complex structures of these products make extraction from plants difficult, and chemical synthesis is limited because of the use of many toxic solvents. Microbial production offers an alternate way to produce these compounds on an industrial scale in a more economical and environment-friendly manner. However, at present microbial production has been achieved only on a laboratory scale and improvements and scale-up of these processes remain challenging. Naringenin and pinocembrin, which are flavonoid scaffolds and precursors for most of the flavonoids, are the model molecules that are key to solving the current issues restricting industrial production of these chemicals. The emergence of systems metabolic engineering, which combines systems biology with synthetic biology and evolutionary engineering at the systems level, offers new perspectives on strain and process optimization. In this review, current challenges in large-scale fermentation processes involving flavonoid scaffolds and the strategies and tools of systems metabolic engineering used to overcome these challenges are summarized. This will offer insights into overcoming the limitations and challenges of large-scale microbial production of these important pharmaceutical compounds. Copyright © 2014 Elsevier B.V. All rights reserved.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

PubMed

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L; de Bruijn, Ino; Andersson, Anders F; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-10-14

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

PubMed Central

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; de Bruijn, Ino; Andersson, Anders F.; Leupin, Olivier X.; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present. PMID:27739431

Emerging engineering principles for yield improvement in microbial cell design.

PubMed

Comba, Santiago; Arabolaza, Ana; Gramajo, Hugo

2012-01-01

Metabolic Engineering has undertaken a rapid transformation in the last ten years making real progress towards the production of a wide range of molecules and fine chemicals using a designed cellular host. However, the maximization of product yields through pathway optimization is a constant and central challenge of this field. Traditional methods used to improve the production of target compounds from engineered biosynthetic pathways in non-native hosts include: codon usage optimization, elimination of the accumulation of toxic intermediates or byproducts, enhanced production of rate-limiting enzymes, selection of appropriate promoter and ribosome binding sites, application of directed evolution of enzymes, and chassis re-circuit. Overall, these approaches tend to be specific for each engineering project rather than a systematic practice based on a more generalizable strategy. In this mini-review, we highlight some novel and extensive approaches and tools intended to address the improvement of a target product formation, founded in sophisticated principles such as dynamic control, pathway genes modularization, and flux modeling.

Emerging engineering principles for yield improvement in microbial cell design

PubMed Central

Comba, Santiago; Arabolaza, Ana; Gramajo, Hugo

2012-01-01

Metabolic Engineering has undertaken a rapid transformation in the last ten years making real progress towards the production of a wide range of molecules and fine chemicals using a designed cellular host. However, the maximization of product yields through pathway optimization is a constant and central challenge of this field. Traditional methods used to improve the production of target compounds from engineered biosynthetic pathways in non-native hosts include: codon usage optimization, elimination of the accumulation of toxic intermediates or byproducts, enhanced production of rate-limiting enzymes, selection of appropriate promoter and ribosome binding sites, application of directed evolution of enzymes, and chassis re-circuit. Overall, these approaches tend to be specific for each engineering project rather than a systematic practice based on a more generalizable strategy. In this mini-review, we highlight some novel and extensive approaches and tools intended to address the improvement of a target product formation, founded in sophisticated principles such as dynamic control, pathway genes modularization, and flux modeling. PMID:24688676

Microbially influenced corrosion communities associated with fuel-grade ethanol environments.

PubMed

Williamson, Charles H D; Jain, Luke A; Mishra, Brajendra; Olson, David L; Spear, John R

2015-08-01

Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these "newer fuels" as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion.

A minimalistic microbial food web in an excavated deep subsurface clay rock.

PubMed

Bagnoud, Alexandre; de Bruijn, Ino; Andersson, Anders F; Diomidis, Nikitas; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

Clay rocks are being considered for radioactive waste disposal, but relatively little is known about the impact of microbes on the long-term safety of geological repositories. Thus, a more complete understanding of microbial community structure and function in these environments would provide further detail for the evaluation of the safety of geological disposal of radioactive waste in clay rocks. It would also provide a unique glimpse into a poorly studied deep subsurface microbial ecosystem. Previous studies concluded that microorganisms were present in pristine Opalinus Clay, but inactive. In this work, we describe the microbial community and assess the metabolic activities taking place within borehole water. Metagenomic sequencing and genome-binning of a porewater sample containing suspended clay particles revealed a remarkably simple heterotrophic microbial community, fueled by sedimentary organic carbon, mainly composed of two organisms: a Pseudomonas sp. fermenting bacterium growing on organic macromolecules and releasing organic acids and H2, and a sulfate-reducing Peptococcaceae able to oxidize organic molecules to CO(2). In Opalinus Clay, this microbial system likely thrives where pore space allows it. In a repository, this may occur where the clay rock has been locally damaged by excavation or in engineered backfills. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

Larsen, Peter; Gilbert, Jack

2013-01-01

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

Microbial Anomalies Encountered on the International Space Station

NASA Technical Reports Server (NTRS)

Bruce, Rebekah J.; Wong, Wing; Pierson, Duane; Castro, Victoria

2010-01-01

Microorganisms in our living environments are unavoidable. A community of microbes arrived in space with the delivery of the first element of the International Space Station (ISS), attached to hardware and on the bodies of the humans tasked with the initial assembly missions. The risk that microorganisms could cause adverse effects in the health of both the human occupants of the ISS as well as the physical integrity of the station environment and life support systems has been both a driver and a function of engineering and operational controls. Scientists and engineers at NASA have gone to extensive measures to control microbial growth at levels safe for the crewmembers and the spacecraft environment. Many of these measures were initiated with the design of the spacecraft and its systems. Materials used in the ISS were tested for resistance to fungi, such as mold and a paint with a fungus-killing chemical was also used. Controlling the humidity of the air in the Station is also an effective way of discouraging microbe growth. The breathing air is reconditioned by the Environmental Control Life Support System (ECLSS) prior to distribution, utilizing High Efficiency Particulate Air (HEPA) filtration. Requirements restricting the accumulation of water condensate in the air handlers and habitable volume of the ISS were other safeguards added. Water for drinking and food rehydration is disinfected or filtered. A robust in-flight housekeeping regimen for the ISS significantly reduces inappropriate growth of microorganisms and includes a regular cleaning of accessible surfaces with disinfectant wipes. Most of these requirements were suggested by microbiologists to mitigate and possibly prevent many microbiological risks. In addition to these controls, before flight monitoring and analyses of the cabin air, exposed surfaces, water and food, consumables, and crew members are conducted to mitigate microbial risk to the crew and spacecraft. Many microbial risks are much

Solvent production by engineered Ralstonia eutropha: channeling carbon to biofuel.

PubMed

Chakravarty, Jayashree; Brigham, Christopher J

2018-06-01

Microbial production of solvents like acetone and butanol was a couple of the first industrial fermentation processes to gain global importance. These solvents are important feedstocks for the chemical and biofuel industry. Ralstonia eutropha is a facultatively chemolithoautotrophic bacterium able to grow with organic substrates or H 2 and CO 2 under aerobic conditions. This bacterium is a natural producer of polyhydroxyalkanoate biopolymers. Recently, with the advances in the development of genetic engineering tools, the range of metabolites R. eutropha can produce has enlarged. Its ability to utilize various carbon sources renders it an interesting candidate host for synthesis of renewable biofuel and solvent production. This review focuses on progress in metabolic engineering of R. eutropha for the production of alcohols, terpenes, methyl ketones, and alka(e)nes using various resources. Biological synthesis of solvents still presents the challenge of high production costs and competition from chemical synthesis. Better understanding of R. eutropha biology will support efforts to engineer and develop superior microbial strains for solvent production. Continued research on multiple fronts is required to engineer R. eutropha for truly sustainable and economical solvent production.

Microbial conversion of biomass into bio-based polymers.

PubMed

Kawaguchi, Hideo; Ogino, Chiaki; Kondo, Akihiko

2017-12-01

The worldwide market for plastics is rapidly growing, and plastics polymers are typically produced from petroleum-based chemicals. The overdependence on petroleum-based chemicals for polymer production raises economic and environmental sustainability concerns. Recent progress in metabolic engineering has expanded fermentation products from existing aliphatic acids or alcohols to include aromatic compounds. This diversity provides an opportunity to expand the development and industrial uses of high-performance bio-based polymers. However, most of the biomonomers are produced from edible sugars or starches that compete directly with food and feed uses. The present review focuses on recent progress in the microbial conversion of biomass into bio-based polymers, in which fermentative products from renewable feedstocks serve as biomonomers for the synthesis of bio-based polymers. In particular, the production of biomonomers from inedible lignocellulosic feedstocks by metabolically engineered microorganisms and the synthesis of bio-based engineered plastics from the biological resources are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial enhancement of oil recovery: Recent advances. Proceedings

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

Premuzic, E.T.; Woodhead, A.D.; Vivirito, K.J.

1992-12-31

During recent years, systematic, scientific, and engineering effort by researchers in the United States and abroad, has established the scientific basis for Microbial Enhanced Oil Recovery (MEOR) technology. The successful application of MEOR technology as an oil recovery process is a goal of the Department of Energy (DOE). Research efforts involving aspects of MEOR in the microbiological, biochemical, and engineering fields led DOE to sponsor an International Conference at Brookhaven National Laboratory in 1992, to facilitate the exchange of information and a discussion of ideas for the future research emphasis. At this, the Fourth International MEOR Conference, where international attendeesmore » from 12 countries presented a total of 35 papers, participants saw an equal distribution between ``research`` and ``field applications.`` In addition, several modeling and ``state-of-the-art`` presentations summed up the present status of MEOR science and engineering. Individual papers in this proceedings have been process separately for inclusion in the Energy Science and Technology Database.« less

Measurements of Tip Vortices from a Full-Scale UH-60A Rotor by Retro- Reflective Background Oriented Schlieren and Stereo Photogrammetry

NASA Technical Reports Server (NTRS)

Schairer, Edward; Kushner, Laura K.; Heineck, James T.

2013-01-01

Positions of vortices shed by a full-scale UH-60A rotor in forward flight were measured during a test in the National Full- Scale Aerodynamics Complex at NASA Ames Research Center. Vortices in a region near the tip of the advancing blade were visualized from two directions by Retro-Reflective Background-Oriented Schlieren (RBOS). Correspondence of points on the vortex in the RBOS images from both cameras was established using epipolar geometry. The object-space coordinates of the vortices were then calculated from the image-plane coordinates using stereo photogrammetry. One vortex from the tip of the blade that had most recently passed was visible in most of the data. The visibility of the vortices was greatest at high thrust and low advance ratios. At these favorable conditions, vortices from the most recent passages of all four blades were detected. The vortex positions were in good agreement with PIV data for a case where PIV measurements were also made. RBOS and photogrammetry provided measurements of the angle at which each vortex passed through the PIV plane.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

Demonstrating the unit hydrograph and flow routing processes involving active student participation - a university lecture experiment

NASA Astrophysics Data System (ADS)

Schulz, Karsten; Burgholzer, Reinhard; Klotz, Daniel; Wesemann, Johannes; Herrnegger, Mathew

2018-05-01

The unit hydrograph (UH) has been one of the most widely employed hydrological modelling techniques to predict rainfall-runoff behaviour of hydrological catchments, and is still used to this day. Its concept is based on the idea that a unit of effective precipitation per time unit (e.g. mm h-1) will always lead to a specific catchment response in runoff. Given its relevance, the UH is an important topic that is addressed in most (engineering) hydrology courses at all academic levels. While the principles of the UH seem to be simple and easy to understand, teaching experiences in the past suggest strong difficulties in students' perception of the UH theory and application. In order to facilitate a deeper understanding of the theory and application of the UH for students, we developed a simple and cheap lecture theatre experiment which involved active student participation. The seating of the students in the lecture theatre represented the hydrological catchment in its size and form. A set of plastic balls, prepared with a piece of magnetic strip to be tacked to any white/black board, each represented a unit amount of effective precipitation. The balls are evenly distributed over the lecture theatre and routed by some given rules down the catchment to the catchment outlet, where the resulting hydrograph is monitored and illustrated at the black/white board. The experiment allowed an illustration of the underlying principles of the UH, including stationarity, linearity, and superposition of the generated runoff and subsequent routing. In addition, some variations of the experimental setup extended the UH concept to demonstrate the impact of elevation, different runoff regimes, and non-uniform precipitation events on the resulting hydrograph. In summary, our own experience in the classroom, a first set of student exams, as well as student feedback and formal evaluation suggest that the integration of such an experiment deepened the learning experience by

Engineering microbial phenotypes through rewiring of genetic networks

PubMed Central

Rodrigues, Rui T.L.; Lee, Sangjin; Haines, Matthew

2017-01-01

Abstract The ability to program cellular behaviour is a major goal of synthetic biology, with applications in health, agriculture and chemicals production. Despite efforts to build ‘orthogonal’ systems, interactions between engineered genetic circuits and the endogenous regulatory network of a host cell can have a significant impact on desired functionality. We have developed a strategy to rewire the endogenous cellular regulatory network of yeast to enhance compatibility with synthetic protein and metabolite production. We found that introducing novel connections in the cellular regulatory network enabled us to increase the production of heterologous proteins and metabolites. This strategy is demonstrated in yeast strains that show significantly enhanced heterologous protein expression and higher titers of terpenoid production. Specifically, we found that the addition of transcriptional regulation between free radical induced signalling and nitrogen regulation provided robust improvement of protein production. Assessment of rewired networks revealed the importance of key topological features such as high betweenness centrality. The generation of rewired transcriptional networks, selection for specific phenotypes, and analysis of resulting library members is a powerful tool for engineering cellular behavior and may enable improved integration of heterologous protein and metabolite pathways. PMID:28369627

Engineering Thermostable Microbial Xylanases Toward its Industrial Applications.

PubMed

Kumar, Vishal; Dangi, Arun Kumar; Shukla, Pratyoosh

2018-03-01

Xylanases are one of the important hydrolytic enzymes which hydrolyze the β-1, 4 xylosidic linkage of the backbone of the xylan polymeric chain which consists of xylose subunits. Xylanases are mainly found in plant cell walls and are produced by several kinds of microorganisms such as fungi, bacteria, yeast, and some protozoans. The fungi are considered as most potent xylanase producers than that of yeast and bacteria. There is a broad series of industrial applications for the thermostable xylanase as an industrial enzyme. Thermostable xylanases have been used in a number of industries such as paper and pulp industry, biofuel industry, food and feed industry, textile industry, etc. The present review explores xylanase-substrate interactions using gene-editing tools toward the comprehension in improvement in industrial stability of xylanases. The various protein-engineering and metabolic-engineering methods have also been explored to improve operational stability of xylanase. Thermostable xylanases have also been used for improvement in animal feed nutritional value. Furthermore, they have been used directly in bakery and breweries, including a major use in paper and pulp industry as a biobleaching agent. This present review envisages some of such applications of thermostable xylanases for their bioengineering.

Synthetic biology and metabolic engineering.

PubMed

Stephanopoulos, Gregory

2012-11-16

Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.

Engineering Escherichia coli coculture systems for the production of biochemical products.

PubMed

Zhang, Haoran; Pereira, Brian; Li, Zhengjun; Stephanopoulos, Gregory

2015-07-07

Engineering microbial consortia to express complex biosynthetic pathways efficiently for the production of valuable compounds is a promising approach for metabolic engineering and synthetic biology. Here, we report the design, optimization, and scale-up of an Escherichia coli-E. coli coculture that successfully overcomes fundamental microbial production limitations, such as high-level intermediate secretion and low-efficiency sugar mixture utilization. For the production of the important chemical cis,cis-muconic acid, we show that the coculture approach achieves a production yield of 0.35 g/g from a glucose/xylose mixture, which is significantly higher than reported in previous reports. By efficiently producing another compound, 4-hydroxybenzoic acid, we also demonstrate that the approach is generally applicable for biosynthesis of other important industrial products.

Application of metabolic engineering for the biotechnological production of L-valine.

PubMed

Oldiges, Marco; Eikmanns, Bernhard J; Blombach, Bastian

2014-07-01

The branched chain amino acid L-valine is an essential nutrient for higher organisms, such as animals and humans. Besides the pharmaceutical application in parenteral nutrition and as synthon for the chemical synthesis of e.g. herbicides or anti-viral drugs, L-valine is now emerging into the feed market, and significant increase of sales and world production is expected. In accordance, well-known microbial production bacteria, such as Escherichia coli and Corynebacterium glutamicum strains, have recently been metabolically engineered for efficient L-valine production under aerobic or anaerobic conditions, and the respective cultivation and production conditions have been optimized. This review summarizes the state of the art in L-valine biosynthesis and its regulation in E. coli and C. glutamicum with respect to optimal metabolic network for microbial L-valine production, genetic strain engineering and bioprocess development for L-valine production, and finally, it will shed light on emerging technologies that have the potential to accelerate strain and bioprocess engineering in the near future.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated

First Microbial Community Assessment of Borehole Fluids from the Deep Underground Science and Engineering Laboratory (DUSEL)

NASA Astrophysics Data System (ADS)

Moser, D. P.; Anderson, C.; Bang, S.; Jones, T. L.; Boutt, D.; Kieft, T.; Sherwood Lollar, B.; Murdoch, L. C.; Pfiffner, S. M.; Bruckner, J.; Fisher, J. C.; Newburn, J.; Wheatley, A.; Onstott, T. C.

2010-12-01

Fluid and gas samples were collected from two flowing boreholes at the 4100 (1,250 m) and 4850 ft (1478 m) levels of the former Homestake Gold Mine in Lead, South Dakota. Service- and flood water samples were also collected as comparative benchmarks. With a maximum depth of 8,000 ft, (2,438 m), this mine currently hosts the Sanford Laboratory and is the proposed location for the US Deep Underground Science and Engineering Laboratory (DUSEL). The uncased 4100L hole is a legacy of mining; whereas, the cased 4850 hole was drilled in 2009 in support of large cavity construction. Both were packered or valved to exclude mine air and sampled anaerobically using aseptic technique. Physical measurements, aquatic and dissolved gas chemistry, cell counts, and microbial community assessments (SSU rRNA libraries) were performed on all samples. This study represents the first at Sanford Lab/DUSEL specifically focused on the deep biosphere rather than mine microbiology. Fluids from the two holes differed markedly, with that from 4100L being characterized by NaHCO3 and 4850 by Na2SO4. pH values of 8.2 vs. 7.5, conductivities (μS) of 1790 vs. 7667 and alkalinities (mg/L) of 767 vs. 187 were obtained from 4100L and 4850, respectively. As expected, the deeper 4850L hole had the higher temperature (38 vs. 30 oC). Neither had measureable nitrate, but both had similar dissolved organic C (DOC) concentrations (0.8 vs. 0.9 mg/L). Sulfate was present at 337 vs. 4,470 mg/L in 4100L and 4850L. Major dissolved gases were N2 (91 and 81 vol%), O2 (12 and 16 vol%) and CH4 (0.07 and 3.35 vol%) in 4100L and 4850L. The δ13C of CH4 was -51 and -56.7 permil in 4100L and 4850, respectively. The uncorrected 14C age of DIC was calculated at 25,310 (+/- 220) and 47,700 (+/-3,100) years for the two fluids. Cell counts were 5.9e3 and 2.01e5 in 4100L and 4850. Microbial community structure was diverse in both holes and distinct from that of service water. A large proportion of rRNA library clones were

Synergizing 13C Metabolic Flux Analysis and Metabolic Engineering for Biochemical Production.

PubMed

Guo, Weihua; Sheng, Jiayuan; Feng, Xueyang

Metabolic engineering of industrial microorganisms to produce chemicals, fuels, and drugs has attracted increasing interest as it provides an environment-friendly and renewable route that does not depend on depleting petroleum sources. However, the microbial metabolism is so complex that metabolic engineering efforts often have difficulty in achieving a satisfactory yield, titer, or productivity of the target chemical. To overcome this challenge, 13 C Metabolic Flux Analysis ( 13 C-MFA) has been developed to investigate rigorously the cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, 13 C-MFA has been widely used in academic labs and the biotechnology industry to pinpoint the key issues related to microbial-based chemical production and to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this chapter we introduce the basics of 13 C-MFA and illustrate how 13 C-MFA has been applied to synergize with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production.

Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities

PubMed Central

Mahadevan, Radhakrishnan; Henson, Michael A.

2012-01-01

Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research. PMID:24688668

Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.

PubMed

Mahadevan, Radhakrishnan; Henson, Michael A

2012-01-01

Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

Counteraction of antibiotic production and degradation stabilizes microbial communities

PubMed Central

Kelsic, Eric D.; Zhao, Jeffrey; Vetsigian, Kalin; Kishony, Roy

2015-01-01

Summary A major challenge in theoretical ecology is understanding how natural microbial communities support species diversity1-8, and in particular how antibiotic producing, sensitive and resistant species coexist9-15. While cyclic “rock-paper-scissors” interactions can stabilize communities in spatial environments9-11, coexistence in unstructured environments remains an enigma12,16. Here, using simulations and analytical models, we show that the opposing actions of antibiotic production and degradation enable coexistence even in well-mixed environments. Coexistence depends on 3-way interactions where an antibiotic degrading species attenuates the inhibitory interactions between two other species. These 3-way interactions enable coexistence that is robust to substantial differences in inherent species growth rates and to invasion by “cheating” species that cease producing or degrading antibiotics. At least two antibiotics are required for stability, with greater numbers of antibiotics enabling more complex communities and diverse dynamical behaviors ranging from stable fixed-points to limit cycles and chaos. Together, these results show how multi-species antibiotic interactions can generate ecological stability in both spatial and mixed microbial communities, suggesting strategies for engineering synthetic ecosystems and highlighting the importance of toxin production and degradation for microbial biodiversity. PMID:25992546

Microbial enhanced oil recovery and wettability research program

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

Thomas, C.P.; Bala, G.A.; Duvall, M.L.

1991-07-01

This report covers research results for the microbial enhanced oil recovery (MEOR) and wettability research program conducted by EG G Idaho, Inc. at the Idaho National Engineering Laboratory (INEL). The isolation and characterization of microbial species collected from various locations including target oil field environments is underway to develop more effective oil recovery systems for specific applications. The wettability research is a multi-year collaborative effort with the New Mexico Petroleum Recovery Research Center (NMPRRC), to evaluate reservoir wettability and its effects on oil recovery. Results from the wettability research will be applied to determine if alteration of wettability is amore » significant contributing mechanism for MEOR systems. Eight facultatively anaerobic surfactant producing isolates able to function in the reservoir conditions of the Minnelusa A Sands of the Powder River Basin in Wyoming were isolated from naturally occurring oil-laden environments. Isolates were characterized according to morphology, thermostability, halotolerance, growth substrates, affinity to crude oil/brine interfaces, degradative effects on crude oils, and biochemical profiles. Research at the INEL has focused on the elucidation of microbial mechanisms by which crude oil may be recovered from a reservoir and the chemical and physical properties of the reservoir that may impact the effectiveness of MEOR. Bacillus licheniformis JF-2 (ATCC 39307) has been used as a benchmark organism to quantify MEOR of medium weight crude oils (17.5 to 38.1{degrees}API) the capacity for oil recovery of Bacillus licheniformis JF-2 utilizing a sucrose-based nutrient has been elucidated using Berea sandstone cores. Spacial distribution of cells after microbial flooding has been analyzed with scanning electron microscopy. Also the effect of microbial surfactants on the interfacial tensions (IFT) of aqueous/crude oil systems has been measured. 87 refs., 60 figs., 15 tabs.« less

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

PubMed

Larsen, Peter; Hamada, Yuki; Gilbert, Jack

2012-07-31

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

Growth and element flux at fine taxonomic resolution in natural microbial communities

NASA Astrophysics Data System (ADS)

Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

2015-04-01

Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

Automated multiplex genome-scale engineering in yeast

PubMed Central

Si, Tong; Chao, Ran; Min, Yuhao; Wu, Yuying; Ren, Wen; Zhao, Huimin

2017-01-01

Genome-scale engineering is indispensable in understanding and engineering microorganisms, but the current tools are mainly limited to bacterial systems. Here we report an automated platform for multiplex genome-scale engineering in Saccharomyces cerevisiae, an important eukaryotic model and widely used microbial cell factory. Standardized genetic parts encoding overexpression and knockdown mutations of >90% yeast genes are created in a single step from a full-length cDNA library. With the aid of CRISPR-Cas, these genetic parts are iteratively integrated into the repetitive genomic sequences in a modular manner using robotic automation. This system allows functional mapping and multiplex optimization on a genome scale for diverse phenotypes including cellulase expression, isobutanol production, glycerol utilization and acetic acid tolerance, and may greatly accelerate future genome-scale engineering endeavours in yeast. PMID:28469255

Mechanistic Understanding of Microbial Plugging for Improved Sweep Efficiency

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

Steven Bryant; Larry Britton

2008-09-30

Microbial plugging has been proposed as an effective low cost method of permeability reduction. Yet there is a dearth of information on the fundamental processes of microbial growth in porous media, and there are no suitable data to model the process of microbial plugging as it relates to sweep efficiency. To optimize the field implementation, better mechanistic and volumetric understanding of biofilm growth within a porous medium is needed. In particular, the engineering design hinges upon a quantitative relationship between amount of nutrient consumption, amount of growth, and degree of permeability reduction. In this project experiments were conducted to obtainmore » new data to elucidate this relationship. Experiments in heterogeneous (layered) beadpacks showed that microbes could grow preferentially in the high permeability layer. Ultimately this caused flow to be equally divided between high and low permeability layers, precisely the behavior needed for MEOR. Remarkably, classical models of microbial nutrient uptake in batch experiments do not explain the nutrient consumption by the same microbes in flow experiments. We propose a simple extension of classical kinetics to account for the self-limiting consumption of nutrient observed in our experiments, and we outline a modeling approach based on architecture and behavior of biofilms. Such a model would account for the changing trend of nutrient consumption by bacteria with the increasing biomass and the onset of biofilm formation. However no existing model can explain the microbial preference for growth in high permeability regions, nor is there any obvious extension of the model for this observation. An attractive conjecture is that quorum sensing is involved in the heterogeneous bead packs.« less

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

PubMed Central

Chodkowski, John L.

2017-01-01

about a diversity of possible microbial interactions that occur in both natural and engineered ecosystems. Author Video: An author video summary of this article is available. PMID:29152587

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.

Microbial Biotechnology 2020; microbiology of fossil fuel resources.

PubMed

Head, Ian M; Gray, Neil D

2016-09-01

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

Cell surface engineering of microorganisms towards adsorption of heavy metals.

PubMed

Li, Peng-Song; Tao, Hu-Chun

2015-06-01

Heavy metal contamination has become a worldwide environmental concern due to its toxicity, non-degradability and food-chain bioaccumulation. Conventional physical and chemical treatment methods for heavy metal removal have disadvantages such as cost-intensiveness, incomplete removal, secondary pollution and the lack of metal specificity. Microbial biomass-based biosorption is one of the approaches gaining increasing attention because it is effective, cheap, and environmental friendly and can work well at low concentrations. To enhance the adsorption properties of microbial cells to heavy metal ions, the cell surface display of various metal-binding proteins/peptides have been performed using a cell surface engineering approach. The surface engineering of Gram-negative bacteria, Gram-positive bacteria and yeast towards the adsorption of heavy metals are reviewed in this article. The problems and future perspectives of this technology are discussed.

Engineering Escherichia coli coculture systems for the production of biochemical products

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

Zhang, Haoran; Pereira, Brian; Li, Zhengjun

Engineering microbial consortia to express complex biosynthetic pathways efficiently for the production of valuable compounds is a promising approach for metabolic engineering and synthetic biology. Here, we report the design, optimization, and scale-up of an Escherichia coli-E. coli coculture that successfully overcomes fundamental microbial production limitations, such as high-level intermediate secretion and low-efficiency sugar mixture utilization. For the production of the important chemical cis,cis-muconic acid, we show that the coculture approach achieves a production yield of 0.35 g/g from a glucose/xylose mixture, which is significantly higher than reported in previous reports. Furthermore, by efficiently producing another compound, 4-hydroxybenzoic acid, wemore » also demonstrate that the approach is generally applicable for biosynthesis of other important industrial products.« less

Engineering Escherichia coli coculture systems for the production of biochemical products

DOE PAGES

Zhang, Haoran; Pereira, Brian; Li, Zhengjun; ...

2015-06-25

Engineering microbial consortia to express complex biosynthetic pathways efficiently for the production of valuable compounds is a promising approach for metabolic engineering and synthetic biology. Here, we report the design, optimization, and scale-up of an Escherichia coli-E. coli coculture that successfully overcomes fundamental microbial production limitations, such as high-level intermediate secretion and low-efficiency sugar mixture utilization. For the production of the important chemical cis,cis-muconic acid, we show that the coculture approach achieves a production yield of 0.35 g/g from a glucose/xylose mixture, which is significantly higher than reported in previous reports. Furthermore, by efficiently producing another compound, 4-hydroxybenzoic acid, wemore » also demonstrate that the approach is generally applicable for biosynthesis of other important industrial products.« less

Methodological flaws introduce strong bias into molecular analysis of microbial populations.

PubMed

Krakat, N; Anjum, R; Demirel, B; Schröder, P

2017-02-01

In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach. The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques. The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured. © 2016 The Society for Applied Microbiology.

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

PubMed Central

Li, Xiaofang; Bond, Philip L.; Van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

2015-01-01

Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

Lycopene overproduction in Saccharomyces cerevisiae through combining pathway engineering with host engineering.

PubMed

Chen, Yan; Xiao, Wenhai; Wang, Ying; Liu, Hong; Li, Xia; Yuan, Yingjin

2016-06-21

Microbial production of lycopene, a commercially and medically important compound, has received increasing concern in recent years. Saccharomyces cerevisiae is regarded as a safer host for lycopene production than Escherichia coli. However, to date, the lycopene yield (mg/g DCW) in S. cerevisiae was lower than that in E. coli and did not facilitate downstream extraction process, which might be attributed to the incompatibility between host cell and heterologous pathway. Therefore, to achieve lycopene overproduction in S. cerevisiae, both host cell and heterologous pathway should be delicately engineered. In this study, lycopene biosynthesis pathway was constructed by integration of CrtE, CrtB and CrtI in S. cerevisiae CEN.PK2. When YPL062W, a distant genetic locus, was deleted, little acetate was accumulated and approximately 100 % increase in cytosolic acetyl-CoA pool was achieved relative to that in parental strain. Through screening CrtE, CrtB and CrtI from diverse species, an optimal carotenogenic enzyme combination was obtained, and CrtI from Blakeslea trispora (BtCrtI) was found to have excellent performance on lycopene production as well as lycopene proportion in carotenoid. Then, the expression level of BtCrtI was fine-tuned and the effect of cell mating types was also evaluated. Finally, potential distant genetic targets (YJL064W, ROX1, and DOS2) were deleted and a stress-responsive transcription factor INO2 was also up-regulated. Through the above modifications between host cell and carotenogenic pathway, lycopene yield was increased by approximately 22-fold (from 2.43 to 54.63 mg/g DCW). Eventually, in fed-batch fermentation, lycopene production reached 55.56 mg/g DCW, which is the highest reported yield in yeasts. Saccharomyces cerevisiae was engineered to produce lycopene in this study. Through combining host engineering (distant genetic loci and cell mating types) with pathway engineering (enzyme screening and gene fine-tuning), lycopene yield was

Systems Metabolic Engineering of Escherichia coli.

PubMed

Choi, Kyeong Rok; Shin, Jae Ho; Cho, Jae Sung; Yang, Dongsoo; Lee, Sang Yup

2016-05-01

Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.

Systems Metabolic Engineering of Escherichia coli.

PubMed

Choi, Kyeong Rok; Shin, Jae Ho; Cho, Jae Sung; Yang, Dongsoo; Lee, Sang Yup

2017-03-01

Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.

Microbial communities inhabiting hypersaline microbial mats from the Abu Dhabi sabkha

NASA Astrophysics Data System (ADS)

Andrade, Luiza; Dutton, Kirsten; Paul, Andreas; van der Land, Cees; Sherry, Angela; Lokier, Stephen; Head, Ian

2017-04-01

Microbial mats are organo-sedimentary structures that are typically found in areas with extreme environmental conditions. Since these ecosystems are considered to be representative of the oldest forms of life on Earth, the study of microbial mats can inform our understanding of the development of life early in the history of our planet. In this study, we used hypersaline microbial mats from the Abu Dhabi sabkha (coastal salt flats). Cores of microbial mats (ca. 90 mm depth) were collected within an intertidal region. The cores were sliced into layers 2-3 mm thick and genomic DNA was extracted from each layer. A fragment of the 16S rRNA encoding gene was amplified in all DNA extracts, using barcoded primers, and the amplicons sequenced with the Ion Torrent platform to investigate the composition of the microbial communities down the depth of the cores. Preliminary results revealed a high proportion of Archaea (15.5-40.8% abundance) in all layers, with Halobacteria appearing to be more significant in the first 40 mm (0.4-10.3% of the total microbial community). Members of the Deltaproteobacteria were dominant in almost all layers of the microbial mat (≤ 48.6% relative abundance); however this dominance was not reflected in the first 8 mm, where the abundance was less than 2%. Chloroflexi and Anaerolinea, representing 93% of bacterial abundance, dominated the first 8 mm depth and decreased at greater depth (≤ 3% relative abundance). Cyanobacteria were found only in the top 10 mm, with unexpected low abundance (≤ 3% of the total number of reads). These results show a vertical zonation of microbial communities and processes in the microbial mats. Further analyses are underway to investigate if these patterns are repeated at other sites along a transect of the sabkha, and to relate the microbial composition to the physical-chemical conditions of the sites.

PanDaTox: A tool for accelerated metabolic engineering

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

Amitai, Gil; Sorek, Rotem

2012-07-18

Metabolic engineering is often facilitated by cloning of genes encoding enzymes from various heterologous organisms into E. coli. Such engineering efforts are frequently hampered by foreign genes that are toxic to the E. coli host. We have developed PanDaTox (www.weizmann.ac.il/pandatox), a web-based resource that provides experimental toxicity information for more than 1.5 million genes from hundreds of different microbial genomes. The toxicity predictions, which were extensively experimentally verified, are based on serial cloning of genes into E. coli as part of the Sanger whole genome shotgun sequencing process. PanDaTox can accelerate metabolic engineering projects by allowing researchers to exclude toxicmore » genes from the engineering plan and verify the clonability of selected genes before the actual metabolic engineering experiments are conducted.« less

Impact of drinking water conditions and copper materials on downstream biofilm microbial communities and legionella pneumophila colonization

EPA Science Inventory

Legionella pneumophila, the medically important species within the genus Legionella, is a concern in engineered water systems. Its ability to amplify within free-living amoebae is well documented, but its interactions/ecology within the microbial community of drinking water biofi...

Microbial Properties Database Editor Tutorial

EPA Science Inventory

A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbial-relevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pat...

Pilot in the Loop CFD Method Development

DTIC Science & Technology

2016-07-31

Aerospace Engineering 231C Hammond Building University Park, PA 16802 Attn: Joseph F. Horn Phone: 814-865-6434, Fax: 814-865-7092 Email: joehorn...larger main rotor provides propulsion and lift, and thus induces significant flow disturbances on the surrounding air . The CFD coupling interface...J., “UH-60A Black Hawk Engineering Simulation Program: Volume I – Mathematical Model,” NASA CR166309, 1981. 5. Transitions/Impact No major

A microbial factory for lactate-based polyesters using a lactate-polymerizing enzyme

PubMed Central

Taguchi, Seiichi; Yamada, Miwa; Matsumoto, Ken'ichiro; Tajima, Kenji; Satoh, Yasuharu; Munekata, Masanobu; Ohno, Katsuhiro; Kohda, Katsunori; Shimamura, Takashi; Kambe, Hiromi; Obata, Shusei

2008-01-01

Polylactate (PLA) is synthesized as a representative bio-based polyester by the chemo-bio process on the basis of metal catalyst-mediated chemical polymerization of lactate (LA) supplied by microbial fermentation. To establish the one-step microbial process for synthesis of LA-based polyesters, we explored whether polyhydroxyalkanoate (PHA) synthase would exhibit polymerizing activity toward a LA-coenzyme A (CoA), based on the fact that PHA monomeric constituents, especially 3-hydroxybutyrate (3HB), are structurally analogous to LA. An engineered PHA synthase was discovered as a candidate by a two-phase in vitro polymerization system previously developed. An LA-CoA producing Escherichia coli strain with a CoA transferase gene was constructed, and the generation of LA-CoA was demonstrated by capillary electrophoresis/MS analysis. Next, when the engineered PHA synthase gene was introduced into the resultant recombinant strain, we confirmed the one-step biosynthesis of the LA-incorporated copolyester, P(6 mol% LA-co-94 mol% 3HB), with a number-average molecular weight of 1.9 × 105, as revealed by gel permeation chromatography, gas chromatography/MS, and NMR. PMID:18978031

Evaluation of engineered foods for Closed Ecological Life Support System (CELSS)

NASA Technical Reports Server (NTRS)

Karel, M.

1981-01-01

A system of conversion of locally regenerated raw materials and of resupplied freeze-dried foods and ingredients into acceptable, safe and nutritious engineered foods is proposed. The first phase of the proposed research has the following objectives: (1) evaluation of feasibility of developing acceptable and reliable engineered foods from a limited selection of plants, supplemented by microbially produced nutrients and a minimum of dehydrated nutrient sources (especially those of animal origin); (2) evaluation of research tasks and specifications of research projects to adapt present technology and food science to expected space conditions (in particular, problems arising from unusual gravity conditions, problems of limited size and the isolation of the food production system, and the opportunities of space conditions are considered); (3) development of scenarios of agricultural production of plant and microbial systems, including the specifications of processing wastes to be recycled.

Enhanced microbial electrosynthesis by using defined co-cultures

PubMed Central

Deutzmann, Jörg S; Spormann, Alfred M

2017-01-01

Microbial uptake of free cathodic electrons presents a poorly understood aspect of microbial physiology. Uptake of cathodic electrons is particularly important in microbial electrosynthesis of sustainable fuel and chemical precursors using only CO2 and electricity as carbon, electron and energy source. Typically, large overpotentials (200 to 400 mV) were reported to be required for cathodic electron uptake during electrosynthesis of, for example, methane and acetate, or low electrosynthesis rates were observed. To address these limitations and to explore conceptual alternatives, we studied defined co-cultures metabolizing cathodic electrons. The Fe(0)-corroding strain IS4 was used to catalyze the electron uptake reaction from the cathode forming molecular hydrogen as intermediate, and Methanococcus maripaludis and Acetobacterium woodii were used as model microorganisms for hydrogenotrophic synthesis of methane and acetate, respectively. The IS4-M. maripaludis co-cultures achieved electromethanogenesis rates of 0.1–0.14 μmol cm−2 h−1 at −400 mV vs standard hydrogen electrode and 0.6–0.9 μmol cm−2 h−1 at −500 mV. Co-cultures of strain IS4 and A. woodii formed acetate at rates of 0.21–0.23 μmol cm−2 h−1 at −400 mV and 0.57–0.74 μmol cm−2 h−1 at −500 mV. These data show that defined co-cultures coupling cathodic electron uptake with synthesis reactions via interspecies hydrogen transfer may lay the foundation for an engineering strategy for microbial electrosynthesis. PMID:27801903

Development of biologically modified anodes for energy harvesting using microbial fuel cells

NASA Astrophysics Data System (ADS)

Sumner, James J.; Ganguli, Rahul; Chmelka, Brad

2012-06-01

Biological fuel cells hold promise as an alternative energy source to batteries for unattended ground sensor applications due to the fact that they can be extremely long lived. This lifetime can be extended over batteries by scavenging fuel from the deployed environment. Microbial fuel cells (MFC) are one class of such sources that produce usable energy from small organic compounds (i.e. sugars, alcohols, organic acids, and biopolymers) which can be easily containerized or scavenged from the environment. The use of microorganisms as the anodic catalysts is what makes these systems unique from other biofuel cell designs. One of the main drawbacks of engineering a sensor system powered by an MFC is that power densities and current flux are extremely low in currently reported systems. The power density is limited by the mass transfer of the fuel source to the catalyst, the metabolism of the microbial catalysts and the electron transfer from the organism to the anode. This presentation will focus on the development of a new style of microbially-modified anodes which will increase power density to a level where a practical power source can be engineered. This is being achieved by developing a three dimensional matrix as an artificial, conductive biofilm. These artificial biofilms will allow the capture of a consortium of microbes designed for efficient metabolism of the available fuel source. Also it will keep the microbes close to the electrode allowing ready access by fuel and providing a low resistance passage of the liberated electrons from fuel oxidation.

Microbial Routes to (2R,3R)-2,3-Butanediol: Recent Advances and Future Prospects.

PubMed

Xie, Neng-Zhong; Chen, Xian-Rui; Wang, Qing-Yan; Chen, Dong; Du, Qi-Shi; Zhou, Guo-Ping; Huang, Ri-Bo

2017-01-01

(2R,3R)-2,3-Butanediol has many industrial applications, such as it is used as an antifreeze agent and low freezing point fuel. In addition, it is particularly important to provide chiral groups in drugs. In recent years, this valuable bio-based chemical has attracted increasing attention, and significant progress has been made in the development of microbial cell factories for (2R,3R)-2,3-butanediol production. This article reviews recent advances and challenges in microbial routes to (2R,3R)-2,3- butanediol production, and highlights the metabolic engineering and synthetic biological approaches used to improve titers, yields, productivities, and optical purities. Finally, a systematic and integrative strategy for developing high-performance microbial cell factories is proposed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

PubMed

Fierer, Noah; Leff, Jonathan W; Adams, Byron J; Nielsen, Uffe N; Bates, Scott Thomas; Lauber, Christian L; Owens, Sarah; Gilbert, Jack A; Wall, Diana H; Caporaso, J Gregory

2012-12-26

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

De Novo Metabolic Engineering and the Promise of Synthetic DNA

NASA Astrophysics Data System (ADS)

Klein-Marcuschamer, Daniel; Yadav, Vikramaditya G.; Ghaderi, Adel; Stephanopoulos, Gregory N.

The uncertain price and tight supply of crude oil and the ever-increasing demand for clean energy have prompted heightened attention to the development of sustainable fuel technologies that ensure continued economic development while maintaining stewardship of the environment. In the face of these enormous challenges, biomass has emerged as a viable alternative to petroleum for the production of energy, chemicals, and materials owing to its abundance, inexpensiveness, and carbon-neutrality. Moreover, the immense ease and efficiency of biological systems at converting biomass-derived feedstocks into fuels, chemicals, and materials has generated renewed interest in biotechnology as a replacement for traditional chemical processes. Aided by the ever-expanding repertoire of microbial genetics and plant biotechnology, improved understanding of gene regulation and cellular metabolism, and incessantly accumulating gene and protein data, scientists are now contemplating engineering microbial cell factories to produce fuels, chemical feedstocks, polymers and pharmaceuticals in an economically and environmentally sustainable way. This goal resonates with that of metabolic engineering - the improvement of cellular properties through the intelligent design, rational modification, or directed evolution of biochemical pathways, and arguably, metabolic engineering seems best positioned to achieve the concomittant goals of environmental stewardship and economic prolificity.

Engineering E. coli–E. coli cocultures for production of muconic acid from glycerol

DOE PAGES

Zhang, Haoran; Li, Zhengjun; Pereira, Brian; ...

2015-09-15

cis, cis-Muconic acid is an important chemical that can be biosynthesized from simple substrates in engineered microorganisms. Recently, it has been shown that engineering microbial cocultures is an emerging and promising approach for biochemical production. In this study, we aim to explore the potential of the E. coli–E. coli coculture system to use a single renewable carbon source, glycerol, for the production of value-added product cis, cis-muconic acid. As a result, two coculture engineering strategies were investigated. In the first strategy, an E. coli strain containing the complete biosynthesis pathway was co-cultivated with another E. coli strain containing only amore » heterologous intermediate-to-product biosynthetic pathway. In the second strategy, the upstream and downstream pathways were accommodated in two separate E. coli strains, each of which was dedicated to one portion of the biosynthesis process. Compared with the monoculture approach, both coculture engineering strategies improved the production significantly. Using a batch bioreactor, the engineered coculture achieved a 2 g/L muconic acid production with a yield of 0.1 g/g. In conclusion, our results demonstrate that coculture engineering is a viable option for producing muconic acid from glycerol. Moreover, microbial coculture systems are shown to have the potential for converting single carbon source to value-added products.« less

Microbial engineering for the production of fatty acids and fatty acid derivatives

DOEpatents

Stephanopoulos, Gregory; Abidi, Syed Hussain Imam

2014-07-01

Some aspects of this invention relate to methods useful for the conversion of a carbon source to a biofuel or biofuel precursor using engineered microbes. Some aspects of this invention relate to the discovery of a key regulator of lipid metabolism in microbes. Some aspects of this invention relate to engineered microbes for biofuel or biofuel precursor production.

Engineering soil organic matter quality: Biodiesel Co-Product (BCP) stimulates exudation of nitrogenous microbial biopolymers

PubMed Central

Redmile-Gordon, Marc A.; Evershed, Richard P.; Kuhl, Alison; Armenise, Elena; White, Rodger P.; Hirsch, Penny R.; Goulding, Keith W.T.; Brookes, Philip C.

2015-01-01

Biodiesel Co-Product (BCP) is a complex organic material formed during the transesterification of lipids. We investigated the effect of BCP on the extracellular microbial matrix or ‘extracellular polymeric substance’ (EPS) in soil which is suspected to be a highly influential fraction of soil organic matter (SOM). It was hypothesised that more N would be transferred to EPS in soil given BCP compared to soil given glycerol. An arable soil was amended with BCP produced from either 1) waste vegetable oils or 2) pure oilseed rape oil, and compared with soil amended with 99% pure glycerol; all were provided with 15N labelled KNO3. We compared transfer of microbially assimilated 15N into the extracellular amino acid pool, and measured concomitant production of exopolysaccharide. Following incubation, the 15N enrichment of total hydrolysable amino acids (THAAs) indicated that intracellular anabolic products had incorporated the labelled N primarily as glutamine and glutamate. A greater proportion of the amino acids in EPS were found to contain 15N than those in the THAA pool, indicating that the increase in EPS was comprised of bioproducts synthesised de novo. Moreover, BCP had increased the EPS production efficiency of the soil microbial community (μg EPS per unit ATP) up to approximately double that of glycerol, and caused transfer of 21% more 15N from soil solution into EPS-amino acids. Given the suspected value of EPS in agricultural soils, the use of BCP to stimulate exudation is an interesting tool to consider in the theme of delivering sustainable intensification. PMID:26635420

Potential roles for microbial endophytes in herbicide tolerance in plants.

PubMed

Tétard-Jones, Catherine; Edwards, Robert

2016-02-01

Herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. A growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. The current evidence for herbicide tolerance being bitrophic, with both free-living and plant-associated endophytes contributing to tolerance in the host plant, has been reviewed. We propose that endophytes can directly contribute to herbicide detoxification through their ability to metabolise xenobiotics. In addition, we explore the paradigm that microbes can 'prime' resistance mechanisms in plants such that they enhance herbicide tolerance by inducing the host's stress responses to withstand the downstream toxicity caused by herbicides. This latter mechanism has the potential to contribute to the growth of non-target-site-based herbicide resistance in weeds. Microbial endophytes already contribute to herbicide detoxification in planta, and there is now significant scope to extend these interactions using synthetic biology approaches to engineer new chemical tolerance traits into crops via microbial engineering. © 2015 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Autoantibodies to two novel peptides in seronegative and early rheumatoid arthritis.

PubMed

De Winter, Liesbeth M; Hansen, Wendy L J; van Steenbergen, Hanna W; Geusens, Piet; Lenaerts, Jan; Somers, Klaartje; Stinissen, Piet; van der Helm-van Mil, Annette H M; Somers, Veerle

2016-08-01

Despite recent progress in biomarker discovery for RA diagnostics, still over one-third of RA patients-and even more in early disease-present without RF or ACPA. The aim of this study was to confirm the presence of previously identified autoantibodies to novel Hasselt University (UH) peptides in early and seronegative RA. Screening for antibodies against novel UH peptides UH-RA.1, UH-RA.9, UH-RA.14 and UH-RA.21, was performed in two large independent cohorts. Peptide ELISAs were developed to screen for the presence of antibodies to UH-RA peptides. First, 292 RA patients (including 39 early patients), 90 rheumatic and 97 healthy controls from UH were studied. Antibody reactivity to two peptides (UH-RA.1 and UH-RA.21) was also evaluated in 600 RA patients, 309 patients with undifferentiated arthritis and 157 rheumatic controls from the Leiden Early Arthritis Clinic cohort. In both cohorts, 38% of RA patients were seronegative for RF and ACPA. Testing for autoantibodies to UH-RA.1 and UH-RA.21 reduced the serological gap from 38% to 29% in the UH cohort (P = 0.03) and from 38% to 32% in the Leiden Early Arthritis Clinic cohort (P = 0.01). Furthermore, 19-33% of early RA patients carried antibodies to these peptides. Specificities in rheumatic controls ranged from 82 to 96%. Whereas antibodies against UH-RA.1 were related to remission, anti-UH-RA.21 antibodies were associated with inflammation, joint erosion and higher tender and swollen joint counts. This study validates the presence of antibody reactivity to novel UH-RA peptides in seronegative and early RA. This might reinforce current diagnostics and improve early diagnosis and intervention in RA. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Microbial communities to mitigate contamination of PAHs in soil--possibilities and challenges: a review.

PubMed

Fernández-Luqueño, F; Valenzuela-Encinas, C; Marsch, R; Martínez-Suárez, C; Vázquez-Núñez, E; Dendooven, L

2011-01-01

Although highly diverse and specialized prokaryotic and eukaryotic microbial communities in soil degrade polycyclic aromatic hydrocarbons (PAHs), most of these are removed slowly. This review will discuss the biotechnological possibilities to increase the microbial dissipation of PAHs from soil as well as the main biological and biotechnological challenges. Microorganism provides effective and economically feasible solutions for soil cleanup and restoration. However, when the PAHs contamination is greater than the microbial ability to dissipate them, then applying genetically modified microorganisms might help to remove the contaminant. Nevertheless, it is necessary to have a more holistic review of the different individual reactions that are simultaneously taking place in a microbial cell and of the interactions microorganism-microorganism, microorganism-plant, microorganism-soil, and microorganisms-PAHs. Elucidating the function of genes from the PAHs-polluted soil and the study in pure cultures of isolated PAHs-degrading organisms as well as the generation of microorganisms in the laboratory that will accelerate the dissipation of PAHs and their safe application in situ have not been studied extensively. There is a latent environmental risk when genetically engineered microorganisms are used to remedy PAHs-contaminated soil.

[Characterization and microbial community shifts of rice strawdegrading microbial consortia].

PubMed

Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

2016-12-04

To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

PubMed Central

Osterstock, Jason B.; Pinchak, William E.; Ishii, Shun’ichi; Nelson, Karen E.

2009-01-01

Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H2) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H2in the rumen. Given the crucial role that H2 plays in ruminant digestion, it is desirable to understand the microbial relationships that control H2 partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research. PMID:20024685

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals.

PubMed

Mukhopadhyay, Aindrila

2015-08-01

During microbial production of solvent-like compounds, such as advanced biofuels and bulk chemicals, accumulation of the final product can negatively impact the cultivation of the host microbe and limit the production levels. Consequently, improving solvent tolerance is becoming an essential aspect of engineering microbial production strains. Mechanisms ranging from chaperones to transcriptional factors have been used to obtain solvent-tolerant strains. However, alleviating growth inhibition does not invariably result in increased production. Transporters specifically have emerged as a powerful category of proteins that bestow tolerance and often improve production but are difficult targets for cellular expression. Here we review strain engineering, primarily as it pertains to bacterial solvent tolerance, and the benefits and challenges associated with the expression of membrane-localized transporters in improving solvent tolerance and production. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development and Operation of an Automatic Rotor Trim Control System for use During the UH-60 Individual Blade Control Wind Tunnel Test

NASA Technical Reports Server (NTRS)

Theodore, Colin R.

2010-01-01

A full-scale wind tunnel test to evaluate the effects of Individual Blade Control (IBC) on the performance, vibration, noise and loads of a UH-60A rotor was recently completed in the National Full-Scale Aerodynamics Complex (NFAC) 40- by 80-Foot Wind Tunnel [1]. A key component of this wind tunnel test was an automatic rotor trim control system that allowed the rotor trim state to be set more precisely, quickly and repeatably than was possible with the rotor operator setting the trim condition manually. The trim control system was also able to maintain the desired trim condition through changes in IBC actuation both in open- and closed-loop IBC modes, and through long-period transients in wind tunnel flow. This ability of the trim control system to automatically set and maintain a steady rotor trim enabled the effects of different IBC inputs to be compared at common trim conditions and to perform these tests quickly without requiring the rotor operator to re-trim the rotor. The trim control system described in this paper was developed specifically for use during the IBC wind tunnel test

Nitrogen removal and microbial communities in a three-stage system simulating a riparian environment.

PubMed

Wang, Ziyuan; Wang, Zhixin; Pei, Yuansheng

2014-06-01

The riparian zone is an active interface for nitrogen removal, in which nitrogen transformations by microorganisms have not been valued. In this study, a three-stage system was constructed to simulate the riparian zone environments, and nitrogen removal as well as the microbial community was investigated in this 'engineered riparian system'. The results demonstrated that stage 1 of this system accounted for 41-51 % of total nitrogen removal. Initial ammonium loading and redox potential significantly impacted the nitrogen removal performances. Stages 1 and 2 were both composed of an anoxic/oxic (A/O) zone and an anaerobic column. The A/O zone removed most of the ammonium load (6.8 g/m(2)/day), while the anaerobic column showed a significant nitrate removal rate (11.1 g/m(2)/day). Molecular biological analysis demonstrated that bacterial diversity was high in the A/O zones, where ammonium-oxidizing bacteria and nitrite-oxidizing bacteria accounted for 8.42 and 3.32 % of the bacterial population, respectively. The denitrifying bacteria Acidovorax sp. and the nitrifying bacteria Nitrosospira/Nitrosomonas were the predominant microorganisms in this engineered riparian system. This three-stage system was established to achieve favorable nitrogen removal and the microbial community in the system was also retained. This investigation should deepen our understanding of biological nitrogen removal in engineered riparian zones.

The contribution of bacterial genome engineering to sustainable development.

PubMed

Reuß, Daniel R; Commichau, Fabian M; Stülke, Jörg

2017-09-01

The United Nations' Sustainable Development Goals define important challenges for the prosperous development of mankind. To reach several of these goals, among them the production of value-added compounds, improved economic and ecologic balance of production processes, prevention of climate change and protection of ecosystems, the use of engineered bacteria can make valuable contributions. We discuss the strategies for genome engineering and how they can be applied to meet the United Nations' goals for sustainable development. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function.

PubMed

Cabrol, Lea; Marone, Antonella; Tapia-Venegas, Estela; Steyer, Jean-Philippe; Ruiz-Filippi, Gonzalo; Trably, Eric

2017-03-01

One of the most important biotechnological challenges is to develop environment friendly technologies to produce new sources of energy. Microbial production of biohydrogen through dark fermentation, by conversion of residual biomass, is an attractive solution for short-term development of bioH2 producing processes. Efficient biohydrogen production relies on complex mixed communities working in tight interaction. Species composition and functional traits are of crucial importance to maintain the ecosystem service. The analysis of microbial community revealed a wide phylogenetic diversity that contributes in different-and still mostly unclear-ways to hydrogen production. Bridging this gap of knowledge between microbial ecology features and ecosystem functionality is essential to optimize the bioprocess and develop strategies toward a maximization of the efficiency and stability of substrate conversion. The aim of this review is to provide a comprehensive overview of the most up-to-date biodata available and discuss the main microbial community features of biohydrogen engineered ecosystems, with a special emphasis on the crucial role of interactions and the relationships between species composition and ecosystem service. The elucidation of intricate relationships between community structure and ecosystem function would make possible to drive ecosystems toward an improved functionality on the basis of microbial ecology principles. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Effects of different vegetation restoration patterns on the diversity of soil nitrogen-fixing microbes in Hulunbeier sandy land, Inner Mongolia of North China].

PubMed

Li, Gang; Wang, Li-Juan; Li, Yu-Jie; Qiao, Jiang; Zhang, Hai-Fang; Song, Xiao-Long; Yang, Dian-Lin

2013-06-01

By using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequence analysis, this paper studied the nifH gene diversity and community structure of soil nitrogen-fixing microbes in Hulunbeier sandy land of Inner Mongolia under four years management of five vegetation restoration modes, i. e., mixed-planting of Agropyron cristatum, Hedysarum fruticosum, Caragana korshinskii, and Elymus nutans (ACHE) and of Agropyron cristatum and Hedysarum fruticosum (AC), and mono-planting of Caragana korshinskii (UC), Agropyron cristatum (UA), and Hedysarum fruticosum (UH), taking the bare land as the control (CK). There existed significant differences in the community composition of nitrogen-fixing microbes among the five vegetation restoration patterns. The Shannon index of the nifH gene was the highest under ACHE, followed by under AC, UC, UA, and UH, and the lowest in CK. Except that UH and CK had less difference in the Shannon index, the other four vegetation restoration modes had a significantly higher Shannon index than CK (P < 0.05). The phylogenetic analysis showed that the soil nitrogen-fixing microbes under UA, UH, and UC were mainly of cyanobacteria, but the soil nitrogen-fixing microbes under AC and ACHE changed obviously, mainly of proteobacteria, and also of cyanobacteria. The canonical correlation analysis showed that the soil total phosphorus, available phosphorus, total nitrogen, and nitrate nitrogen contents under the five vegetation restoration modes had significant effects on the nitrogen-fixing microbial communities, and there existed significant correlations among the soil total phosphorus, available phosphorus, total nitrogen, and nitrate nitrogen. It was suggested that the variations of the community composition of soil nitrogen-fixing microbes under the five vegetation restoration modes were resulted from the interactive and combined effects of the soil physical and chemical factors.

Metabolic engineering of strains: from industrial-scale to lab-scale chemical production.

PubMed

Sun, Jie; Alper, Hal S

2015-03-01

A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5-50 g/L), and lab-scale (0-5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.

Microbial properties database editor tutorial

USDA-ARS?s Scientific Manuscript database

A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbialrelevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pathogens. Physical prop...

Clostridia: a flexible microbial platform for the production of alcohols.

PubMed

Ren, Cong; Wen, Zhiqiang; Xu, Yan; Jiang, Weihong; Gu, Yang

2016-12-01

Solventogenic clostridia are native producers of ethanol and many higher alcohols employing a broad range of cheap renewable substrates, such as lignocellulosic materials and C1 gases (CO and CO 2 ). These characteristics enable solventogenic clostridia to act as flexible microbial platforms for the production of liquid biofuels. With the rapid development of genetic tools in recent years, the intrinsic intractability of clostridia has been largely overcome, thus, engineering clostridia for production of chemicals and fuels has attracted increasing interests. Here, we provide an overview of recent progress in the production of alcohols based on solventogenic clostridia. Saccharolytic, cellulolytic and gas-fermenting clostridia are discussed, with a special focus on strategies for metabolic engineering to enable and to improve clostridia for the production of higher alcohols. Copyright © 2016 Elsevier Ltd. All rights reserved.

Applications of Microbial Cell Sensors

NASA Astrophysics Data System (ADS)

Shimomura-Shimizu, Mifumi; Karube, Isao

Since the first microbial cell sensor was studied by Karube et al. in 1977, many types of microbial cell sensors have been developed as analytical tools. The microbial cell sensor utilizes microbes as a sensing element and a transducer. The characteristics of microbial cell sensors as sensing devices are a complete contrast to those of enzyme sensors or immunosensors, which are highly specific for the substrates of interest, although the specificity of the microbial cell sensor has been improved by genetic modification of the microbe used as the sensing element. Microbial cell sensors have the advantages of tolerance to measuring conditions, a long lifetime, and good cost performance, and have the disadvantage of a long response time. In this review, applications of microbial cell sensors are summarized.

Microbial Source Tracking: Current and Future Molecular Tools in Microbial Water Quality Forensics

EPA Science Inventory

Current regulations in the United States stipulate that the microbial quality of waters used for consumption and recreational activities should be determined regularly by measuring microbial indicators of fecal pollution. Hence, the microbial risk associated with these waters is...

Shape recognition of microbial cells by colloidal cell imprints

NASA Astrophysics Data System (ADS)

Borovička, Josef; Stoyanov, Simeon D.; Paunov, Vesselin N.

2013-08-01

We have engineered a class of colloids which can recognize the shape and size of targeted microbial cells and selectively bind to their surfaces. These imprinted colloid particles, which we called ``colloid antibodies'', were fabricated by partial fragmentation of silica shells obtained by templating the targeted microbial cells. We successfully demonstrated the shape and size recognition between such colloidal imprints and matching microbial cells. High percentage of binding events of colloidal imprints with the size matching target particles was achieved. We demonstrated selective binding of colloidal imprints to target microbial cells in a binary mixture of cells of different shapes and sizes, which also resulted in high binding selectivity. We explored the role of the electrostatic interactions between the target cells and their colloid imprints by pre-coating both of them with polyelectrolytes. Selective binding occurred predominantly in the case of opposite surface charges of the colloid cell imprint and the targeted cells. The mechanism of the recognition is based on the amplification of the surface adhesion in the case of shape and size match due to the increased contact area between the target cell and the colloidal imprint. We also tested the selective binding for colloid imprints of particles of fixed shape and varying sizes. The concept of cell recognition by colloid imprints could be used for development of colloid antibodies for shape-selective binding of microbes. Such colloid antibodies could be additionally functionalized with surface groups to enhance their binding efficiency to cells of specific shape and deliver a drug payload directly to their surface or allow them to be manipulated using external fields. They could benefit the pharmaceutical industry in developing selective antimicrobial therapies and formulations.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

An ancient Chinese wisdom for metabolic engineering: Yin-Yang

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

Wu, Stephen G.; He, Lian; Wang, Qingzhao

In ancient Chinese philosophy, Yin-Yang describes two contrary forces that are interconnected and interdependent. This concept also holds true in microbial cell factories, where Yin represents energy metabolism in the form of ATP, and Yang represents carbon metabolism. Current biotechnology can effectively edit the microbial genome or introduce novel enzymes to redirect carbon fluxes. On the other hand, microbial metabolism loses significant free energy as heat when converting sugar into ATP; while maintenance energy expenditures further aggravate ATP shortage. The limitation of cell “powerhouse” prevents hosts from achieving high carbon yields and rates. Via an Escherichia coli flux balance analysismore » model, we further demonstrate the penalty of ATP cost on biofuel synthesis. To ensure cell powerhouse being sufficient in microbial cell factories, we propose five principles: 1. Take advantage of native pathways for product synthesis. 2. Pursue biosynthesis relying only on pathways or genetic parts without significant ATP burden. 3. Combine microbial production with chemical conversions (semi-biosynthesis) to reduce biosynthesis steps. 4. Create “minimal cells” or use non-model microbial hosts with higher energy fitness. 5. Develop a photosynthesis chassis that can utilize light energy and cheap carbon feedstocks. Meanwhile, metabolic flux analysis can be used to quantify both carbon and energy metabolisms. The fluxomics results are essential to evaluate the industrial potential of laboratory strains, avoiding false starts and dead ends during metabolic engineering« less

An ancient Chinese wisdom for metabolic engineering: Yin-Yang

DOE PAGES

Wu, Stephen G.; He, Lian; Wang, Qingzhao; ...

2015-03-20

In ancient Chinese philosophy, Yin-Yang describes two contrary forces that are interconnected and interdependent. This concept also holds true in microbial cell factories, where Yin represents energy metabolism in the form of ATP, and Yang represents carbon metabolism. Current biotechnology can effectively edit the microbial genome or introduce novel enzymes to redirect carbon fluxes. On the other hand, microbial metabolism loses significant free energy as heat when converting sugar into ATP; while maintenance energy expenditures further aggravate ATP shortage. The limitation of cell “powerhouse” prevents hosts from achieving high carbon yields and rates. Via an Escherichia coli flux balance analysismore » model, we further demonstrate the penalty of ATP cost on biofuel synthesis. To ensure cell powerhouse being sufficient in microbial cell factories, we propose five principles: 1. Take advantage of native pathways for product synthesis. 2. Pursue biosynthesis relying only on pathways or genetic parts without significant ATP burden. 3. Combine microbial production with chemical conversions (semi-biosynthesis) to reduce biosynthesis steps. 4. Create “minimal cells” or use non-model microbial hosts with higher energy fitness. 5. Develop a photosynthesis chassis that can utilize light energy and cheap carbon feedstocks. Meanwhile, metabolic flux analysis can be used to quantify both carbon and energy metabolisms. The fluxomics results are essential to evaluate the industrial potential of laboratory strains, avoiding false starts and dead ends during metabolic engineering« less

Microbial P450 Enzymes in Bioremediation and Drug Discovery: Emerging Potentials and Challenges.

PubMed

Bhattacharya, Sukanta S; Yadav, Jagjit S

2018-01-01

Cytochrome P450 enzymes are a structurally conserved but functionally diverse group of heme-containing mixed function oxidases found across both prokaryotic and eukaryotic forms of the microbial world. Microbial P450s are known to perform diverse functions ranging from the synthesis of cell wall components to xenobiotic/drug metabolism to biodegradation of environmental chemicals. Conventionally, many microbial systems have been reported to mimic mammalian P450-like activation of drugs and were proposed as the in-vitro models of mammalian drug metabolism. Recent reports suggest that native or engineered forms of specific microbial P450s from these and other microbial systems could be employed for desired specific biotransformation reactions toward natural and synthetic (drug) compounds underscoring their emerging potential in drug improvement and discovery. On the other hand, microorganisms particularly fungi and actinomycetes have been shown to possess catabolic P450s with unusual potential to degrade toxic environmental chemicals including persistent organic pollutants (POPs). Wood-rotting basidiomycete fungi in particular have revealed the presence of exceptionally large P450 repertoire (P450ome) in their genomes, majority of which are however orphan (with no known function). Our pre- and post-genomic studies have led to functional characterization of several fungal P450s inducible in response to exposure to several environmental toxicants and demonstration of their potential in bioremediation of these chemicals. This review is an attempt to summarize the postgenomic unveiling of this versatile enzyme superfamily in microbial systems and investigation of their potential to synthesize new drugs and degrade persistent pollutants, among other biotechnological applications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The Universal R-Matrix for the Jordanian Deformation of sl(2), and the Contracted Forms of so(4)

NASA Astrophysics Data System (ADS)

Shariati, A.; Aghamohammadi, A.; Khorrami, M.

We introduce a universal R-matrix for the Jordanian deformation of U(sl(2)). Using Uh(so(4))=Uh(sl(2)) ⊕ U-h(sl(2)), we obtain the universal R-matrix for Uh(so(4)). Applying the graded contractions on the universal R-matrix of Uh(so(4)), we show that there exist three distinct R-matrices for all the contracted algebras. It is shown that Uh(sl(2)), Uh(so(4)), and all of these contracted algebras are triangular.

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

PubMed

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

2015-05-19

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

Expedition Six Flight Engineer Pettit uses a chemical/microbial analysis bag to collect water sample

NASA Image and Video Library

2002-12-18

ISS006-E-08628 (18 December 2002) --- Astronaut Donald R. Pettit, Expedition Six NASA ISS science officer, is pictured in the Zvezda Service Module on the International Space Station (ISS) during the scheduled Week 3 potable water sampling and on-orbit chemical/microbial analysis of the SM environment control and life support system.

Expedition Six Flight Engineer Pettit uses a chemical/microbial analysis bag to collect water sample

NASA Image and Video Library

2002-12-18

ISS006-E-08616 (18 December 2002) --- Astronaut Donald R. Pettit, Expedition Six NASA ISS science officer, is pictured in the Zvezda Service Module on the International Space Station (ISS) during the scheduled Week 3 potable water sampling and on-orbit chemical/microbial analysis of the SM environment control and life support system.

Genetic Engineering Strategies for Enhanced Biodiesel Production.

PubMed

Hegde, Krishnamoorthy; Chandra, Niharika; Sarma, Saurabh Jyoti; Brar, Satinder Kaur; Veeranki, Venkata Dasu

2015-07-01

The focus on biodiesel research has shown a tremendous growth over the last few years. Several microbial and plant sources are being explored for the sustainable biodiesel production to replace the petroleum diesel. Conventional methods of biodiesel production have several limitations related to yield and quality, which led to development of new engineering strategies to improve the biodiesel production in plants, and microorganisms. Substantial progress in utilizing algae, yeast, and Escherichia coli for the renewable production of biodiesel feedstock via genetic engineering of fatty acid metabolic pathways has been reported in the past few years. However, in most of the cases, the successful commercialization of such engineering strategies for sustainable biodiesel production is yet to be seen. This paper systematically presents the drawbacks in the conventional methods for biodiesel production and an exhaustive review on the present status of research in genetic engineering strategies for production of biodiesel in plants, and microorganisms. Further, we summarize the technical challenges need to be tackled to make genetic engineering technology economically sustainable. Finally, the need and prospects of genetic engineering technology for the sustainable biodiesel production and the recommendations for the future research are discussed.

Microbial electrosynthetic cells

DOEpatents

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

2018-01-30

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

Microbial pesticides

Treesearch

Michael L. McManus

1991-01-01

Interest in the use of microbial pesticides has intensified because of public concern about the safety of chemical pesticides and their impact in the environment. Characteristics of the five groups of entomopathogens that have potential as microbial pesticides are briefly discussed and an update is provided on research and development activities underway to enhance the...

Silencing of meiosis-critical genes for engineering male sterility in plants

USDA-ARS?s Scientific Manuscript database

Engineering sterile traits in plants through the tissue-specific expression of a cytotoxic gene provides an effective way for containing transgene flow; however, the microbial origin of cytotoxic genes has raised concerns. In an attempt to develop a safe alternative, we have chosen the meiosis-crit...

Microbial Energy Conversion

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

Buckley, Merry; Wall, Judy D.

2006-10-01

The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array ofmore » potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil

Ecology, Microbial

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

Konopka, Allan

2009-05-15

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Microbial bioinformatics 2020.

PubMed

Pallen, Mark J

2016-09-01

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

Proton transfer in microbial electrolysis cells

DOE PAGES

Borole, Abhijeet P.; Lewis, Alex J.

2017-02-15

Proton transfer and electron transfer are of prime importance in the development of microbial electrochemical cells. While electron transfer is primarily controlled by biology, proton transfer is controlled by process engineering and cell design. To develop commercially feasible technologies around the concept of a bioelectrochemical cell, real feedstocks have to be explored and associated limitations have to be identified. Here in this study, the proton transfer rate was quantified for a microbial electrolysis cell (MEC) and its dependence on process parameters was investigated using a proton balance model. The reaction system consisted of a biomass-derived pyrolytic aqueous stream as amore » substrate producing hydrogen in a flow-through MEC. The proton transfer rate increased with anode flow rate and organic loading rate up to a maximum of 0.36 ± 0.01 moles per m 2 per h, equivalent to a hydrogen production rate of 9.08 L per L per day. Higher rates of hydrogen production, reaching 11.7 ± 0.2 L per L per day were achieved, when additional protons were provided via the cathode buffer. Electrochemical impedance spectroscopy shows that proton transfer was the dominant resistance in the production of hydrogen. The quantification of proton transfer rates for MECs with potential for biorefinery application and the demonstration of high hydrogen production rates approaching those required for commercial consideration indicate the strong potential of this technology for renewable hydrogen production. Understanding the transport phenomenon in bioelectrochemical cells is of great significance since these systems have potential for wide-ranging applications including energy production, bioremediation, chemical and nanomaterial synthesis, electro-fermentation, energy storage, desalination, and produced water treatment. Electron transfer in anode biofilms has been investigated extensively, but proton transfer studies are also important, since many cathodic half reactions

Proton transfer in microbial electrolysis cells

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

Borole, Abhijeet P.; Lewis, Alex J.

Proton transfer and electron transfer are of prime importance in the development of microbial electrochemical cells. While electron transfer is primarily controlled by biology, proton transfer is controlled by process engineering and cell design. To develop commercially feasible technologies around the concept of a bioelectrochemical cell, real feedstocks have to be explored and associated limitations have to be identified. Here in this study, the proton transfer rate was quantified for a microbial electrolysis cell (MEC) and its dependence on process parameters was investigated using a proton balance model. The reaction system consisted of a biomass-derived pyrolytic aqueous stream as amore » substrate producing hydrogen in a flow-through MEC. The proton transfer rate increased with anode flow rate and organic loading rate up to a maximum of 0.36 ± 0.01 moles per m 2 per h, equivalent to a hydrogen production rate of 9.08 L per L per day. Higher rates of hydrogen production, reaching 11.7 ± 0.2 L per L per day were achieved, when additional protons were provided via the cathode buffer. Electrochemical impedance spectroscopy shows that proton transfer was the dominant resistance in the production of hydrogen. The quantification of proton transfer rates for MECs with potential for biorefinery application and the demonstration of high hydrogen production rates approaching those required for commercial consideration indicate the strong potential of this technology for renewable hydrogen production. Understanding the transport phenomenon in bioelectrochemical cells is of great significance since these systems have potential for wide-ranging applications including energy production, bioremediation, chemical and nanomaterial synthesis, electro-fermentation, energy storage, desalination, and produced water treatment. Electron transfer in anode biofilms has been investigated extensively, but proton transfer studies are also important, since many cathodic half reactions

Thermochemical Wastewater Valorization via Enhanced Microbial Toxicity Tolerance

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

Beckham, Gregg T; Thelhawadigedara, Lahiru Niroshan Jayakody; Johnson, Christopher W

Thermochemical (TC) biomass conversion processes such as pyrolysis and liquefaction generate considerable amounts of wastewater, which often contains highly toxic compounds that are incredibly challenging to convert via standard wastewater treatment approaches such as anaerobic digestion. These streams represent a cost for TC biorefineries, and a potential valorization opportunity, if effective conversion methods are developed. The primary challenge hindering microbial conversion of TC wastewater is toxicity. In this study, we employ a robust bacterium, Pseudomonas putida, with TC wastewater streams to demonstrate that aldehydes are the most inhibitory compounds in these streams. Proteomics, transcriptomics, and fluorescence-based immunoassays of P. putidamore » grown in a representative wastewater stream indicate that stress results from protein damage, which we hypothesize is a primary toxicity mechanism. Constitutive overexpression of the chaperone genes, groEL, groES, and clpB, in a genome-reduced P. putida strain improves the tolerance towards multiple TC wastewater samples up to 200-fold. Moreover, the concentration ranges of TC wastewater are industrially relevant for further bioprocess development for all wastewater streams examined here, representing different TC process configurations. Furthermore, we demonstrate proof-of-concept polyhydroxyalkanoate production from the usable carbon in an exemplary TC wastewater stream. Overall, this study demonstrates that protein quality control machinery and repair mechanisms can enable substantial gains in microbial tolerance to highly toxic substrates, including heterogeneous waste streams. When coupled to other metabolic engineering advances such as expanded substrate utilization and enhanced product accumulation, this study generally enables new strategies for biological conversion of highly-toxic, organic-rich wastewater via engineered aerobic monocultures or designer consortia.« less

Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains

DOE PAGES

Lian, Jiazhang; Bao, Zehua; Hu, Sumeng; ...

2018-02-20

The CRISPR/Cas9 system has been widely used for multiplex genome engineering of Saccharomyces cerevisiae. Furthermore, its application in manipulating industrial yeast strains is less successful, probably due to the genome complexity and low copy numbers of gRNA expression plasmids. Here we developed an efficient CRISPR/Cas9 system for industrial yeast strain engineering by using our previously engineered plasmids with increased copy numbers. Four genes in both a diploid strain (Ethanol Red, 8 alleles in total) and a triploid strain (ATCC 4124, 12 alleles in total) were knocked out in a single step with 100% efficiency. This system was used to constructmore » xylose-fermenting, lactate-producing industrial yeast strains, in which ALD6, PHO13, LEU2, and URA3 were disrupted in a single step followed by the introduction of a xylose utilization pathway and a lactate biosynthetic pathway on auxotrophic marker plasmids. The optimized CRISPR/Cas9 system provides a powerful tool for the development of industrial yeast based microbial cell factories.« less

Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains

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

Lian, Jiazhang; Bao, Zehua; Hu, Sumeng

The CRISPR/Cas9 system has been widely used for multiplex genome engineering of Saccharomyces cerevisiae. Furthermore, its application in manipulating industrial yeast strains is less successful, probably due to the genome complexity and low copy numbers of gRNA expression plasmids. Here we developed an efficient CRISPR/Cas9 system for industrial yeast strain engineering by using our previously engineered plasmids with increased copy numbers. Four genes in both a diploid strain (Ethanol Red, 8 alleles in total) and a triploid strain (ATCC 4124, 12 alleles in total) were knocked out in a single step with 100% efficiency. This system was used to constructmore » xylose-fermenting, lactate-producing industrial yeast strains, in which ALD6, PHO13, LEU2, and URA3 were disrupted in a single step followed by the introduction of a xylose utilization pathway and a lactate biosynthetic pathway on auxotrophic marker plasmids. The optimized CRISPR/Cas9 system provides a powerful tool for the development of industrial yeast based microbial cell factories.« less

Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains.

PubMed

Lian, Jiazhang; Bao, Zehua; Hu, Sumeng; Zhao, Huimin

2018-06-01

The CRISPR/Cas9 system has been widely used for multiplex genome engineering of Saccharomyces cerevisiae. However, its application in manipulating industrial yeast strains is less successful, probably due to the genome complexity and low copy numbers of gRNA expression plasmids. Here we developed an efficient CRISPR/Cas9 system for industrial yeast strain engineering by using our previously engineered plasmids with increased copy numbers. Four genes in both a diploid strain (Ethanol Red, 8 alleles in total) and a triploid strain (ATCC 4124, 12 alleles in total) were knocked out in a single step with 100% efficiency. This system was used to construct xylose-fermenting, lactate-producing industrial yeast strains, in which ALD6, PHO13, LEU2, and URA3 were disrupted in a single step followed by the introduction of a xylose utilization pathway and a lactate biosynthetic pathway on auxotrophic marker plasmids. The optimized CRISPR/Cas9 system provides a powerful tool for the development of industrial yeast based microbial cell factories. © 2018 Wiley Periodicals, Inc.

Microbial production of rhamnolipids using sugars as carbon sources.

PubMed

Tan, Yun Nian; Li, Qingxin

2018-06-08

Rhamnolipids are a class of biosurfactants with effective surface-active properties. The high cost of microbial production of rhamnolipids largely affects their commercial applications. To reduce the production post, research has been carried out in screening more powerful strains, engineering microbes with higher biosurfactant yields and exploring cheaper substrates to reduce the production cost. Extensive refining is required for biosurfactant production using oils and oil-containing wastes, necessitating the use of complex and expensive biosurfactant recovery methods such as extraction with solvents or acid precipitation. As raw materials normally can account for 10-30% of the overall production cost, sugars have been proven to be an alternative carbon source for microbial production of rhamnolipids due to its lower costs and straightforward processing techniques. Studies have thus been focused on using tropical agroindustrial crop residues as renewable substrates. Herein, we reviewed studies that are using sugar-containing substrates as carbon sources for producing rhamnolipids. We speculate that sugars derived from agricultural wastes rich in cellulose and sugar-containing wastes are potential carbon sources in fermentation while challenges still remain in large scales.

Microbial bioreporters of trace explosives.

PubMed

Shemer, Benjamin; Koshet, Ori; Yagur-Kroll, Sharon; Belkin, Shimshon

2017-06-01

Since its introduction as an explosive in the late 19th century, 2,4,6-trinitrotoluene (TNT), along with other explosive compounds, has left numerous environmental marks. One of these is widespread soil and water pollution by trace explosives in military proving grounds, manufacturing facilities, or actual battlefields. Another dramatic impact is that exerted by the millions of landmines and other explosive devices buried in large parts of the world, causing extensive loss of life, injuries, and economical damage. In this review we highlight recent advances in the design and construction of microbial bioreporters, molecularly engineered to generate a quantifiable dose-dependent signal in the presence of trace amounts of explosives. Such sensor strains may be employed for monitoring environmental pollution as well as for the remote detection of buried landmines. Copyright © 2017 Elsevier Ltd. All rights reserved.

Novel technologies provide more engineering strategies for amino acid-producing microorganisms.

PubMed

Gu, Pengfei; Su, Tianyuan; Qi, Qingsheng

2016-03-01

Traditionally, amino acid-producing strains were obtained by random mutagenesis and subsequent selection. With the development of genetic and metabolic engineering techniques, various microorganisms with high amino acid production yields are now constructed by rational design of targeted biosynthetic pathways. Recently, novel technologies derived from systems and synthetic biology have emerged and open a new promising avenue towards the engineering of amino acid production microorganisms. In this review, these approaches, including rational engineering of rate-limiting enzymes, real-time sensing of end-products, pathway optimization on the chromosome, transcription factor-mediated strain improvement, and metabolic modeling and flux analysis, were summarized with regard to their application in microbial amino acid production.

Oh No, Henrietta Got Out!

ERIC Educational Resources Information Center

Lottero-Perdue, Pamela; Grabia, Kathryn; Sandifer, Cody

2017-01-01

In a kindergarten classroom, exclamations like "Oh no!" may be causes for concern. However, when the students in Mrs. Grabia's classroom shouted "Oh no!" and "Uh oh!" during an engineering-infused 5E lesson, it meant that a persistent little robot had pushed its way out of the fences they had created. It also meant…

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

PubMed

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

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

White, G.J.

1996-08-01

Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus ismore » on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.« less

A Theoretical Reassessment of Microbial Maintenance and Implications for Microbial Ecology Modeling

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

Wang, Gangsheng; Post, Wilfred M

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a critical reassessment. We provided a rigorous proof that the true growth yield coefficient (YG) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert ( max,H) is higher than those in the other twomore » models ( max,P and max,C), and the difference is the physiological maintenance factor (mq = a); and (3) the overall maintenance coefficient (mT) is more sensitive to mq than to the specific growth rate ( G) and YG. Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.« less

[Effect of microbial nutrient concentration on improvement of municipal sewage sludge dewaterability through bioleaching].

PubMed

Song, Yong-wei; Liu, Fen-wu; Zhou, Li-xiang

2012-08-01

In this study, shaking flask batch experiments and practical engineering application tests were performed to investigate the effect of microbial nutrient concentration on the dewaterability of municipal sewage sludge with 2%, 3%, 4% and 5% solid contents via bioleaching. Meanwhile, the changes of pH value and the utilization efficiency of microbial nutrients during bioleaching were analyzed in this study. The results showed that the pH value decreased gradually at the beginning and then maintained a stable state in the treatments with different solid contents, and the nutrients were completely used up by the microorganisms after 2 days of bioleaching. It was found that the SRF of 2%, 3%, 4%, 5% sludges decreased quickly and then rose gradually with the extension of bioleaching time. In addition, the higher solid content the greater the increase. It was determined that the optimum microbial nutrient dosage for sludge with solid content of 2%, 3%, 4% and 5% were 3.0 g x L(-1), 4.5 g x L(-1), 8.3 g x L(-1) and 12.8 g x L(-1) respectively. At this point, the lowest SRF of sludge with each solid content were 0.61 x 10(12) m x kg(-1), 1.22 x 10(12) m x kg(-1), 3.09 x 10(12) m x kg(-1) and 4.83 x 10(12) m x kg(-1), respectively. Through the engineering application, it was showed that diluting the solid content of sewage sludge from 5% to 3% before bioleaching was feasible. It could not only improve the dewaterability of bioleached sewage sludge (the SRF declined from 3.29 x 10(12) m x kg(-1) to 1.10 x 10(12) m x kg(-1)), but also shorten the sludge nutrient time (shortened from 4 days to 2.35 days) and reduce the operation costs. Therefore, the results of this study have important significance for the engineering application of bioleaching of municipal sewage sludge with high solid content.

Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

PubMed Central

Yrjälä, Kim; Alakukku, Laura; Palojärvi, Ansa

2012-01-01

The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy. PMID:22983972

Engineered passive bioreactive barriers: risk-managing the legacy of industrial soil and groundwater pollution.

PubMed

Kalin, Robert M

2004-06-01

Permeable reactive barriers are a technology that is one decade old, with most full-scale applications based on abiotic mechanisms. Though there is extensive literature on engineered bioreactors, natural biodegradation potential, and in situ remediation, it is only recently that engineered passive bioreactive barrier technology is being considered at the commercial scale to manage contaminated soil and groundwater risks. Recent full-scale studies are providing the scientific confidence in our understanding of coupled microbial (and genetic), hydrogeologic, and geochemical processes in this approach and have highlighted the need to further integrate engineering and science tools.

Engineering microbes for isoprene production.

PubMed

Ye, Lidan; Lv, Xiaomei; Yu, Hongwei

2016-11-01

Isoprene is facing a growing global market due to its wide industrial applications. Current industrial production of isoprene is almost entirely petroleum-based, which is influenced by the shrinking C5 supply, while the natural emission of isoprene is predominantly contributed by plants. To bridge the need gap, a highly efficient fermentation-based process for isoprene production might be a suitable and sustainable solution, and extensive research works have been performed to achieve this goal. Here we review the accomplishments in this field by summarizing the history and prospects of microbial isoprene production. The natural producers and biosynthesis pathways of isoprene, the key enzyme isoprene synthase and the metabolic engineering strategies adopted for developing isoprene-producing microorganisms are introduced. In particular, strategies employed for achieving engineered strains with improved performance indices are discussed based on the published papers and patents. The perspectives on further performance improvements and potential future strategies are presented as well. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Chimeric microbial rhodopsins for optical activation of Gs-proteins

PubMed Central

Yoshida, Kazuho; Yamashita, Takahiro; Sasaki, Kengo; Inoue, Keiichi; Shichida, Yoshinori; Kandori, Hideki

2017-01-01

We previously showed that the chimeric proteins of microbial rhodopsins, such as light-driven proton pump bacteriorhodopsin (BR) and Gloeobacter rhodopsin (GR) that contain cytoplasmic loops of bovine rhodopsin, are able to activate Gt protein upon light absorption. These facts suggest similar protein structural changes in both the light-driven proton pump and animal rhodopsin. Here we report two trials to engineer chimeric rhodopsins, one for the inserted loop, and another for the microbial rhodopsin template. For the former, we successfully activated Gs protein by light through the incorporation of the cytoplasmic loop of β2-adrenergic receptor (β2AR). For the latter, we did not observe any G-protein activation for the light-driven sodium pump from Indibacter alkaliphilus (IndiR2) or a light-driven chloride pump halorhodopsin from Natronomonas pharaonis (NpHR), whereas the light-driven proton pump GR showed light-dependent G-protein activation. This fact suggests that a helix opening motion is common to G protein coupled receptor (GPCR) and GR, but not to IndiR2 and NpHR. Light-induced difference FTIR spectroscopy revealed similar structural changes between WT and the third loop chimera for each light-driven pump. A helical structural perturbation, which was largest for GR, was further enhanced in the chimera. We conclude that similar structural dynamics that occur on the cytoplasmic side of GPCR are needed to design chimeric microbial rhodopsins. PMID:29362703

Construction of PAH-degrading mixed microbial consortia by induced selection in soil.

PubMed

Zafra, German; Absalón, Ángel E; Anducho-Reyes, Miguel Ángel; Fernandez, Francisco J; Cortés-Espinosa, Diana V

2017-04-01

Bioremediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soils through the biostimulation and bioaugmentation processes can be a strategy for the clean-up of oil spills and environmental accidents. In this work, an induced microbial selection method using PAH-polluted soils was successfully used to construct two microbial consortia exhibiting high degradation levels of low and high molecular weight PAHs. Six fungal and seven bacterial native strains were used to construct mixed consortia with the ability to tolerate high amounts of phenanthrene (Phe), pyrene (Pyr) and benzo(a)pyrene (BaP) and utilize these compounds as a sole carbon source. In addition, we used two engineered PAH-degrading fungal strains producing heterologous ligninolytic enzymes. After a previous selection using microbial antagonism tests, the selection was performed in microcosm systems and monitored using PCR-DGGE, CO 2 evolution and PAH quantitation. The resulting consortia (i.e., C1 and C2) were able to degrade up to 92% of Phe, 64% of Pyr and 65% of BaP out of 1000 mg kg -1 of a mixture of Phe, Pyr and BaP (1:1:1) after a two-week incubation. The results indicate that constructed microbial consortia have high potential for soil bioremediation by bioaugmentation and biostimulation and may be effective for the treatment of sites polluted with PAHs due to their elevated tolerance to aromatic compounds, their capacity to utilize them as energy source. Copyright © 2016 Elsevier Ltd. All rights reserved.

Developing methanogenic microbial consortia from diverse coal sources and environments

DOE PAGES

Fuertez, John; Boakye, Richard; McLennan, John; ...

2017-08-18

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor

Developing methanogenic microbial consortia from diverse coal sources and environments

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

Fuertez, John; Boakye, Richard; McLennan, John

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor

Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation.

PubMed

Praveschotinunt, Pichet; Dorval Courchesne, Noémie-Manuelle; den Hartog, Ilona; Lu, Chaochen; Kim, Jessica J; Nguyen, Peter Q; Joshi, Neel S

2018-06-15

The rapidly growing field of microbiome research presents a need for better methods of monitoring gut microbes in vivo with high spatial and temporal resolution. We report a method of tracking microbes in vivo within the gastrointestinal tract by programming them to incorporate nonstandard amino acids (NSAA) and labeling them via click chemistry. Using established machinery constituting an orthogonal translation system (OTS), we engineered Escherichia coli to incorporate p-azido-l-phenylalanine (pAzF) in place of the UAG (amber) stop codon. We also introduced a mutant gene encoding for a cell surface protein (CsgA) that was altered to contain an in-frame UAG codon. After pAzF incorporation and extracellular display, the engineered strains could be covalently labeled via copper-free click reaction with a Cy5 dye conjugated to the dibenzocyclooctyl (DBCO) group. We confirmed the functionality of the labeling strategy in vivo using a murine model. Labeling of the engineered strain could be observed using oral administration of the dye to mice several days after colonization of the gastrointestinal tract. This work sets the foundation for the development of in vivo tracking microbial strategies that may be compatible with noninvasive imaging modalities and are capable of longitudinal spatiotemporal monitoring of specific microbial populations.

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures.

PubMed

Liang, Shaobo; Gliniewicz, Karol; Mendes-Soares, Helena; Settles, Matthew L; Forney, Larry J; Coats, Erik R; McDonald, Armando G

2015-03-01

Three undefined mixed cultures (activated sludge) from different municipal wastewater treatment plants were used as seeds in a novel lactic acid fermentation process fed with potato peel waste (PPW). Anaerobic sequencing batch fermenters were run under identical conditions to produce predominantly lactic acid. Illumina sequencing was used to examine the 16S rRNA genes of bacteria in the three seeds and fermenters. Results showed that the structure of microbial communities of three seeds were different. All three fermentation products had unique community structures that were dominated (>96%) by species of the genus Lactobacillus, while members of this genus constituted <0.1% in seeds. The species of Lactobacillus sp. differed among the three fermentations. Results of this study suggest the structure of microbial communities in lactic acid fermentation of PPW with undefined mixed cultures were robust and resilient, which provided engineering prospects for the microbial utilization of carbohydrate wastes to produce lactic acid. Copyright © 2014 Elsevier Ltd. All rights reserved.

A portable bioelectronic sensing system (BESSY) for environmental deployment incorporating differential microbial sensing in miniaturized reactors

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

Zhou, Alyssa Y.; Baruch, Moshe; Ajo-Franklin, Caroline M.

Current technologies are lacking in the area of deployable, in situ monitoring of complex chemicals in environmental applications. Microorganisms metabolize various chemical compounds and can be engineered to be analyte-specific making them naturally suited for robust chemical sensing. But, current electrochemical microbial biosensors use large and expensive electrochemistry equipment not suitable for on-site, real-time environmental analysis. We demonstrate a miniaturized, autonomous bioelectronic sensing system (BESSY) suitable for deployment for instantaneous and continuous sensing applications. We developed a 2x2 cm footprint, low power, two-channel, three-electrode electrochemical potentiostat which wirelessly transmits data for on-site microbial sensing. Furthermore, we designed a new waymore » of fabricating self-contained, submersible, miniaturized reactors (m-reactors) to encapsulate the bacteria, working, and counter electrodes. We have validated the BESSY’s ability to specifically detect a chemical amongst environmental perturbations using differential current measurements. This work paves the way for in situ microbial sensing outside of a controlled laboratory environment.« less

A portable bioelectronic sensing system (BESSY) for environmental deployment incorporating differential microbial sensing in miniaturized reactors

DOE PAGES

Zhou, Alyssa Y.; Baruch, Moshe; Ajo-Franklin, Caroline M.; ...

2017-09-15

Current technologies are lacking in the area of deployable, in situ monitoring of complex chemicals in environmental applications. Microorganisms metabolize various chemical compounds and can be engineered to be analyte-specific making them naturally suited for robust chemical sensing. But, current electrochemical microbial biosensors use large and expensive electrochemistry equipment not suitable for on-site, real-time environmental analysis. We demonstrate a miniaturized, autonomous bioelectronic sensing system (BESSY) suitable for deployment for instantaneous and continuous sensing applications. We developed a 2x2 cm footprint, low power, two-channel, three-electrode electrochemical potentiostat which wirelessly transmits data for on-site microbial sensing. Furthermore, we designed a new waymore » of fabricating self-contained, submersible, miniaturized reactors (m-reactors) to encapsulate the bacteria, working, and counter electrodes. We have validated the BESSY’s ability to specifically detect a chemical amongst environmental perturbations using differential current measurements. This work paves the way for in situ microbial sensing outside of a controlled laboratory environment.« less

Monitoring engineered remediation with borehole radar

USGS Publications Warehouse

Lane, J.W.; Day-Lewis, F. D.; Joesten, P.K.

2007-01-01

The success of engineered remediation is predicated on correct emplacement of either amendments (e.g., vegetable-oil emulsion, lactate, molasses, etc.) or permeable reactive barriers (e.g., vegetable oil, zero-valent iron, etc.) to enhance microbial or geochemical breakdown of contaminants and treat contaminants. Currently, site managers have limited tools to provide information about the distribution of injected materials; the existence of gaps or holes in barriers; and breakdown or transformation of injected materials over time. ?? 2007 Society of Exploration Geophysicists.

Computer applications making rapid advances in high throughput microbial proteomics (HTMP).

PubMed

Anandkumar, Balakrishna; Haga, Steve W; Wu, Hui-Fen

2014-02-01

The last few decades have seen the rise of widely-available proteomics tools. From new data acquisition devices, such as MALDI-MS and 2DE to new database searching softwares, these new products have paved the way for high throughput microbial proteomics (HTMP). These tools are enabling researchers to gain new insights into microbial metabolism, and are opening up new areas of study, such as protein-protein interactions (interactomics) discovery. Computer software is a key part of these emerging fields. This current review considers: 1) software tools for identifying the proteome, such as MASCOT or PDQuest, 2) online databases of proteomes, such as SWISS-PROT, Proteome Web, or the Proteomics Facility of the Pathogen Functional Genomics Resource Center, and 3) software tools for applying proteomic data, such as PSI-BLAST or VESPA. These tools allow for research in network biology, protein identification, functional annotation, target identification/validation, protein expression, protein structural analysis, metabolic pathway engineering and drug discovery.

Combinatorial pathway optimization in Escherichia coli by directed co-evolution of rate-limiting enzymes and modular pathway engineering.

PubMed

Lv, Xiaomei; Gu, Jiali; Wang, Fan; Xie, Wenping; Liu, Min; Ye, Lidan; Yu, Hongwei

2016-12-01

Metabolic engineering of microorganisms for heterologous biosynthesis is a promising route to sustainable chemical production which attracts increasing research and industrial interest. However, the efficiency of microbial biosynthesis is often restricted by insufficient activity of pathway enzymes and unbalanced utilization of metabolic intermediates. This work presents a combinatorial strategy integrating modification of multiple rate-limiting enzymes and modular pathway engineering to simultaneously improve intra- and inter-pathway balance, which might be applicable for a range of products, using isoprene as an example product. For intra-module engineering within the methylerythritol-phosphate (MEP) pathway, directed co-evolution of DXS/DXR/IDI was performed adopting a lycopene-indicated high-throughput screening method developed herein, leading to 60% improvement of isoprene production. In addition, inter-module engineering between the upstream MEP pathway and the downstream isoprene-forming pathway was conducted via promoter manipulation, which further increased isoprene production by 2.94-fold compared to the recombinant strain with solely protein engineering and 4.7-fold compared to the control strain containing wild-type enzymes. These results demonstrated the potential of pathway optimization in isoprene overproduction as well as the effectiveness of combining metabolic regulation and protein engineering in improvement of microbial biosynthesis. Biotechnol. Bioeng. 2016;113: 2661-2669. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Metabolic engineering for improved microbial pentose fermentation.

PubMed

Fernandes, Sara; Murray, Patrick

2010-01-01

Global concern over the depletion of fossil fuel reserves, and the detrimental impact that combustion of these materials has on the environment, is focusing attention on initiatives to create sustainable approaches for the production and use of biofuels from various biomass substrates. The development of a low-cost, safe and eco-friendly process for the utilization of renewable resources to generate value-added products with biotechnological potential as well as robust microorganisms capable of efficient fermentation of all types of sugars are essential to underpin the economic production of biofuels from biomass feedstocks. Saccharomyces cerevisiae, the most established fermentation yeast used in large scale bioconversion strategies, does not however metabolise the pentose sugars, xylose and arabinose and bioengineering is required for introduction of efficient pentose metabolic pathways and pentose sugar transport proteins for bioconversion of these substrates. Our approach provided a basis for future experiments that may ultimately lead to the development of industrial S. cerevisiae strains engineered to express pentose metabolising proteins from thermophilic fungi living on decaying plant material and here we expand our original article and discuss the strategies implemented to improve pentose fermentation. © 2010 Landes Bioscience

Rhizosphere engineering: Enhancing sustainable plant ecosystem productivity

DOE PAGES

Ahkami, Amir H.; White, III, Richard Allen; Handakumbura, Pubudu P.; ...

2017-04-21

Here, the rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a diverse microbial consortium of bacteria, archaea, viruses, and microeukaryotes. Understanding, predicting and controlling the structure and function of the rhizosphere will allow us to harness plant-microbe interactions and other rhizosphere activities as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage. Here, we review critical knowledge gaps in rhizosphere science, and how mechanistic understandingmore » of rhizosphere interactions can be leveraged in rhizosphere engineering efforts with the goal of maintaining sustainable plant ecosystem services for food and bioenergy production in an ever changing global climate.« less

Rhizosphere engineering: Enhancing sustainable plant ecosystem productivity

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

Ahkami, Amir H.; White, III, Richard Allen; Handakumbura, Pubudu P.

Here, the rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a diverse microbial consortium of bacteria, archaea, viruses, and microeukaryotes. Understanding, predicting and controlling the structure and function of the rhizosphere will allow us to harness plant-microbe interactions and other rhizosphere activities as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage. Here, we review critical knowledge gaps in rhizosphere science, and how mechanistic understandingmore » of rhizosphere interactions can be leveraged in rhizosphere engineering efforts with the goal of maintaining sustainable plant ecosystem services for food and bioenergy production in an ever changing global climate.« less

Department of Defense In-House RDT and E Activities

DTIC Science & Technology

1977-10-30

SUPPRFSSI’N CWAMRFR, CAM EVAL & REF CEN, FUEL CELL t RTRY TEST STAS, ELEC PROPULSTON KTM, MPPS POWER TEST CELLS, nFRG TEST HANGAR, MORILE STRESS ANAL...TRIDENT,6S8,ETC) DESGNDEV E FVAL OF U/W TARGET SYSTEMS C MORILE /FIXD U/H TEST RANGES INTRODUCE TO FLEET C IN-SERVICE ENGINEERING OF MK 4S

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes.

PubMed

Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca; Luo, Hao; Herrgård, Markus J

2018-05-11

Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical has been successfully achieved through evolutionary engineering by coupling production to cellular growth.

Reactive powder based concretes: Mechanical properties, durability and hybrid use with OPC

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

Cwirzen, A.; Penttala, V.; Vornanen, C.

2008-10-15

The basic mechanical properties, frost durability and the bond strength with normal strength concretes of the ultra high strength (UHS) mortars and concretes were studied. The produced mixes had plastic or fluid-like consistency. The 28-day compressive strength varied between 170 and 202 MPa for the heat-treated specimens and between 130 and 150 MPa for the non-heat-treated specimens. The shrinkage values were two times higher for the UHS mortars in comparison with the UHS concretes. After the initial shrinkage, swelling was noticed in the UHS mortars. The lowest creep values were measured for the non-heat-treated UHS concretes. The frost-deicing salts durabilitymore » of the UHS mortars and concretes appeared to be very good even despite the increased water uptake of the UHS concretes. The study of the hybrid concrete beams indicated the formation of low strength transition zone between the UHS mortar and normal strength concrete.« less

Biotechnological Aspects of Microbial Extracellular Electron Transfer

PubMed Central

Kato, Souichiro

2015-01-01

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

Production of succinic acid by metabolically engineered microorganisms.

PubMed

Ahn, Jung Ho; Jang, Yu-Sin; Lee, Sang Yup

2016-12-01

Succinic acid (SA) has been recognized as one of the most important bio-based building block chemicals due to its numerous potential applications. For the economical bio-based production of SA, extensive research works have been performed on developing microbial strains by metabolic engineering as well as fermentation and downstream processes. Here we review metabolic engineering strategies applied for bio-based production of SA using representative microorganisms, including Saccharomyces cerevisiae, Pichia kudriavzevii, Escherichia coli, Mannheimia succiniciproducens, Basfia succiniciproducens, Actinobacillus succinogenes, and Corynebacterium glutamicum. In particular, strategies employed for developing engineered strains of these microorganisms leading to the best performance indices (titer, yield, and productivity) are showcased based on the published papers as well as patents. Those processes currently under commercialization are also analyzed and future perspectives are provided. Copyright © 2016 Elsevier Ltd. All rights reserved.

A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

PubMed

Wang, Gangsheng; Post, Wilfred M

2012-09-01

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models. © This article is a US government work and is in the public domain in the USA.

Wind Tunnel Measurements of the Wake of a Full-Scale UH-60A Rotor in Forward Flight

NASA Technical Reports Server (NTRS)

Wadcock, Alan J.; Yamauchi, Gloria K.; Schairer, Edward T.

2013-01-01

A full-scale UH-60A rotor was tested in the National Full-Scale Aerodynamics Complex (NFAC) 40- by 80-Foot Wind Tunnel in May 2010. The test was designed to acquire a suite of measurements to validate state-of-the-art modeling tools. Measurements include blade airloads (from a single pressure-instrumented blade), blade structural loads (strain gages), rotor performance (rotor balance and torque measurements), blade deformation (stereo-photogrammetry), and rotor wake measurements (Particle Image Velocimetry (PIV) and Retro-reflective Backward Oriented Schlieren (RBOS)). During the test, PIV measurements of flow field velocities were acquired in a stationary cross-flow plane located on the advancing side of the rotor disk at approximately 90 deg rotor azimuth. At each test condition, blade position relative to the measurement plane was varied. The region of interest (ROI) was 4-ft high by 14-ft wide and covered the outer half of the blade radius. Although PIV measurements were acquired in only one plane, much information can be gleaned by studying the rotor wake trajectory in this plane, especially when such measurements are augmented by blade airloads and RBOS data. This paper will provide a comparison between PIV and RBOS measurements of tip vortex position and vortex filament orientation for multiple rotor test conditions. Blade displacement measurements over the complete rotor disk will also be presented documenting blade-to-blade differences in tip-path-plane and providing additional information for correlation with PIV and RBOS measurements of tip vortex location. In addition, PIV measurements of tip vortex core diameter and strength will be presented. Vortex strength will be compared with measurements of maximum bound circulation on the rotor blade determined from pressure distributions obtained from 235 pressure sensors distributed over 9 radial stations.

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

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

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

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes asmore » time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates« less

Diverse Class 2 CRISPR-Cas Effector Proteins for Genome Engineering Applications.

PubMed

Pyzocha, Neena K; Chen, Sidi

2018-02-16

CRISPR-Cas genome editing technologies have revolutionized modern molecular biology by making targeted DNA edits simple and scalable. These technologies are developed by domesticating naturally occurring microbial adaptive immune systems that display wide diversity of functionality for targeted nucleic acid cleavage. Several CRISPR-Cas single effector enzymes have been characterized and engineered for use in mammalian cells. The unique properties of the single effector enzymes can make a critical difference in experimental use or targeting specificity. This review describes known single effector enzymes and discusses their use in genome engineering applications.

Production of caffeoylmalic acid from glucose in engineered Escherichia coli.

PubMed

Li, Tianzhen; Zhou, Wei; Bi, Huiping; Zhuang, Yibin; Zhang, Tongcun; Liu, Tao

2018-07-01

To achieve biosynthesis of caffeoylmalic acid from glucose in engineered Escherichia coli. We constructed the biosynthetic pathway of caffeoylmalic acid in E. coli by co-expression of heterologous genes RgTAL, HpaBC, At4CL2 and HCT2. To enhance the production of caffeoylmalic acid, we optimized the tyrosine metabolic pathway of E. coli to increase the supply of the substrate caffeic acid. Consequently, an E. coli-E. coli co-culture system was used for the efficient production of caffeoylmalic acid. The final titer of caffeoylmalic acid reached 570.1 mg/L. Microbial production of caffeoylmalic acid using glucose has application potential. In addition, microbial co-culture is an efficient tool for producing caffeic acid esters.

Long-Term Effects of Multiwalled Carbon Nanotubes and Graphene on Microbial Communities in Dry Soil.

PubMed

Ge, Yuan; Priester, John H; Mortimer, Monika; Chang, Chong Hyun; Ji, Zhaoxia; Schimel, Joshua P; Holden, Patricia A

2016-04-05

Little is known about the long-term effects of engineered carbonaceous nanomaterials (ECNMs) on soil microbial communities, especially when compared to possible effects of natural or industrial carbonaceous materials. To address these issues, we exposed dry grassland soil for 1 year to 1 mg g(-1) of either natural nanostructured material (biochar), industrial carbon black, three types of multiwalled carbon nanotubes (MWCNTs), or graphene. Soil microbial biomass was assessed by substrate induced respiration and by extractable DNA. Bacterial and fungal communities were examined by terminal restriction fragment length polymorphism (T-RFLP). Microbial activity was assessed by soil basal respiration. At day 0, there was no treatment effect on soil DNA or T-RFLP profiles, indicating negligible interference between the amended materials and the methods for DNA extraction, quantification, and community analysis. After a 1-year exposure, compared to the no amendment control, some treatments reduced soil DNA (e.g., biochar, all three MWCNT types, and graphene; P < 0.05) and altered bacterial communities (e.g., biochar, carbon black, narrow MWCNTs, and graphene); however, there were no significant differences across the amended treatments. These findings suggest that ECNMs may moderately affect dry soil microbial communities but that the effects are similar to those from natural and industrial carbonaceous materials, even after 1-year exposure.

Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering.

PubMed

Liu, Yang; Liu, Ye; Wang, Meng

2017-01-01

The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors.

Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering

PubMed Central

Liu, Yang; Liu, Ye; Wang, Meng

2017-01-01

The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors. PMID:29089935

Inferring Microbial Fitness Landscapes

DTIC Science & Technology

2016-02-25

infer from data the determinants of microbial evolution with sufficient resolution that we can quantify 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...Distribution Unlimited UU UU UU UU 25-02-2016 1-Oct-2012 30-Sep-2015 Final Report: Inferring Microbial Fitness Landscapes The views, opinions and/or findings...Triangle Park, NC 27709-2211 evolution, fitness landscapes, epistasis, microbial populations REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT

Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells.

PubMed

Liu, Qian; Liu, Bingfeng; Li, Wei; Zhao, Xin; Zuo, Wenjing; Xing, Defeng

2017-01-01

The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter , which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs.

Quorum sensing and microbial drug resistance.

PubMed

Chen, Yu-fan; Liu, Shi-yin; Liang, Zhi-bin; Lv, Ming-fa; Zhou, Jia-nuan; Zhang, Lian-hui

2016-10-20

Microbial drug resistance has become a serious problem of global concern, and the evolution and regulatory mechanisms of microbial drug resistance has become a hotspot of research in recent years. Recent studies showed that certain microbial resistance mechanisms are regulated by quorum sensing system. Quorum sensing is a ubiquitous cell-cell communication system in the microbial world, which associates with cell density. High-density microbial cells produce sufficient amount of small signal molecules, activating a range of downstream cellular processes including virulence and drug resistance mechanisms, which increases bacterial drug tolerance and causes infections on host organisms. In this review, the general mechanisms of microbial drug resistance and quorum-sensing systems are summarized with a focus on the association of quorum sensing and chemical signaling systems with microbial drug resistance mechanisms, including biofilm formation and drug efflux pump. The potential use of quorum quenching as a new strategy to control microbial resistance is also discussed.

Deep sea microbial fuel cell output as a proxy for microbial activity

NASA Astrophysics Data System (ADS)

Richter, K.; George, R.; Hardy, K. R.

2016-02-01

Abstract: Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The current is chiefly limited by the rate of microbial metabolism at the anode and serves as a proxy for microbial activity. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions and studies of important environmental parameters that affect fuel cell performance. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>4000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. We are pursuing a field efforts to deploy a microbial fuel cell in progressively deeper water, record in situ power and temperature over several weeks, and retrieve the fuel cell along with sediment samples for analysis. We are also pursuing a laboratory effort to build a matching microbial fuel cell in a pressure vessel capable of matching the pressure and temperature of deep water, and stocking the pressure vessel with deep water sediment in order to take measurements analogous to those in the field. We also hope to determine whether bacteria growing on the anode are different from bacteria growing in the bulk sediment via DNA analysis. The current progress and results from this work at SPAWAR will be presented.

State Estimation of Main Rotor Flap and Lead-Lag Using Accelerometers and Laser Transducers on the RASCAL UH-60 Helicopter

NASA Technical Reports Server (NTRS)

Fletcher, Jay W.; Chen, Robert T. N.; Strasilla, Eric; Aiken, Edwin W. (Technical Monitor)

1995-01-01

Modern rotorcraft flight control system designs which promise to yield high vehicle response bandwidth and good gust rejection can benefit from the use of rotor-state feedbacks. The measurement of main rotor blade motions is also desirable to validate and improve rotorcraft simulation models, to identify high-order linear flight dynamics models, to provide rotor system health monitoring; during flight test, and to provide for correlation with acoustic measurements from wind tunnel and flight tests. However, few attempts have been made to instrument a flight vehicle in this manner, and no previous system has had the robustness and accuracy required for these diverse applications. A rotor blade motion measurement and estimation system has been developed by NASA and the U.S. Army for use on the Rotorcraft Aircrew Systems Concepts Airborne Laboratory (RASCAL) helicopter. RASCAL is a UH-60 Blackhawk which is being modified at Ames Research Center in a phased development program for use in flight dynamics and controls, navigation, airspace management, and rotorcraft human factors research. The aircraft will feature a full-authority, digital, fly-by-wire research flight control system; a coupled ring laser gyro, differential GPS based navigation system; a stereoscopic color wide field of view helmet, mounted display; programmable panel mounted displays; and advanced navigation sensors. The rotor blade motion system is currently installed for data acquisition only, but will be integrated with the research flight control system when it is installed later this year.

Metabolic engineering of yeast for production of fuels and chemicals.

PubMed

Nielsen, Jens; Larsson, Christer; van Maris, Antonius; Pronk, Jack

2013-06-01

Microbial production of fuels and chemicals from renewable carbohydrate feedstocks offers sustainable and economically attractive alternatives to their petroleum-based production. The yeast Saccharomyces cerevisiae offers many advantages as a platform cell factory for such applications. Already applied on a huge scale for bioethanol production, this yeast is easy to genetically engineer, its physiology, metabolism and genetics have been intensively studied and its robustness enables it to handle harsh industrial conditions. Introduction of novel pathways and optimization of its native cellular processes by metabolic engineering are rapidly expanding its range of cell-factory applications. Here we review recent scientific progress in metabolic engineering of S. cerevisiae for the production of bioethanol, advanced biofuels, and chemicals. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microbial-processing of fruit and vegetable wastes for production of vital enzymes and organic acids: Biotechnology and scopes.

PubMed

Panda, Sandeep K; Mishra, Swati S; Kayitesi, Eugenie; Ray, Ramesh C

2016-04-01

Wastes generated from fruits and vegetables are organic in nature and contribute a major share in soil and water pollution. Also, green house gas emission caused by fruit and vegetable wastes (FVWs) is a matter of serious environmental concern. This review addresses the developments over the last one decade on microbial processing technologies for production of enzymes and organic acids from FVWs. The advances in genetic engineering for improvement of microbial strains in order to enhance the production of the value added bio-products as well as the concept of zero-waste economy have been briefly discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Regulatory RNA-assisted genome engineering in microorganisms.

PubMed

Si, Tong; HamediRad, Mohammad; Zhao, Huimin

2015-12-01

Regulatory RNAs are increasingly recognized and utilized as key modulators of gene expression in diverse organisms. Thanks to their modular and programmable nature, trans-acting regulatory RNAs are especially attractive in genome-scale applications. Here we discuss the recent examples in microbial genome engineering implementing various trans-acting RNA platforms, including sRNA, RNAi, asRNA and CRISRP-Cas. In particular, we focus on how the scalable and multiplex nature of trans-acting RNAs has been used to tackle the challenges in creating genome-wide and combinatorial diversity for functional genomics and metabolic engineering applications. Advances in computational design and context-dependent regulation are also discussed for their contribution in improving fine-tuning capabilities of trans-acting RNAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

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

Matter, J.; Chandran, K.

2013-05-31

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

Microbial diversity--insights from population genetics.

PubMed

Mes, Ted H M

2008-01-01

Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities.

PubMed

Zhao, Yang-Guo; Zhang, Yi; She, Zonglian; Shi, Yue; Wang, Min; Gao, Mengchun; Guo, Liang

2017-09-01

Performance of microbial fuel cells (MFCs) was monitored during the influent nutrient change from lactate to glucose/acetate/propionate and then to lactate. Meanwhile, anodic microbial communities were characterized by culture-independent molecular biotechnologies. Results showed MFC performance recovered rapidly when the lactate was replaced by one of its metabolic intermediates acetate, while it needed a longer time to recover if lactate substrate was converted to glucose/propionate or acetate to lactate. Secondary lactate feed enhanced the enrichment of bacterial populations dominating in first lactate feed. Electricity-producing bacteria, Geobacter spp., and beneficial helpers, Anaeromusa spp. and Pseudomonas spp., revived from a low abundance as lactate secondary supply, but microbial communities were hard to achieve former profiles in structure and composition. Hence, microbial community profiles tended to recover when outside environmental condition were restored. Different substrates selected unique functional microbial populations.

Engineering redox homeostasis to develop efficient alcohol-producing microbial cell factories.

PubMed

Zhao, Chunhua; Zhao, Qiuwei; Li, Yin; Zhang, Yanping

2017-06-24

The biosynthetic pathways of most alcohols are linked to intracellular redox homeostasis, which is crucial for life. This crucial balance is primarily controlled by the generation of reducing equivalents, as well as the (reduction)-oxidation metabolic cycle and the thiol redox homeostasis system. As a main oxidation pathway of reducing equivalents, the biosynthesis of most alcohols includes redox reactions, which are dependent on cofactors such as NADH or NADPH. Thus, when engineering alcohol-producing strains, the availability of cofactors and redox homeostasis must be considered. In this review, recent advances on the engineering of cellular redox homeostasis systems to accelerate alcohol biosynthesis are summarized. Recent approaches include improving cofactor availability, manipulating the affinity of redox enzymes to specific cofactors, as well as globally controlling redox reactions, indicating the power of these approaches, and opening a path towards improving the production of a number of different industrially-relevant alcohols in the near future.

Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell.

PubMed

Miceli, Joseph F; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I; Krajmalnik-Brown, Rosa

2014-10-01

Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (∼ 11A/m(2)) and Coulombic efficiency (∼ 70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ∼ 80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed microbial cultures containing complementing biochemical pathways. Copyright © 2014 Elsevier Ltd. All rights reserved.

Interspecies interactions are an integral determinant of microbial community dynamics

PubMed Central

Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

2015-01-01

This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

NASA Astrophysics Data System (ADS)

Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

2001-12-01

Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.

Genomic perspectives in microbial oceanography.

PubMed

DeLong, Edward F; Karl, David M

2005-09-15

The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

NASA Astrophysics Data System (ADS)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

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

Global microbialization of coral reefs.

PubMed

Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

2016-04-25

Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

Non-enzymatic palladium recovery on microbial and synthetic surfaces.

PubMed

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

2012-08-01

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

Microbial enhanced oil recovery research. Annex 5, Summary annual report 1990--1991

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

Sharma, M.M.; Georgiou, G.

1991-12-31

The objective of this work is to develop an engineering framework for the exploitation of microorganisms to enhance oil recovery. Specific goals include: (1) the production, isolation, chemical characterization and study of the physical properties of microbially produced surfactants; (2) development of simulators for MEOR; (3) model studies in sandstone cores for the characterization of the interactions between growing microbially cultures and oil reservoirs,; (4) design of operation strategies for the sequential injection of microorganisms and nutrient in reservoirs. Accomplishments are: (1) ultra low interfacial tensions (0.003 mN/M) were obtained between decane and 5% NaCl brine using biosurfactants obtained frommore » Bacillus Licheniformis, JF-2 which is the lowest IFT ever reported for biosurfactants; (2) a method to was developed isolate the biosurfactant from the growth medium; (3) the structure of the isolated biosurfactant has been determined; (4) several techniques have been proposed to increase the yield of the surfactant; and (5) an MEOR simulator has been completed.« less

Soil Microbial Forensics.

PubMed

Santiago-Rodriguez, Tasha M; Cano, Raúl J

2016-08-01

Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.

The Microbial Olympics

PubMed Central

Youle, Merry; Rohwer, Forest; Stacy, Apollo; Whiteley, Marvin; Steel, Bradley C.; Delalez, Nicolas J.; Nord, Ashley L.; Berry, Richard M.; Armitage, Judith P.; Kamoun, Sophien; Hogenhout, Saskia; Diggle, Stephen P.; Gurney, James; Pollitt, Eric J. G.; Boetius, Antje; Cary, S. Craig

2014-01-01

Every four years, the Olympic Games plays host to competitors who have built on their natural talent by training for many years to become the best in their chosen discipline. Similar spirit and endeavour can be found throughout the microbial world, in which every day is a competition to survive and thrive. Microorganisms are trained through evolution to become the fittest and the best adapted to a particular environmental niche or lifestyle, and to innovate when the ‘rules of the game’ are changed by alterations to their natural habitats. In this Essay, we honour the best competitors in the microbial world by inviting them to take part in the inaugural Microbial Olympics. PMID:22796885

Bearing restoration by grinding

NASA Technical Reports Server (NTRS)

Hanau, H.; Parker, R. J.; Zaretsky, E. V.; Chen, S. M.; Bull, H. L.

1976-01-01

A joint program was undertaken by the NASA Lewis Research Center and the Army Aviation Systems Command to restore by grinding those rolling-element bearings which are currently being discarded at aircraft engine and transmission overhaul. Three bearing types were selected from the UH-1 helicopter engine (T-53) and transmission for the pilot program. No bearing failures occurred related to the restoration by grinding process. The risk and cost of a bearing restoration by grinding programs was analyzed. A microeconomic impact analysis was performed.

Microbial safety in space

NASA Astrophysics Data System (ADS)

Krooneman, Janneke; Harmsen, Hermie; Landini, Paolo; Zinn, Manfred; Munaut, Françoise; van der Meer, Walter; Beimfohr, Claudia; Reichert, Bas; Preuß, Andrea

2005-10-01

Microbial hygiene is important in our daily lives; preventing and combating microbial infections is increasingly important in society. In hospitals, strict monitoring and control is exercised for people and infrastructure alike. In modern buildings, air-conditioning system are screened for harmful bacteria such as Legionella. More recently, concerns about SARS (virus) and anthrax (bacteria) have added pressure on the scientific community to come up with adequate monitoring and control techniques to assure microbial hygiene. Additionally, the use of biotechnological recycling and cleaning processes for sustainability brings the need for reliable monitoring tools and preventive or riks-reducing strategies. In the manned space environment, similar problems need to be solved and efforts have already been made to study the behaviour of micro-organisms and microbial hygiene onboard space stations.

Control of microbial contamination.

NASA Technical Reports Server (NTRS)

Mcdade, J. J.

1971-01-01

Two specific applications are discussed of microbial contamination control in planetary quarantine. Under the first concept, using the clean room to control environmental microorganisms, the objective is to reduce the microbial species and keep the numbers of microorganisms within an enclosure at a low level. The clean room concept is aimed at obtaining a product that has a controlled and reduced level of microbial contamination. Under the second concept, using the microbiological barrier to control microbial contamination of a specific product, the barrier techniques are designed to prevent the entry of any microorganisms into a sterile work area. Thus the assembly of space flight hardware within the confines of a microbiological barrier is aimed at obtaining a sterile product. In theory and practice, both approaches are shown to be applicable to the planetary quarantine program.

Biosynthesis and engineering of kaempferol in Saccharomyces cerevisiae.

PubMed

Duan, Lijin; Ding, Wentao; Liu, Xiaonan; Cheng, Xiaozhi; Cai, Jing; Hua, Erbing; Jiang, Huifeng

2017-09-26

Kaempferol is a flavonol with broad bioactivity of anti-oxidant, anti-cancer, anti-diabetic, anti-microbial, cardio-protective and anti-asthma. Microbial synthesis of kaempferol is a promising strategy because of the low content in primary plant source. In this study, the biosynthesis pathway of kaempferol was constructed in the budding yeast Saccharomyces cerevisiae to produce kaempferol de novo, and several biological measures were taken for high production. Firstly, a high efficient flavonol synthases (FLS) from Populus deltoides was introduced into the biosynthetic pathway of kaempferol. Secondly, a S. cerevisiae recombinant was constructed for de novo synthesis of kaempferol, which generated about 6.97 mg/L kaempferol from glucose. To further promote kaempferol production, the acetyl-CoA biosynthetic pathway was overexpressed and p-coumarate was supplied as substrate, which improved kaempferol titer by about 23 and 120%, respectively. Finally, a fed-batch process was developed for better kaempferol fermentation performance, and the production reached 66.29 mg/L in 40 h. The titer of kaempferol in our engineered yeast is 2.5 times of the highest reported titer. Our study provides a possible strategy to produce kaempferol using microbial cell factory.

Microbially induced and microbially catalysed precipitation: two different carbonate factories

NASA Astrophysics Data System (ADS)

Meister, Patrick

2016-04-01

The landmark paper by Schlager (2003) has revealed three types of benthic carbonate production referred to as "carbonate factories", operative at different locations at different times in Earth history. The tropical or T-factory comprises the classical platforms and fringing reefs and is dominated by carbonate precipitation by autotrophic calcifying metazoans ("biotically controlled" precipitation). The cool or C-factory is also biotically controlled but via heterotrophic, calcifying metazoans in cold and deep waters at the continental margins. A further type is the mud-mound or M-factory, where carbonate precipitation is supported by microorganisms but not controlled by a specific enzymatic pathway ("biotically induced" precipitation). How exactly the microbes influence precipitation is still poorly understood. Based on recent experimental and field studies, the microbial influence on modern mud mound and microbialite growth includes two fundamentally different processes: (1) Metabolic activity of microbes may increase the saturation state with respect to a particular mineral phase, thereby indirectly driving the precipitation of the mineral phase: microbially induced precipitation. (2) In a situation, where a solution is already supersaturated but precipitation of the mineral is inhibited by a kinetic barrier, microbes may act as a catalyser, i.e. they lower the kinetic barrier: microbially catalysed precipitation. Such a catalytic effect can occur e.g. via secreted polymeric substances or specific chemical groups on the cell surface, at which the minerals nucleate or which facilitate mechanistically the bonding of new ions to the mineral surface. Based on these latest developments in microbialite formation, I propose to extend the scheme of benthic carbonate factories of Schlager et al. (2003) by introducing an additional branch distinguishing microbially induced from microbially catalysed precipitation. Although both mechanisms could be operative in a M

Engineering acyl carrier protein to enhance production of shortened fatty acids.

PubMed

Liu, Xueliang; Hicks, Wade M; Silver, Pamela A; Way, Jeffrey C

2016-01-01

The acyl carrier protein (ACP) is an essential and ubiquitous component of microbial synthesis of fatty acids, the natural precursor to biofuels. Natural fatty acids usually contain long chains of 16 or more carbon atoms. Shorter carbon chains, with increased fuel volatility, are desired for internal combustion engines. Engineering the length specificity of key proteins in fatty acid metabolism, such as ACP, may enable microbial synthesis of these shorter chain fatty acids. We constructed a homology model of the Synechococcus elongatus ACP, showing a hydrophobic pocket harboring the growing acyl chain. Amino acids within the pocket were mutated to increase steric hindrance to the acyl chain. Certain mutant ACPs, when over-expressed in Escherichia coli, increased the proportion of shorter chain lipids; I75 W and I75Y showed the strongest effects. Expression of I75 W and I75Y mutant ACPs also increased production of lauric acid in E. coli that expressed the C12-specific acyl-ACP thioesterase from Cuphea palustris. We engineered the specificity of the ACP, an essential protein of fatty acid metabolism, to alter the E. coli lipid pool and enhance production of medium-chain fatty acids as biofuel precursors. These results indicate that modification of ACP itself could be combined with enzymes affecting length specificity in fatty acid synthesis to enhance production of commodity chemicals based on fatty acids.

Metabolic engineering approaches for production of biochemicals in food and medicinal plants.

PubMed

Wilson, Sarah A; Roberts, Susan C

2014-04-01

Historically, plants are a vital source of nutrients and pharmaceuticals. Recent advances in metabolic engineering have made it possible to not only increase the concentration of desired compounds, but also introduce novel biosynthetic pathways to a variety of species, allowing for enhanced nutritional or commercial value. To improve metabolic engineering capabilities, new transformation techniques have been developed to allow for gene specific silencing strategies or stacking of multiple genes within the same region of the chromosome. The 'omics' era has provided a new resource for elucidation of uncharacterized biosynthetic pathways, enabling novel metabolic engineering approaches. These resources are now allowing for advanced metabolic engineering of plant production systems, as well as the synthesis of increasingly complex products in engineered microbial hosts. The status of current metabolic engineering efforts is highlighted for the in vitro production of paclitaxel and the in vivo production of β-carotene in Golden Rice and other food crops. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cell-free synthetic biology for in vitro prototype engineering.

PubMed

Moore, Simon J; MacDonald, James T; Freemont, Paul S

2017-06-15

Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).

Cell-free synthetic biology for in vitro prototype engineering

PubMed Central

Moore, Simon J.; MacDonald, James T.

2017-01-01

Cell-free transcription–translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. PMID:28620040

The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications.

PubMed

Park, Young-Kyoung; Nicaud, Jean-Marc; Ledesma-Amaro, Rodrigo

2018-03-01

Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering modular ester fermentative pathways in Escherichia coli.

PubMed

Layton, Donovan S; Trinh, Cong T

2014-11-01

Sensation profiles are observed all around us and are made up of many different molecules, such as esters. These profiles can be mimicked in everyday items for their uses in foods, beverages, cosmetics, perfumes, solvents, and biofuels. Here, we developed a systematic 'natural' way to derive these products via fermentative biosynthesis. Each ester fermentative pathway was designed as an exchangeable ester production module for generating two precursors- alcohols and acyl-CoAs that were condensed by an alcohol acyltransferase to produce a combinatorial library of unique esters. As a proof-of-principle, we coupled these ester modules with an engineered, modular, Escherichia coli chassis in a plug-and-play fashion to create microbial cell factories for enhanced anaerobic production of a butyrate ester library. We demonstrated tight coupling between the modular chassis and ester modules for enhanced product biosynthesis, an engineered phenotype useful for directed metabolic pathway evolution. Compared to the wildtype, the engineered cell factories yielded up to 48 fold increase in butyrate ester production from glucose. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Microbial Fuel Cells and Microbial Electrolyzers

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

Borole, Abhijeet P

2015-01-01

Microbial Fuel Cells and microbial electrolyzers represent an upcoming technology for production of electricity and hydrogen using a hybrid electrocatalytic-biocatalytic approach. The combined catalytic efficiency of these processes has potential to make this technology highly efficient among the various renewable energy production alternatives. This field has attracted electrochemists, biologists and many other disciplines due to its potential to contribute to the energy, water and environment sectors. A brief introduction to the technology is provided followed by current research needs from a bioelectrochemical perspective. Insights into the operation and limitations of these systems achieved via cyclic voltammetry and impedance spectroscopy aremore » discussed along with the power management needs to develop the application aspects. Besides energy production, other potential applications in bioenergy, bioelectronics, chemical production and remediation are also highlighted.« less

EVA-Compatible Microbial Swab Tool

NASA Technical Reports Server (NTRS)

Rucker, Michelle A.

2016-01-01

When we send humans to search for life on Mars, we'll need to know what we brought with us versus what may already be there. To ensure our crewed spacecraft meet planetary protection requirements—and to protect our science from human contamination—we'll need to know whether micro-organisms are leaking/venting from our ships and spacesuits. This is easily done by swabbing external vents and suit surfaces for analysis, but requires a specialized tool for the job. Engineers at the National Aeronautics and Space Administration (NASA) recently developed an Extravehicular Activity (EVA)-compatible swab tool that can be used to sample current space suits and life support systems. Data collected now will influence Mars life support and EVA hardware early in the planning process, before design changes become difficult and expensive.NASA’s EVA swab tool pairs a Space Shuttle-era tool handle with a commercially available swab tip mounted into a custom-designed end effector. A glove-compatible release mechanism allows the handle to quickly switch between swab tips, much like a shaving razor handle can snap onto a disposable blade cartridge. Swab tips are stowed inside individual sterile containers, each fitted with a microbial filter that allows the container to equalize atmospheric pressure, but prevents cabin contaminants from rushing into the container when passing from the EVA environment into a pressurized cabin. A bank of containers arrayed inside a tool caddy allows up to six individual samples to be collected during a given spacewalk.NASA plans to use the tool in 2016 to collect samples from various spacesuits during ground testing to determine what (if any) human-borne microbial contamination leaks from the suit under simulated thermal vacuum conditions. Next, the tool will be used on board the International Space Station to assess the types of microbial contaminants found on external environmental control and life support system vents. Data will support

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate.

PubMed

Wang, Zejie; Lee, Taekwon; Lim, Bongsu; Choi, Chansoo; Park, Joonhong

2014-01-17

The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate

PubMed Central

2014-01-01

Background The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. Results The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. Conclusion The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were

[Advances in microbial solar cells--A review].

PubMed

Guo, Xiaoyun; Yu, Changping; Zheng, Tianling

2015-08-04

The energy crisis has become one of the major problems hindering the development of the world. The emergence of microbial fuel cells provides a new solution to the energy crisis. Microbial solar cells, integrating photosynthetic organisms such as plants and microalgae into microbial fuel cells, can convert solar energy into electrical energy. Microbial solar cell has steady electric energy, and broad application prospects in wastewater treatment, biodiesel processing and intermediate metabolites production. Here we reviewed recent progress of microbial solar cells from the perspective of the role of photosynthetic organisms in microbial fuel cells, based on a vast amount of literature, and discussed their advantages and deficiency. At last, brief analysis of the facing problems and research needs of microbial fuel cells are undertaken. This work was expected to be beneficial for the application of the microbial solar cells technology.

Deep subsurface microbial processes

USGS Publications Warehouse

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

The maturing of microbial ecology.

PubMed

Schmidt, Thomas M

2006-09-01

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

Microbial reduction of uranium

USGS Publications Warehouse

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

1991-01-01

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

Phosphoketolase pathway engineering for carbon-efficient biocatalysis

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

Henard, Calvin Andrew; Freed, Emily Frances; Guarnieri, Michael Thomas

2015-12-01

Recent advances in metabolic engineering have facilitated the development of microbial biocatalysts capable of producing an array of bio-products, ranging from fuels to drug molecules. These bio-products are commonly generated through an acetyl-CoA intermediate, which serves as a key precursor in the biological conversion of carbon substrates. Moreover, conventional biocatalytic upgrading strategies proceeding through this route are limited by low carbon efficiencies, in large part due to carbon losses associated with pyruvate decarboxylation to acetyl-CoA. Bypass of pyruvate decarboxylation offers a means to dramatically enhance carbon yields and, in turn, bioprocess economics. Here, we discuss recent advances and prospects formore » employing the phosphoketolase pathway for direct biosynthesis of acetyl-CoA from carbon substrates, and phosphoketolase-based metabolic engineering strategies for carbon efficient biocatalysis.« less

Effects of microbial inoculum composition on rumen microbial ecology of dairy calves

USDA-ARS?s Scientific Manuscript database

The objective of this study was to determine if microbial inoculum composition affects dairy calf rumen microbial ecology. Holstein bull calves (n=20) were removed from their dam at birth and individually housed in calf hutches with sand bedding. Responses were studied using a randomized complete bl...

Metabolic engineering of Corynebacterium glutamicum for fermentative production of chemicals in biorefinery.

PubMed

Baritugo, Kei-Anne; Kim, Hee Taek; David, Yokimiko; Choi, Jong-Il; Hong, Soon Ho; Jeong, Ki Jun; Choi, Jong Hyun; Joo, Jeong Chan; Park, Si Jae

2018-05-01

Bio-based production of industrially important chemicals provides an eco-friendly alternative to current petrochemical-based processes. Because of the limited supply of fossil fuel reserves, various technologies utilizing microbial host strains for the sustainable production of platform chemicals from renewable biomass have been developed. Corynebacterium glutamicum is a non-pathogenic industrial microbial species traditionally used for L-glutamate and L-lysine production. It is a promising species for industrial production of bio-based chemicals because of its flexible metabolism that allows the utilization of a broad spectrum of carbon sources and the production of various amino acids. Classical breeding, systems, synthetic biology, and metabolic engineering approaches have been used to improve its applications, ranging from traditional amino-acid production to modern biorefinery systems for production of value-added platform chemicals. This review describes recent advances in the development of genetic engineering tools and techniques for the establishment and optimization of metabolic pathways for bio-based production of major C2-C6 platform chemicals using recombinant C. glutamicum.

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

PubMed

Timmers, Ruud A; Rothballer, Michael; Strik, David P B T B; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-04-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.

Synthetic Klebsiella pneumoniae-Shewanella oneidensis Consortium Enables Glycerol-Fed High-Performance Microbial Fuel Cells.